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	<title>Soft Matter and Interfaces - User contributions [en]</title>
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	<updated>2026-05-21T11:43:41Z</updated>
	<subtitle>User contributions</subtitle>
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	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=258</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=258"/>
		<updated>2025-10-14T09:10:25Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&lt;br /&gt;
* Ana Vila Verde&#039;s office is located at (see also map): Lotharstr. 1, 47057 Duisburg, Germany, building MF, office 246 (2nd floor). &#039;&#039;&#039;Make sure&#039;&#039;&#039; you input both street and postal code when you use navigation systems, because there is another Lotharstrasse  in Duisburg that is 17 km away!&lt;br /&gt;
&lt;br /&gt;
** &#039;&#039;&#039;Campus map:&#039;&#039;&#039;&lt;br /&gt;
[[Image:HowToReachUs2.png|frameless|upright=3]] &lt;br /&gt;
* &#039;&#039;&#039;Getting here:&#039;&#039;&#039;&lt;br /&gt;
** &#039;&#039;&#039;By car:&#039;&#039;&#039;  &amp;quot;Carl-Benz-Strasse 201 parking, 47057 Duisburg, Germany&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
** &#039;&#039;&#039;By train/public transportation/taxi:&#039;&#039;&#039;  Take a train to Duisburg Hbf (schedules in the [https://www.bahn.de Deutsche Bahn website]), exit the train station on the West side (walk towards platform 1), then take a taxi (about 20 EUR) or take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
*** Walking from Duisburg HBf to my office (~25 mins): exit the train station on the East side (walk towards platform 13), then follow this [https://www.google.com/maps/dir/Kammerstra%C3%9Fe+2,+47057+Duisburg/Lotharstra%C3%9Fe+1,+47058+Duisburg/@51.4307165,6.7834752,16z/data=!4m15!4m14!1m5!1m1!1s0x47b8bf6b85f35131:0xeaf219ffe70b6780!2m2!1d6.7774698!2d51.4293734!1m5!1m1!1s0x47b8c09d4664abbb:0x4148433935ab58e!2m2!1d6.7999517!2d51.4332526!3e2!5i1?entry=ttu route].&lt;br /&gt;
** &#039;&#039;&#039;By plane:&#039;&#039;&#039; &lt;br /&gt;
*** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent (multiple per hour).   &lt;br /&gt;
**** To get to Duisburg HBf from Düsseldorf airport, buy a VRR “B” train ticket for a single ride (&amp;quot;Eizelnticket&amp;quot;; about 7 EUR) at the VRR or Deutsche Bahn machines.  This ticket gives you access to all the RE and S trains, but NOT the ICE trains.  &lt;br /&gt;
**** The ticket machines are on the floor above the train platforms, if memory does not fail me.   &lt;br /&gt;
**** The machine gives you the option of buying it already with a time stamp, or without a time stamp.  If you take the second option, remember to validate it before you enter the train in the validation box next to the ticket machine.  &lt;br /&gt;
**** You &#039;&#039;&#039;cannot buy&#039;&#039;&#039; tickets or validate them inside the train.&lt;br /&gt;
**** &lt;br /&gt;
*** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf and Frankfurt airport; in this case, your destination &amp;quot;airport&amp;quot; should be &amp;quot;QDU&amp;quot; (in &amp;quot;airport code&amp;quot;), corresponding to Düsseldorf Hbf.   &lt;br /&gt;
**** The combined ticket is advantageous because the train part of the trip functions as another flight (eg., in case of delays or cancellations). &lt;br /&gt;
**** Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket for the QDU-Duisburg part.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=257</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=257"/>
		<updated>2025-07-03T11:37:33Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&lt;br /&gt;
* &#039;&#039;&#039;Campus map:&#039;&#039;&#039;&lt;br /&gt;
[[Image:HowToReachUs2.png|frameless|upright=3]] &lt;br /&gt;
* &#039;&#039;&#039;By car:&#039;&#039;&#039;  &amp;quot;Carl-Benz-Strasse 201 parking, 47057 Duisburg&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
* &#039;&#039;&#039;By train/public transportation/taxi:&#039;&#039;&#039;  Take a train to Duisburg Hbf (schedules in the [https://www.bahn.de Deutsche Bahn website]), exit the train station on the West side (walk towards platform 1), then take a taxi (destination: Lotharstrasse 1, 47057 Duisburg; about 20 EUR) or take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
** Walking from Duisburg HBf to my office (~25 mins): exit the train station on the East side (walk towards platform 13), then follow this [https://www.google.com/maps/dir/Kammerstra%C3%9Fe+2,+47057+Duisburg/Lotharstra%C3%9Fe+1,+47058+Duisburg/@51.4307165,6.7834752,16z/data=!4m15!4m14!1m5!1m1!1s0x47b8bf6b85f35131:0xeaf219ffe70b6780!2m2!1d6.7774698!2d51.4293734!1m5!1m1!1s0x47b8c09d4664abbb:0x4148433935ab58e!2m2!1d6.7999517!2d51.4332526!3e2!5i1?entry=ttu route].&lt;br /&gt;
* &#039;&#039;&#039;By plane:&#039;&#039;&#039; &lt;br /&gt;
** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent (multiple per hour).   &lt;br /&gt;
*** To get to Duisburg HBf from Düsseldorf airport, buy a VRR “B” train ticket for a single ride (&amp;quot;Eizelnticket&amp;quot;; about 7 EUR) at the VRR or Deutsche Bahn machines.  This ticket gives you access to all the RE and S trains, but NOT the ICE trains.  &lt;br /&gt;
*** The ticket machines are on the floor above the train platforms, if memory does not fail me.   &lt;br /&gt;
*** The machine gives you the option of buying it already with a time stamp, or without a time stamp.  If take the second option, remember to validate it before you enter the train in the validation box next to the ticket machine.  &lt;br /&gt;
*** You &#039;&#039;&#039;cannot buy&#039;&#039;&#039; tickets or validate them inside the train.&lt;br /&gt;
*** &lt;br /&gt;
** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf (&amp;quot;QDU&amp;quot; in &amp;quot;airport code notation&amp;quot;)  and Frankfurt airport.   &lt;br /&gt;
*** The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). &lt;br /&gt;
*** Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Lbox-hints&amp;diff=256</id>
		<title>Lbox-hints</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Lbox-hints&amp;diff=256"/>
		<updated>2025-06-05T13:10:01Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt; Here are minimal instructions to get started in the group:&lt;br /&gt;
&lt;br /&gt;
== Printers ==&lt;br /&gt;
* Herr Thiele&#039;s office (MC 373), mfc373.comphys.uni-due.de (134.91.161.242) &lt;br /&gt;
* MF 245, HL-5270DN series [00807786944d] &lt;br /&gt;
&lt;br /&gt;
To print, you need to SWITCH OFF the wlan in your computer and instead have a cable internet connection.&lt;br /&gt;
&amp;lt;!--* Behind the tea kitchen:  depbrother.comphys.uni-due.de (134.91.161.248)--&amp;gt; &lt;br /&gt;
&amp;lt;!---* AVV&#039;s office (MC 362):  office362.comphys.uni-duisburg-essen.de (134.91.161.247)---&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Sciebo cloud==&lt;br /&gt;
Sciebo is a statewide (NRW) cloud service for research, studies and teaching, which is operated from the university in Münster.&lt;br /&gt;
&lt;br /&gt;
* Create your account using [https://www.uni-due.de/zim/services/sciebo/ this link]; look for registrierung.  (If the link doesn&#039;t work, do a search for DUE Sciebo Anmeldung to get the right link, and then remind AVV to update this page.)&lt;br /&gt;
** If interested, there&#039;s also a client you can download so you can see the documents offline more easily.&lt;br /&gt;
* Once the account is created, your username will have the format &amp;quot;xxxxxxx@uni-duisburg-essen.de&amp;quot;, where xxxxxxx is your uni-Kennung.&lt;br /&gt;
* At the moment, Sciebo unfortunately does not deal well with collaborative online work (e.g., word docs) where users simultaneously (or quasi) modify the same file. Use it for files that you want to send someone else, not for intense collaborative work.&lt;br /&gt;
&lt;br /&gt;
== Zoom ==&lt;br /&gt;
* DUE Zoom can be found [https://uni-due.zoom.us here].  &lt;br /&gt;
&lt;br /&gt;
==Seminars==&lt;br /&gt;
* [https://www.uni-due.de/physik/veranstaltungen/physikalisches_kolloquium_en.php Physical Colloquium of the Faculty of Physics]: Wednesdays at 13h. Register to get the email announcements [https://lists.uni-due.de/mailman/listinfo/physik.kolloquium here].  It is the main event of the Physics faculty.&lt;br /&gt;
* [https://udue.de/TheoKoll Theorie Colloquium]: Fridays at 14h&lt;br /&gt;
* [https://www.uni-due.de/physik/veranstaltungen/kolloquium.php Other seminars in the physics department]&lt;br /&gt;
&lt;br /&gt;
==Home office==&lt;br /&gt;
* You can do home office 2 days per week, provided you do not miss in person events (seminars, etc).  Inform the group no later than 9 am using the group Signal chat.&lt;br /&gt;
* More frequent home office is in principle possible given sufficiently substantial motives, but needs to be discussed with AVV BEFORE it takes place.&lt;br /&gt;
&lt;br /&gt;
===Working remotely===&lt;br /&gt;
*  lbox needs to run the LXDE virtual desktop (ask Lothar); your laptop needs to run an [https://wiki.x2go.org/doku.php/download:start X2GO client]&lt;br /&gt;
*  DUE has a [https://www.uni-due.de/zim/services/software/office-ma.php campus license for Microsoft Office]; use it for home laptops/desktops to avoid formatting issues when exchanging files.  &lt;br /&gt;
** The DUE website does not have instructions for Mac OSX; you&#039;ll have to search for how to include the license for this system&lt;br /&gt;
* There&#039;s a list of Campus Software that can be installed in the lbox/personal computers [https://www.uni-due.de/zim/services/software/softwareliste-ma here].  For some of them, you can download the software by following the links there but afterwards you&#039;ll need to insert a license; if this happens, Lothar is whom you need.&lt;br /&gt;
&lt;br /&gt;
==Kitchen==&lt;br /&gt;
* We&#039;re responsible for keeping the tea kitchen (MG 268) clean.  This means that each of us should:&lt;br /&gt;
** Take care of the kitchen (as described in the schedule posted there) when it is our turn.&lt;br /&gt;
** Switch on the dish washer if it is completely full.&lt;br /&gt;
** Wipe microwave/table/counters/fridge to clean up own mess.&lt;br /&gt;
** Place used cuttlery and crockery in the dish washer.  Used items may be left in the sink IF AND ONLY IF the dish washer is completely full or is working. &lt;br /&gt;
&lt;br /&gt;
==Vacations/Sickness==&lt;br /&gt;
* UDE regulations regarding vacation can be found [https://www.uni-due.de/verwaltung/abwesenheiten/erholungsurlaub.php here]. A request for vacation should be initially discussed with AVV. Once everything is cleared up, remember to fill in and send AVV (via email) the relevant [https://www.uni-due.de/imperia/md/content/zentralverwaltung/formulare/antrag_urlaub-sonderurlaub-freizeitausgleich.pdf form], BEFORE you go on vacation.  If you have a E-Signature you can digitally sign it, otherwise you need to print it, sign it, make a pdf and then send it to AVV via email.&lt;br /&gt;
* UDE regulations regarding sickness can be found [https://www.uni-due.de/verwaltung/abwesenheiten/erkrankung.php here].&lt;br /&gt;
&lt;br /&gt;
==Enrolling as a PhD student at UDE==&lt;br /&gt;
* The relevant regulations are [https://www.uni-due.de/physik/studium/promotion_en.php here].&lt;br /&gt;
==Being environmentally friendly==&lt;br /&gt;
* Screens and lights MUST be switched off at the end of the workday (power consumption is approximately 30 W).&lt;br /&gt;
&amp;lt;!--* Your lbox MUST be left on standby (&amp;quot;suspend&amp;quot; mode) at the end of the workday (power consumption is 3 W in suspended mode, wherease it is 60 W when left on).&lt;br /&gt;
** To reactive your lbox when working remotely (username = your comphys username): &amp;lt;code&amp;gt; ssh username@cps.comphys.uni-due.de wakeup&amp;lt;/code&amp;gt;  --&amp;gt; &lt;br /&gt;
* Take carboard/plastic/old gadgets/etc to the recycling bins yourself (there&#039;s no DUE service to take care of this): they are in the &amp;quot;backyard&amp;quot; after you exit the buildings next to MB 022 (a janitor&#039;s office).&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=255</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=255"/>
		<updated>2025-03-06T13:23:37Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|Copyright:  R. Baege. &amp;lt;br&amp;gt;&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper] and [ https://doi.org/10.1002/pro.5241 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper]) that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;100px&amp;quot; &amp;gt;&lt;br /&gt;
File:XiaociHu.jpeg | Xiaoci Hu (starting 15.09.2024)&lt;br /&gt;
File:Elio.png | Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID [https://www.webofscience.com/wos/woscc/summary/0ab0654b-aad6-4775-99d6-4ecfe0e66778-014f9429d8/date-descending/1 (H-7805-2013) in Web of Science].&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&amp;lt;!--I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]--&amp;gt; &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
* 25.01.: We use MD simulations and IR-solvation shell spectroscopy done the group of [https://www.ruhr-uni-bochum.de/pc2/petersen/ Poul Petersen at the Ruhr University Bochum], to show that protein hydration shells of halophilic proteins are - surprisingly - equally as robust to changes in KCl concentration as normal (i.e., mesophilic) proteins. See our paper in [https://doi.org/10.1002/pro.5241 Protein Science].&lt;br /&gt;
* 24.09.15: From September 15 onwards, Xiaoci Hu will join us for three years as a PhD student. Welcome Xiaoci!&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically explain  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
&lt;br /&gt;
=== Research guidelines ===&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  &lt;br /&gt;
* RESOLV-affiliated students and post-docs may also contact the [https://www.solvation.de/about/intranet/igss-intranet/ombudsperson-1 RESOLV ombudspersons]&lt;br /&gt;
&lt;br /&gt;
The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
&lt;br /&gt;
=== Support for non-scientific issues ===&lt;br /&gt;
The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. &lt;br /&gt;
&lt;br /&gt;
GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
&lt;br /&gt;
Both GEOs and the PR are under &amp;lt;strong&amp;gt;[https://de.wikipedia.org/wiki/Verschwiegenheitspflicht Schweigepflicht] (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
&lt;br /&gt;
=== Computing resouces ===&lt;br /&gt;
&lt;br /&gt;
[https://udue.de/acluster Group cluster]&lt;br /&gt;
&lt;br /&gt;
=== Group info ===&lt;br /&gt;
&lt;br /&gt;
[[lbox-hints| Practical stuff]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;&amp;lt;big&amp;gt;Click here for directions&amp;lt;/big&amp;gt;&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=254</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=254"/>
		<updated>2025-03-06T13:20:04Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|Copyright:  R. Baege. &amp;lt;br&amp;gt;&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;100px&amp;quot; &amp;gt;&lt;br /&gt;
File:XiaociHu.jpeg | Xiaoci Hu (starting 15.09.2024)&lt;br /&gt;
File:Elio.png | Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID [https://www.webofscience.com/wos/woscc/summary/0ab0654b-aad6-4775-99d6-4ecfe0e66778-014f9429d8/date-descending/1 (H-7805-2013) in Web of Science].&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&amp;lt;!--I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]--&amp;gt; &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
* 25.01.: We use MD simulations and IR-solvation shell spectroscopy done the group of [https://www.ruhr-uni-bochum.de/pc2/petersen/ Poul Petersen at the Ruhr University Bochum], to show that protein hydration shells of halophilic proteins are - surprisingly - equally as robust to changes in KCl concentration as normal (i.e., mesophilic) proteins. See our paper in [https://doi.org/10.1002/pro.5241 Protein Science].&lt;br /&gt;
* 24.09.15: From September 15 onwards, Xiaoci Hu will join us for three years as a PhD student. Welcome Xiaoci!&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically explain  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
&lt;br /&gt;
=== Research guidelines ===&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  &lt;br /&gt;
* RESOLV-affiliated students and post-docs may also contact the [https://www.solvation.de/about/intranet/igss-intranet/ombudsperson-1 RESOLV ombudspersons]&lt;br /&gt;
&lt;br /&gt;
The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
&lt;br /&gt;
=== Support for non-scientific issues ===&lt;br /&gt;
The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. &lt;br /&gt;
&lt;br /&gt;
GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
&lt;br /&gt;
Both GEOs and the PR are under &amp;lt;strong&amp;gt;[https://de.wikipedia.org/wiki/Verschwiegenheitspflicht Schweigepflicht] (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
&lt;br /&gt;
=== Computing resouces ===&lt;br /&gt;
&lt;br /&gt;
[https://udue.de/acluster Group cluster]&lt;br /&gt;
&lt;br /&gt;
=== Group info ===&lt;br /&gt;
&lt;br /&gt;
[[lbox-hints| Practical stuff]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;&amp;lt;big&amp;gt;Click here for directions&amp;lt;/big&amp;gt;&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Making-movies&amp;diff=253</id>
		<title>Making-movies</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Making-movies&amp;diff=253"/>
		<updated>2024-12-03T14:26:22Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: Created page with &amp;quot;=== Making movies in VMD ===   &amp;#039;&amp;#039;&amp;#039;General stuff:&amp;#039;&amp;#039;&amp;#039; * Animated gifs can be dropped into Power Point or into a browser to play. I normally used this format. * mp4 movies are also OK * Unusual (and very beautiful) representations can be created in VMD using renderers other than Snapshot, but they take longer to produce, so I don&amp;#039;t mention them here. * In all cases, load the relevant trajectories and format how it looks. * In VMD Main-&amp;gt;Display-&amp;gt;Render Mode, chose GLSL to en...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== Making movies in VMD ===&lt;br /&gt;
 &lt;br /&gt;
&#039;&#039;&#039;General stuff:&#039;&#039;&#039;&lt;br /&gt;
* Animated gifs can be dropped into Power Point or into a browser to play. I normally used this format.&lt;br /&gt;
* mp4 movies are also OK&lt;br /&gt;
* Unusual (and very beautiful) representations can be created in VMD using renderers other than Snapshot, but they take longer to produce, so I don&#039;t mention them here.&lt;br /&gt;
* In all cases, load the relevant trajectories and format how it looks.&lt;br /&gt;
* In VMD Main-&amp;gt;Display-&amp;gt;Render Mode, chose GLSL to enable transparent materials.&lt;br /&gt;
* Save the visualization state as a *vmd file, in case you want to make modifications in the future.&lt;br /&gt;
* There are specialized tutorials to learn how to use the visualization capabilities of VMD.  Search for them... Here I only summarize a few topics for which guidelines appear to be harder to find.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Drawing an arrow at the pulled end (for pulling simulations)&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
In pulling simulations, it is sometimes useful to draw an arrow at the pulled end for visualization purposes.  Steps to do this in VMD:&lt;br /&gt;
&lt;br /&gt;
# Modify  script script_drawArrow.tcl to your needs, to specify the atom where the arrow starts and direction of arrow.&lt;br /&gt;
# Run script (by typing at the VMD TkConsole &amp;quot;source script_drawArrow.tcl &amp;quot;; the &amp;quot;&amp;quot; are not typed in...)&lt;br /&gt;
# Move the bar in VMD main from the beginning to the end of the trajectory, so the script executes for each frame&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Update the secondary structure at every frame&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Some representations (e.g. NewCartoon) depend on the secondary structure of the amino acids, but by default VMD does not update it every frame to keep things light.  If you need it updated at every frame:&lt;br /&gt;
&lt;br /&gt;
# Save the script  [https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/sscache.tcl sscache.tcl ] somewhere in your machine, and then source it within VMD (by typing at the VMD Tkconsole &amp;quot;source sscache.tcl&amp;quot;)&lt;br /&gt;
# Source the script named [https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/stride.tcl stride.tcl] (in the same way as in 1)&lt;br /&gt;
# Type at the TkConsole    &amp;quot;start_sscache&amp;quot;&lt;br /&gt;
# Move the bar in VMD main from the beginning to the end of the trajectory, so the SS is cached.  You should be able to see now that it is updated at every frame.&lt;br /&gt;
&lt;br /&gt;
To turn off the trace, use the command stop_sscache, which also takes the molecule number. There must be one stop_sscache for each start_sscache. The command clear_sscache resets the saved secondary structure data for all the molecules and all the frames. More info in https://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node256.html&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Making movies (A)&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
This option is OK for trajectories that are not too jumpy to begin with.&lt;br /&gt;
&lt;br /&gt;
In VMD Main -&amp;gt; Extensions -&amp;gt; Movie Maker:&lt;br /&gt;
# renderer snapshot&lt;br /&gt;
# movie settings: trajectory ; leave option to delete all files on&lt;br /&gt;
# format: Animated GIF (image magick)&lt;br /&gt;
#  Select an empty working directory&lt;br /&gt;
# Click on &amp;quot;Make Movie&amp;quot;, and wait until it completes&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Making movies (B)&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
This option is better if your trajectory is jumpy.&lt;br /&gt;
&lt;br /&gt;
Step 1: In VMD Main -&amp;gt; Extensions -&amp;gt; Move Maker:&lt;br /&gt;
# renderer snapshot&lt;br /&gt;
# movie settings: trajectory ; deselect option to delete all files&lt;br /&gt;
# format: jpeg (image magick)&lt;br /&gt;
# Select an empty working directory&lt;br /&gt;
# Click on &amp;quot;Make Movie&amp;quot;, and wait until it completes&lt;br /&gt;
&lt;br /&gt;
Step 2: In a Linux machine, in the directory with the jpeg images, run command&lt;br /&gt;
convert -delay 30 myImageName.*.jpg myMovie-delay-30.gif&lt;br /&gt;
&lt;br /&gt;
Try several delay values (5 to 50 is a good range) to find something that works. Remember to rename the movies according to the delay so at the end you can chose the best one.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=252</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=252"/>
		<updated>2024-11-11T08:28:18Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&lt;br /&gt;
* &#039;&#039;&#039;Campus map:&#039;&#039;&#039;&lt;br /&gt;
[[Image:HowToReachUs2.png|frameless|upright=3]] &lt;br /&gt;
* &#039;&#039;&#039;By car:&#039;&#039;&#039;  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
* &#039;&#039;&#039;By train/public transportation/taxi:&#039;&#039;&#039;  Take a train to Duisburg Hbf (schedules in the [https://www.bahn.de Deutsche Bahn website]), exit the train station on the West side (walk towards platform 1), then take a taxi (destination: Lotharstrasse 1, 47057 Duisburg; about 20 EUR) or take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
** Walking from Duisburg HBf to my office (~25 mins): exit the train station on the East side (walk towards platform 13), then follow this [https://www.google.com/maps/dir/Kammerstra%C3%9Fe+2,+47057+Duisburg/Lotharstra%C3%9Fe+1,+47058+Duisburg/@51.4307165,6.7834752,16z/data=!4m15!4m14!1m5!1m1!1s0x47b8bf6b85f35131:0xeaf219ffe70b6780!2m2!1d6.7774698!2d51.4293734!1m5!1m1!1s0x47b8c09d4664abbb:0x4148433935ab58e!2m2!1d6.7999517!2d51.4332526!3e2!5i1?entry=ttu route].&lt;br /&gt;
* &#039;&#039;&#039;By plane:&#039;&#039;&#039; &lt;br /&gt;
** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent (multiple per hour).   &lt;br /&gt;
*** To get to Duisburg HBf from Düsseldorf airport, buy a VRR “B” train ticket for a single ride (&amp;quot;Eizelnticket&amp;quot;; about 7 EUR) at the VRR or Deutsche Bahn machines.  This ticket gives you access to all the RE and S trains, but NOT the ICE trains.  &lt;br /&gt;
*** The ticket machines are on the floor above the train platforms, if memory does not fail me.   &lt;br /&gt;
*** The machine gives you the option of buying it already with a time stamp, or without a time stamp.  If take the second option, remember to validate it before you enter the train in the validation box next to the ticket machine.  &lt;br /&gt;
*** You &#039;&#039;&#039;cannot buy&#039;&#039;&#039; tickets or validate them inside the train.&lt;br /&gt;
*** &lt;br /&gt;
** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf (&amp;quot;QDU&amp;quot; in &amp;quot;airport code notation&amp;quot;)  and Frankfurt airport.   &lt;br /&gt;
*** The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). &lt;br /&gt;
*** Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Lbox-hints&amp;diff=251</id>
		<title>Lbox-hints</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Lbox-hints&amp;diff=251"/>
		<updated>2024-09-18T13:00:53Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt; Here are minimal instructions to get started in the group:&lt;br /&gt;
&lt;br /&gt;
== Printers ==&lt;br /&gt;
* Herr Thiele&#039;s office (MC 373), mfc373.comphys.uni-due.de (134.91.161.242) &lt;br /&gt;
* MF 245, HL-5270DN series [00807786944d] &lt;br /&gt;
&lt;br /&gt;
To print, you need to SWITCH OFF the wlan in your computer and instead have a cable internet connection.&lt;br /&gt;
&amp;lt;!--* Behind the tea kitchen:  depbrother.comphys.uni-due.de (134.91.161.248)--&amp;gt; &lt;br /&gt;
&amp;lt;!---* AVV&#039;s office (MC 362):  office362.comphys.uni-duisburg-essen.de (134.91.161.247)---&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Sciebo cloud==&lt;br /&gt;
Sciebo is a statewide (NRW) cloud service for research, studies and teaching, which is operated from the university in Münster.&lt;br /&gt;
&lt;br /&gt;
* Create your account using [https://www.uni-due.de/zim/services/sciebo/ this link]; look for registrierung.  (If the link doesn&#039;t work, do a search for DUE Sciebo Anmeldung to get the right link, and then remind AVV to update this page.)&lt;br /&gt;
** If interested, there&#039;s also a client you can download so you can see the documents offline more easily.&lt;br /&gt;
* Once the account is created, your username will have the format &amp;quot;xxxxxxx@uni-duisburg-essen.de&amp;quot;, where xxxxxxx is your uni-Kennung.&lt;br /&gt;
* At the moment, Sciebo unfortunately does not deal well with collaborative online work (e.g., word docs) where users simultaneously (or quasi) modify the same file. Use it for files that you want to send someone else, not for intense collaborative work.&lt;br /&gt;
&lt;br /&gt;
== Zoom ==&lt;br /&gt;
* DUE Zoom can be found [https://uni-due.zoom.us here].  &lt;br /&gt;
&lt;br /&gt;
==Seminars==&lt;br /&gt;
* [https://www.uni-due.de/physik/veranstaltungen/physikalisches_kolloquium_en.php Physical Colloquium of the Faculty of Physics]: Wednesdays at 13h. Register to get the email announcements [https://lists.uni-due.de/mailman/listinfo/physik.kolloquium here].  It is the main event of the Physics faculty.&lt;br /&gt;
* [https://udue.de/TheoKoll Theorie Colloquium]: Fridays at 14h&lt;br /&gt;
* [https://www.uni-due.de/physik/veranstaltungen/kolloquium.php Other seminars in the physics department]&lt;br /&gt;
&lt;br /&gt;
==Home office==&lt;br /&gt;
* You can do home office 2 days per week, provided you do not miss in person events (seminars, etc).  Inform the group no later than 9 am using the group Signal chat.&lt;br /&gt;
* More frequent home office is in principle possible given sufficiently substantial motives, but needs to be discussed with AVV BEFORE it takes place.&lt;br /&gt;
&lt;br /&gt;
===Working remotely===&lt;br /&gt;
*  lbox needs to run the LXDE virtual desktop (ask Lothar); your laptop needs to run an [https://wiki.x2go.org/doku.php/download:start X2GO client]&lt;br /&gt;
*  DUE has a [https://www.uni-due.de/zim/services/software/office-ma.php campus license for Microsoft Office]; use it for home laptops/desktops to avoid formatting issues when exchanging files.  &lt;br /&gt;
** The DUE website does not have instructions for Mac OSX; you&#039;ll have to search for how to include the license for this system&lt;br /&gt;
* There&#039;s a list of Campus Software that can be installed in the lbox/personal computers [https://www.uni-due.de/zim/services/software/softwareliste-ma here].  For some of them, you can download the software by following the links there but afterwards you&#039;ll need to insert a license; if this happens, Lothar is whom you need.&lt;br /&gt;
&lt;br /&gt;
==Kitchen==&lt;br /&gt;
* We&#039;re responsible for keeping the tea kitchen (MG 268) clean.  This means that each of us should:&lt;br /&gt;
** Take care of the kitchen (as described in the schedule posted there) when it is our turn.&lt;br /&gt;
** Switch on the dish washer if it is completely full.&lt;br /&gt;
** Wipe microwave/table/counters/fridge to clean up own mess.&lt;br /&gt;
** Place used cuttlery and crockery in the dish washer.  Used items may be left in the sink IF AND ONLY IF the dish washer is completely full or is working. &lt;br /&gt;
&lt;br /&gt;
==Vacations/Sickness==&lt;br /&gt;
* UDE regulations regarding vacation can be found [https://www.uni-due.de/verwaltung/abwesenheiten/erholungsurlaub.php here]. A request for vacation should be initially discussed with AVV. Once everything is cleared up, remember to fill in, print out, sign and hand in the relevant form to Ingo Thiele BEFORE you go on vacation.&lt;br /&gt;
* UDE regulations regarding sickness can be found [https://www.unidue.de/verwaltung/abwesenheiten/erkrankung_englisch.php here].&lt;br /&gt;
&lt;br /&gt;
==Enrolling as a PhD student at UDE==&lt;br /&gt;
* The relevant regulations are [https://www.uni-due.de/physik/studium/promotion_en.php here].&lt;br /&gt;
==Being environmentally friendly==&lt;br /&gt;
* Screens and lights MUST be switched off at the end of the workday (power consumption is approximately 30 W).&lt;br /&gt;
&amp;lt;!--* Your lbox MUST be left on standby (&amp;quot;suspend&amp;quot; mode) at the end of the workday (power consumption is 3 W in suspended mode, wherease it is 60 W when left on).&lt;br /&gt;
** To reactive your lbox when working remotely (username = your comphys username): &amp;lt;code&amp;gt; ssh username@cps.comphys.uni-due.de wakeup&amp;lt;/code&amp;gt;  --&amp;gt; &lt;br /&gt;
* Take carboard/plastic/old gadgets/etc to the recycling bins yourself (there&#039;s no DUE service to take care of this): they are in the &amp;quot;backyard&amp;quot; after you exit the buildings next to MB 022 (a janitor&#039;s office).&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=250</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=250"/>
		<updated>2024-09-17T11:40:27Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|Copyright:  R. Baege. &amp;lt;br&amp;gt;&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;100px&amp;quot; &amp;gt;&lt;br /&gt;
File:XiaociHu.jpeg | Xiaoci Hu (starting 15.09.2024)&lt;br /&gt;
File:Elio.png | Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&amp;lt;!--I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]--&amp;gt; &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
* 24.09.15: From September 15 onwards, Xiaoci Hu will join us for three years as a PhD student. Welcome Xiaoci!&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
&lt;br /&gt;
=== Research guidelines ===&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  &lt;br /&gt;
* RESOLV-affiliated students and post-docs may also contact the [https://www.solvation.de/about/intranet/igss-intranet/ombudsperson-1 RESOLV ombudspersons]&lt;br /&gt;
&lt;br /&gt;
The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
&lt;br /&gt;
=== Support for non-scientific issues ===&lt;br /&gt;
The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. &lt;br /&gt;
&lt;br /&gt;
GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
&lt;br /&gt;
Both GEOs and the PR are under &amp;lt;strong&amp;gt;[https://de.wikipedia.org/wiki/Verschwiegenheitspflicht Schweigepflicht] (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
&lt;br /&gt;
=== Computing resouces ===&lt;br /&gt;
&lt;br /&gt;
[https://udue.de/acluster Group cluster]&lt;br /&gt;
&lt;br /&gt;
=== Group info ===&lt;br /&gt;
&lt;br /&gt;
[[lbox-hints| Practical stuff]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;&amp;lt;big&amp;gt;Click here for directions&amp;lt;/big&amp;gt;&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
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		<author><name>Vilaverde</name></author>
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	<entry>
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		<title>Main Page</title>
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		<updated>2024-09-17T11:23:04Z</updated>

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&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|Copyright:  R. Baege. &amp;lt;br&amp;gt;&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Xiaoci hu (starting 15.09.2024)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&amp;lt;!--I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]--&amp;gt; &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
&lt;br /&gt;
=== Research guidelines ===&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  &lt;br /&gt;
* RESOLV-affiliated students and post-docs may also contact the [https://www.solvation.de/about/intranet/igss-intranet/ombudsperson-1 RESOLV ombudspersons]&lt;br /&gt;
&lt;br /&gt;
The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
&lt;br /&gt;
=== Support for non-scientific issues ===&lt;br /&gt;
The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. &lt;br /&gt;
&lt;br /&gt;
GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
&lt;br /&gt;
Both GEOs and the PR are under &amp;lt;strong&amp;gt;[https://de.wikipedia.org/wiki/Verschwiegenheitspflicht Schweigepflicht] (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
&lt;br /&gt;
=== Computing resouces ===&lt;br /&gt;
&lt;br /&gt;
[https://udue.de/acluster Group cluster]&lt;br /&gt;
&lt;br /&gt;
=== Group info ===&lt;br /&gt;
&lt;br /&gt;
[[lbox-hints| Practical stuff]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;&amp;lt;big&amp;gt;Click here for directions&amp;lt;/big&amp;gt;&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=247</id>
		<title>Jobs</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=247"/>
		<updated>2024-08-01T13:35:40Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__TOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--- ==Open positions==&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
 [https://www.linkedin.com/jobs/view/2971284979  PhD position - Probing the structure and thermodynamics of solvation and of aggregation of fluorinated molecules with simulations]&lt;br /&gt;
&lt;br /&gt;
08.2022: There is an open PhD position in the group. &lt;br /&gt;
&lt;br /&gt;
---&amp;gt;&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
==How to prepare for your first interview==&lt;br /&gt;
* The interview will take approximately between 15 and 25 mins.  &lt;br /&gt;
* I must be able to clearly see you and hear you; please ensure a stable internet connection.&lt;br /&gt;
* Be punctual. If you are experiencing internet problems and you cannot connect over Zoom, please email me about it within 5 minutes of the start time of the interview.&lt;br /&gt;
* If you claim that you can program, I will ask that you write, in real time and with screen sharing, a short program in the language of your preference.  Please ensure that you have a working environment to do this (python, C++...).&lt;br /&gt;
* I will ask basic questions about undergraduate math/chemistry/physics.&lt;br /&gt;
&lt;br /&gt;
==How to prepare for your second interview==&lt;br /&gt;
* The interview will take approximately 1h.  &lt;br /&gt;
* I must be able to clearly see you and hear you; please ensure a stable internet connection.&lt;br /&gt;
* Be punctual. If you are experiencing internet problems and you cannot connect over Zoom, please email me about it within 5 minutes of the start time of the interview.  &lt;br /&gt;
* You should prepare a 15 to 20 min long talk about your prior research.  The talk should be supported by presentation slides. &lt;br /&gt;
# The first slide should be about you: remind me of the main points of your application (e.g., your BSc. and MSc. grades, topics of BSc. projects). Emphasize your STRONGEST points (e.g., research work initiated by you or done independently; prior expertise that matches the requirements of the position for which you are applying).  Explain unusual events in your CV (e.g., long time to complete your MSc. because of sickness; an MSc. thesis with few results because of limited computational resources).  Keep it short (&amp;lt; 3 min).&lt;br /&gt;
# Focus on ONE research topic (for PhD candidates, this would be the research you did towards you Master degree).  I encourage you to show your slides to colleagues so that they are clear and have no obvious mistakes, and also that you practice the talk in front of them.    Structure the talk so that a listener understands: &lt;br /&gt;
## What is the scientific question motivating that work;  &lt;br /&gt;
## Why is that question important;  &lt;br /&gt;
## How you approached the question (which methods you used and why are they appropriate); &lt;br /&gt;
## What are your results and what can be learned from them. &lt;br /&gt;
# Things to keep in mind: &lt;br /&gt;
## Make sure you understand the physical meaning of the observables you show, and the units in which these observables are expressed.&lt;br /&gt;
## Have the mathematical expression used to calculate the observables either in the main slide or in a support slide.  Make sure it is correct (!) and that you understand what you calculated.&lt;br /&gt;
&lt;br /&gt;
* During the talk I will interrupt you many times with questions; don&#039;t be put off by this.&lt;br /&gt;
&lt;br /&gt;
* After the talk I will answer your questions about the project I am offering, my group, life in Duisburg, etc... &lt;br /&gt;
** I have noticed that many applicants barely ask me questions, perhaps out of shyness or out of concern they will appear rude or pushy.  To be clear:  I typically get a favorable impression about applicants that ask questions that will enable them to decide whether the project, my group, the University of Duisburg-Essen and the city of Duisburg are good fits for them.  Not asking questions is more likely to count against you than in your favor...&lt;br /&gt;
* We keep going until we are both out of questions or the time is up, whichever comes first.  By the end of it, we should both be in a position to decide whether we&#039;d work well together on the project for which you apply.&lt;br /&gt;
* I do interviews so I can assess your intellectual maturity,  your ability to communicate in English, and if your expectations and mine are a good fit so that the project can be carried out successfully. I want to get a feel for your level of understanding about fundamental knowledge from your undergraduate degree and your own prior research work, as well as your ability to think like a scientist.&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Lbox-hints&amp;diff=246</id>
		<title>Lbox-hints</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Lbox-hints&amp;diff=246"/>
		<updated>2024-08-01T13:11:37Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt; Here are minimal instructions to get started in the group:&lt;br /&gt;
&lt;br /&gt;
== Printers ==&lt;br /&gt;
* Herr Thiele&#039;s office (MC 373), mfc373.comphys.uni-due.de (134.91.161.242) &lt;br /&gt;
* MF 245, HL-5270DN series [00807786944d] &lt;br /&gt;
&lt;br /&gt;
To print, you need to SWITCH OFF the wlan in your computer and instead have a cable internet connection.&lt;br /&gt;
&amp;lt;!--* Behind the tea kitchen:  depbrother.comphys.uni-due.de (134.91.161.248)--&amp;gt; &lt;br /&gt;
&amp;lt;!---* AVV&#039;s office (MC 362):  office362.comphys.uni-duisburg-essen.de (134.91.161.247)---&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Sciebo cloud==&lt;br /&gt;
Sciebo is a statewide (NRW) cloud service for research, studies and teaching, which is operated from the university in Münster.&lt;br /&gt;
&lt;br /&gt;
* Create your account using [https://www.uni-due.de/zim/services/sciebo/ this link]; look for registrierung.  (If the link doesn&#039;t work, do a search for DUE Sciebo Anmeldung to get the right link, and then remind AVV to update this page.)&lt;br /&gt;
** If interested, there&#039;s also a client you can download so you can see the documents offline more easily.&lt;br /&gt;
* Once the account is created, your username will have the format &amp;quot;xxxxxxx@uni-duisburg-essen.de&amp;quot;, where xxxxxxx is your uni-Kennung.&lt;br /&gt;
* At the moment, Sciebo unfortunately does not deal well with collaborative online work (e.g., word docs) where users simultaneously (or quasi) modify the same file. Use it for files that you want to send someone else, not for intense collaborative work.&lt;br /&gt;
&lt;br /&gt;
== Zoom ==&lt;br /&gt;
* DUE Zoom can be found [https://uni-due.zoom.us here].  &lt;br /&gt;
&lt;br /&gt;
==Seminars==&lt;br /&gt;
* [https://www.uni-due.de/physik/veranstaltungen/physikalisches_kolloquium_en.php Physical Colloquium of the Faculty of Physics]: Wednesdays at 13h. Register to get the email announcements [https://lists.uni-due.de/mailman/listinfo/physik.kolloquium here].  It is the main event of the Physics faculty.&lt;br /&gt;
* [https://udue.de/TheoKoll Theorie Colloquium]: Fridays at 14h&lt;br /&gt;
* [https://www.uni-due.de/physik/veranstaltungen/kolloquium.php Other seminars in the physics department]&lt;br /&gt;
&lt;br /&gt;
==Home office==&lt;br /&gt;
* You can do home office 2 days per week, provided you do not miss in person events (seminars, etc).  Inform the group no later than 9 am using the group Signal chat.&lt;br /&gt;
* More frequent home office is in principle possible given sufficiently substantial motives, but needs to be discussed with AVV BEFORE it takes place.&lt;br /&gt;
&lt;br /&gt;
===Working remotely===&lt;br /&gt;
*  lbox needs to run the LXDE virtual desktop (ask Lothar); your laptop needs to run an [https://wiki.x2go.org/doku.php/download:start X2GO client]&lt;br /&gt;
*  DUE has a [https://www.uni-due.de/zim/services/software/office-ma.php campus license for Microsoft Office]; use it for home laptops/desktops to avoid formatting issues when exchanging files.  &lt;br /&gt;
** The DUE website does not have instructions for Mac OSX; you&#039;ll have to search for how to include the license for this system&lt;br /&gt;
* There&#039;s a list of Campus Software that can be installed in the lbox/personal computers [https://www.uni-due.de/zim/services/software/softwareliste-ma here].  For some of them, you can download the software by following the links there but afterwards you&#039;ll need to insert a license; if this happens, Lothar is whom you need.&lt;br /&gt;
&lt;br /&gt;
==Kitchen==&lt;br /&gt;
* We&#039;re responsible for keeping the tea kitchen (MG 268) clean.  This means that each of us should:&lt;br /&gt;
** Take care of the kitchen (as described in the schedule posted there) when it is our turn.&lt;br /&gt;
** Switch on the dish washer if it is completely full.&lt;br /&gt;
** Wipe microwave/table/counters/fridge to clean up own mess.&lt;br /&gt;
** Place used cuttlery and crockery in the dish washer.  Used items may be left in the sink IF AND ONLY IF the dish washer is completely full or is working. &lt;br /&gt;
&lt;br /&gt;
==Being environmentally friendly==&lt;br /&gt;
* Screens and lights MUST be switched off at the end of the workday (power consumption is approximately 30 W).&lt;br /&gt;
&amp;lt;!--* Your lbox MUST be left on standby (&amp;quot;suspend&amp;quot; mode) at the end of the workday (power consumption is 3 W in suspended mode, wherease it is 60 W when left on).&lt;br /&gt;
** To reactive your lbox when working remotely (username = your comphys username): &amp;lt;code&amp;gt; ssh username@cps.comphys.uni-due.de wakeup&amp;lt;/code&amp;gt;  --&amp;gt; &lt;br /&gt;
* Take carboard/plastic/old gadgets/etc to the recycling bins yourself (there&#039;s no DUE service to take care of this): they are in the &amp;quot;backyard&amp;quot; after you exit the buildings next to MB 022 (a janitor&#039;s office).&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=245</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=245"/>
		<updated>2024-08-01T12:50:12Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|Copyright:  R. Baege. &amp;lt;br&amp;gt;&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&amp;lt;!--I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]--&amp;gt; &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
&lt;br /&gt;
=== Research guidelines ===&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  &lt;br /&gt;
* RESOLV-affiliated students and post-docs may also contact the [https://www.solvation.de/about/intranet/igss-intranet/ombudsperson-1 RESOLV ombudspersons]&lt;br /&gt;
&lt;br /&gt;
The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
&lt;br /&gt;
=== Support for non-scientific issues ===&lt;br /&gt;
The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. &lt;br /&gt;
&lt;br /&gt;
GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
&lt;br /&gt;
Both GEOs and the PR are under &amp;lt;strong&amp;gt;[https://de.wikipedia.org/wiki/Verschwiegenheitspflicht Schweigepflicht] (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
&lt;br /&gt;
=== Computing resouces ===&lt;br /&gt;
&lt;br /&gt;
[https://udue.de/acluster Group cluster]&lt;br /&gt;
&lt;br /&gt;
=== Group info ===&lt;br /&gt;
&lt;br /&gt;
[[lbox-hints| Practical stuff]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;&amp;lt;big&amp;gt;Click here for directions&amp;lt;/big&amp;gt;&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=244</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=244"/>
		<updated>2024-08-01T12:45:07Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|Copyright:  R. Baege. &amp;lt;br&amp;gt;&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]&lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
&lt;br /&gt;
=== Research guidelines ===&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  &lt;br /&gt;
* RESOLV-affiliated students and post-docs may also contact the [https://www.solvation.de/about/intranet/igss-intranet/ombudsperson-1 RESOLV ombudspersons]&lt;br /&gt;
&lt;br /&gt;
The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
&lt;br /&gt;
=== Support for non-scientific issues ===&lt;br /&gt;
The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. &lt;br /&gt;
&lt;br /&gt;
GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
&lt;br /&gt;
Both GEOs and the PR are under &amp;lt;strong&amp;gt;[https://de.wikipedia.org/wiki/Verschwiegenheitspflicht Schweigepflicht] (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
&lt;br /&gt;
=== Computing resouces ===&lt;br /&gt;
&lt;br /&gt;
[https://udue.de/acluster Group cluster]&lt;br /&gt;
&lt;br /&gt;
=== Group info ===&lt;br /&gt;
&lt;br /&gt;
[[lbox-hints| Practical stuff]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;&amp;lt;big&amp;gt;Click here for directions&amp;lt;/big&amp;gt;&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=243</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=243"/>
		<updated>2024-08-01T12:19:45Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|Copyright:  R. Baege. &amp;lt;br&amp;gt;&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]&lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=File:AnaVilaVerde.JPG&amp;diff=242</id>
		<title>File:AnaVilaVerde.JPG</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=File:AnaVilaVerde.JPG&amp;diff=242"/>
		<updated>2024-08-01T12:06:38Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: Vilaverde uploaded a new version of File:AnaVilaVerde.JPG&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=241</id>
		<title>Jobs</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=241"/>
		<updated>2024-05-16T15:58:58Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: /* How to prepare for your interview */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__TOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--- ==Open positions==&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
 [https://www.linkedin.com/jobs/view/2971284979  PhD position - Probing the structure and thermodynamics of solvation and of aggregation of fluorinated molecules with simulations]&lt;br /&gt;
&lt;br /&gt;
08.2022: There is an open PhD position in the group. &lt;br /&gt;
&lt;br /&gt;
---&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==How to prepare for your interview==&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
* The interview will take approximately 1h.  &lt;br /&gt;
* I must be able to clearly see you and hear you; please ensure a stable internet connection.  &lt;br /&gt;
* You should prepare a 15 to 20 min long talk about your prior research.  The talk should be supported by presentation slides. &lt;br /&gt;
# The first slide should be about you: remind me of the main points of your application (e.g., your BSc. and MSc. grades, topics of BSc. projects). Emphasize your STRONGEST points (e.g., research work initiated by you or done independently; prior expertise that matches the requirements of the position for which you are applying).  Explain unusual events in your CV (e.g., long time to complete your MSc. because of sickness; an MSc. thesis with few results because of limited computational resources).  Keep it short (&amp;lt; 3 min).&lt;br /&gt;
# Focus on ONE research topic (for PhD candidates, this would be the research you did towards you Master degree).  I encourage you to show your slides to colleagues so that they are clear and have no obvious mistakes, and also that you practice the talk in front of them.    Structure the talk so that a listener understands: &lt;br /&gt;
## What is the scientific question motivating that work;  &lt;br /&gt;
## Why is that question important;  &lt;br /&gt;
## How you approached the question (which methods you used and why are they appropriate); &lt;br /&gt;
## What are your results and what can be learned from them. &lt;br /&gt;
# Things to keep in mind: &lt;br /&gt;
## Make sure you understand the physical meaning of the observables you show, and the units in which these observables are expressed.&lt;br /&gt;
## Have the mathematical expression used to calculate the observables either in the main slide or in a support slide.  Make sure it is correct (!) and that you understand what you calculated.&lt;br /&gt;
&lt;br /&gt;
* During the talk I will interrupt you many times with questions; don&#039;t be put off by this.&lt;br /&gt;
* If you claim that you can program, I will ask that you write, in real time and with screen sharing, a short program in the language of your preference.  Please ensure that you have a working environment to do this (python, C++...).&lt;br /&gt;
* After the talk I will answer your questions about the project I am offering, my group, life in Duisburg, etc... &lt;br /&gt;
** I have noticed that many applicants barely ask me questions, perhaps out of shyness or out of concern they will appear rude or pushy.  To be clear:  I typically get a favorable impression about applicants that ask questions that will enable them to decide whether the project, my group, the University of Duisburg-Essen and the city of Duisburg are good fits for them.  Not asking questions is more likely to count against you than in your favor...&lt;br /&gt;
* We keep going until we are both out of questions or the time is up, whichever comes first.  By the end of it, we should both be in a position to decide whether we&#039;d work well together on the project for which you apply.&lt;br /&gt;
* I do interviews so I can assess your intellectual maturity,  your ability to communicate in English, and if your expectations and mine are a good fit so that the project can be carried out successfully. I want to get a feel for your level of understanding about fundamental knowledge from your undergraduate degree and your own prior research work, as well as your ability to think like a scientist.&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=240</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=240"/>
		<updated>2024-05-16T15:57:04Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: /* Jobs */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
I have an open PhD position; see job ad [https://psi-k.net/jobs/phd-position-dept-of-physics-duisburg-uni-d/ here]&lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=239</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=239"/>
		<updated>2024-04-03T08:03:31Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&lt;br /&gt;
* Campus map:&lt;br /&gt;
[[Image:HowToReachUs2.png|frameless|upright=3]] &lt;br /&gt;
* By car:  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
* By train/public transportation/taxi:  Take a train to Duisburg Hbf (schedules in the [https://www.bahn.de Deutsche Bahn website]), exit the train station on the West side (walk towards platform 1), then take a taxi (destination: Lotharstrasse 1, 47057 Duisburg; about 20 EUR) or take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
** Walking from Duisburg HBf to my office (~25 mins): exit the train station on the East side (walk towards platform 13), then follow this [https://www.google.com/maps/dir/Kammerstra%C3%9Fe+2,+47057+Duisburg/Lotharstra%C3%9Fe+1,+47058+Duisburg/@51.4307165,6.7834752,16z/data=!4m15!4m14!1m5!1m1!1s0x47b8bf6b85f35131:0xeaf219ffe70b6780!2m2!1d6.7774698!2d51.4293734!1m5!1m1!1s0x47b8c09d4664abbb:0x4148433935ab58e!2m2!1d6.7999517!2d51.4332526!3e2!5i1?entry=ttu route].&lt;br /&gt;
* By plane: &lt;br /&gt;
** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent.   &lt;br /&gt;
** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf (&amp;quot;QDU&amp;quot; in &amp;quot;airport code notation&amp;quot;)  and Frankfurt airport.   The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=238</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=238"/>
		<updated>2024-03-11T04:38:02Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: /* News */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
*  24.02.23: Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- * 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]--&amp;gt;&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=237</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=237"/>
		<updated>2024-03-11T04:35:26Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&#039;&#039;&#039; Guests&#039;&#039;&#039;--&amp;gt;&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://www.linkedin.com/in/robin-singh-736087116/?midToken=AQE3lZQzky82aw&amp;amp;midSig=13j0sg2ymv3qc1&amp;amp;trk=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta&amp;amp;trkEmail=eml-email_m2m_invite_single_01-hero-4-prof%7Ecta-null-s9gah%7El0zc8joi%7E3o-null-neptune%2Fprofile%7Evanity%2Eview Robin Singh], currently at [https://www.linkedin.com/company/gravity-pcm-institute/ Gravity PCM Institute].  &lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the [https://iasbs.ac.ir Institute for Advanced Studies in Basic Sciences], Zanjan, Iran, visited us for 6 months on a RESOLV fellowship. &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Publications ==&lt;br /&gt;
&lt;br /&gt;
Best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
My CV, funding, referee activities can be seen in my [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
*  Hosein Geraili and collaborators in the group of [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Rasmus Linser] mechanistically expalin  using simulation and NMR that the non-monotonic and non-linear impact of salt on protein dynamics stems from electrostatics, rather than from changes in the hydrophobic effect as previously believed.  See our paper in [https://doi.org/10.1002/cbic.202400057 ChemBioChem].&lt;br /&gt;
&lt;br /&gt;
=== Olds ===&lt;br /&gt;
&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=236</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=236"/>
		<updated>2024-02-05T09:56:13Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: /* Recent and current collaborators */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
=== Olds ===&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/proin/mitarbeiter/prof/index.html.en Prof. Dr. Christian Herrmann], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=235</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=235"/>
		<updated>2024-01-03T10:45:12Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
=== Olds ===&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]) (in collaboration with [https://www.chem.purdue.edu/bendor/ Dor Ben-Amotz].&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
We have clarified the structure of MgSO4 solutions ([https://doi.org/10.1039/C9CP06845G here]; in collaboration with [https://www.ruhr-uni-bochum.de/pc2/ Martina Havenith]) and that both additive and non-additive effects impact water dynamics at high MgSO4 concentrations ([https://10.1021/jp4059802 here] and [http://10.1039/c5cp05726d here])&lt;br /&gt;
&lt;br /&gt;
==== Force field development ====&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://orcid.org/0000-0001-7059-7568 Dr. Sulejman Skoko] (starting 01.09.2023).  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/ Prof. Dr. Martina Havenith], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=234</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=234"/>
		<updated>2024-01-03T10:29:50Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
=== Olds ===&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
=== Halophilic proteins ===&lt;br /&gt;
Understanding the origin of their surprising functionality at high salt concentrations. We&#039;ve shown (in [https://www.cell.com/biophysj/fulltext/S0006-3495(21)00444-6 this paper]) that the solvation shell of mesophilic (&amp;quot;normal&amp;quot;) proteins is just as robust to changes in salt concentration as that of halophilic proteins, and (in [https://www.sciencedirect.com/science/article/pii/S0006349523003235 this paper] that acidic amino acids on proteins, potassium ions and water can have stabilizing interactions.&lt;br /&gt;
&lt;br /&gt;
=== Fluorinated (bio)molecules ===&lt;br /&gt;
How fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation.  &lt;br /&gt;
&lt;br /&gt;
We&#039;ve shown that and how fluorination has unexpected impact in the hydrophobicity of fluorinated amino acids ([https://10.1016/j.chempr.2017.09.012 here] and [https://10.1039/c8cp07025c here]; in collaboration with the experimental group of [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html Beate Koksch]), and in specific how solvation shells are perturbed by the introduction of one or more CF bonds: ([https://10.1021/jacs.9b06862 CF3 groups], [https://10.1039/D0CP04205F, CF, CF2 and CF3 groups], and [https://10.1021/acs.jpcb.1c08601 CF2 groups in linear diols]).&lt;br /&gt;
&lt;br /&gt;
=== Proteins under force ===&lt;br /&gt;
Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani] [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 we were able to show] that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
&lt;br /&gt;
=== Hydrated ions ===&lt;br /&gt;
Hydration of inorganic and organic ions; ion-ion interactions. &lt;br /&gt;
&lt;br /&gt;
=== Force field development ===&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Useful information for grad students and post-docs ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators ==&lt;br /&gt;
In no particular order:&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=233</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=233"/>
		<updated>2024-01-03T10:02:12Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Research Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators, in no particular order ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=232</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=232"/>
		<updated>2024-01-03T10:00:06Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators, in no particular order ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to reach me/contact me ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; Lotharstr. 1, 47057 Duisburg, building MF, office 246 (2nd floor). [[How_To_Reach_Us| &#039;&#039;&#039;Click here for directions&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=231</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=231"/>
		<updated>2024-01-03T08:56:27Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* Campus map:&lt;br /&gt;
[[Image:HowToReachUs2.png|frameless|upright=3]] &lt;br /&gt;
* By car:  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
* By train/public transportation/taxi:  Take a train to Duisburg Hbf (schedules in the [https://www.bahn.de Deutsche Bahn website]), exit the train station on the West side (walk towards platform 1), then take a taxi (destination: Lotharstrasse 1, 47057 Duisburg; about 20 EUR) or take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
** Walking from Duisburg HBf to my office (~25 mins): exit the train station on the East side (walk towards platform 13), then follow this [https://www.google.com/maps/dir/Kammerstra%C3%9Fe+2,+47057+Duisburg/Lotharstra%C3%9Fe+1,+47058+Duisburg/@51.4307165,6.7834752,16z/data=!4m15!4m14!1m5!1m1!1s0x47b8bf6b85f35131:0xeaf219ffe70b6780!2m2!1d6.7774698!2d51.4293734!1m5!1m1!1s0x47b8c09d4664abbb:0x4148433935ab58e!2m2!1d6.7999517!2d51.4332526!3e2!5i1?entry=ttu route].&lt;br /&gt;
* By plane: &lt;br /&gt;
** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent.   &lt;br /&gt;
** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf (&amp;quot;QDU&amp;quot; in &amp;quot;airport code notation&amp;quot;)  and Frankfurt airport.   The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=File:HowToReachUs2.png&amp;diff=230</id>
		<title>File:HowToReachUs2.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=File:HowToReachUs2.png&amp;diff=230"/>
		<updated>2024-01-03T08:54:48Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=File:HowToReachUs.png&amp;diff=229</id>
		<title>File:HowToReachUs.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=File:HowToReachUs.png&amp;diff=229"/>
		<updated>2024-01-03T08:45:47Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: Revised instructions accounting for closed parking lots.&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Summary ==&lt;br /&gt;
Revised instructions accounting for closed parking lots.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=227</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=227"/>
		<updated>2024-01-03T08:24:30Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* Campus map:&lt;br /&gt;
[[Image:HowToReachUs.png|frameless|upright=3]] &lt;br /&gt;
* By car:  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
* By train/public transportation/taxi:  Take a train to Duisburg Hbf (schedules in the [https://www.bahn.de Deutsche Bahn website]), exit the train station on the West side (walk towards platform 1), then take a taxi (destination: Lotharstrasse 1, 47057 Duisburg; about 20 EUR) or take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
** Walking from Duisburg HBf to my office (~25 mins): exit the train station on the East side (walk towards platform 13), then follow this [https://www.google.com/maps/dir/Kammerstra%C3%9Fe+2,+47057+Duisburg/Lotharstra%C3%9Fe+1,+47058+Duisburg/@51.4307165,6.7834752,16z/data=!4m15!4m14!1m5!1m1!1s0x47b8bf6b85f35131:0xeaf219ffe70b6780!2m2!1d6.7774698!2d51.4293734!1m5!1m1!1s0x47b8c09d4664abbb:0x4148433935ab58e!2m2!1d6.7999517!2d51.4332526!3e2!5i1?entry=ttu route].&lt;br /&gt;
* By plane: &lt;br /&gt;
** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent.   &lt;br /&gt;
** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf (&amp;quot;QDU&amp;quot; in &amp;quot;airport code notation&amp;quot;)  and Frankfurt airport.   The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=226</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=226"/>
		<updated>2024-01-03T08:02:02Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* Campus map:&lt;br /&gt;
[[Image:HowToReachUs.png|frameless|upright=3]] &lt;br /&gt;
* By car:  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
* By train/public transportation/taxi:  Take a train to Duisburg Hbf, exit the train station on the West side (walk towards platform 1), then take a taxi or take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
** Walking from Duisburg HBf to my office: exit the train station on the East side (walk towards platform 13), then follow this [route https://www.google.com/maps/dir/Kammerstra%C3%9Fe+2,+47057+Duisburg/Lotharstra%C3%9Fe+1,+47058+Duisburg/@51.4307165,6.7834752,16z/data=!4m15!4m14!1m5!1m1!1s0x47b8bf6b85f35131:0xeaf219ffe70b6780!2m2!1d6.7774698!2d51.4293734!1m5!1m1!1s0x47b8c09d4664abbb:0x4148433935ab58e!2m2!1d6.7999517!2d51.4332526!3e2!5i1?entry=ttu]&lt;br /&gt;
* By plane: &lt;br /&gt;
** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent.   &lt;br /&gt;
** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf (&amp;quot;QDU&amp;quot; in &amp;quot;airport code notation&amp;quot;)  and Frankfurt airport.   The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=225</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=225"/>
		<updated>2023-08-09T14:46:47Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: /* Collaborators */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany. [[How_To_Reach_Us| &#039;&#039;&#039;Here&#039;s how to find me.&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Recent and current collaborators, in no particular order ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
* [https://www.omilletlab.com/oscar-millet Dr. Óscar Millet], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://www.ikerbasque.net/en/gabriel-ortega-quintanilla Dr. Gabriel Ortega], CIC bioGUNE, Derio, Bizkaia, Spain.&lt;br /&gt;
* [https://cranslab.colostate.edu Prof. Debbie Crans], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [https://levingerlab.colostate.edu/people/ Prof. Nancy Levinger], Colorado State University, Fort Collins, Colorado.&lt;br /&gt;
* [http://www.nedaaee.com/nedaaee.com/ Prof. Seyed Ehsan Nedaaee Oskoee], Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.&lt;br /&gt;
* [https://www.kth.se/profile/tyrode/ Prof. Eric Tyrode], KTH Royal Institute of Technology, Stockholm, Sweden.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=224</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=224"/>
		<updated>2023-07-27T09:55:05Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: /* Useful information */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany. [[How_To_Reach_Us| &#039;&#039;&#039;Here&#039;s how to find me.&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* Guidelines for &amp;lt;strong&amp;gt;good teaching and scientific practice&amp;lt;/strong&amp;gt;, and contact details for ombudspersons and ethics committees of DUE are [https://www.uni-due.de/en/good-research-practice/ here].  The ombudsperson may be contacted &amp;lt;strong&amp;gt;confidentially&amp;lt;/strong&amp;gt; by students or post-docs if you have conflicts of a scientific nature with your advisor that you feel you cannot address by a direct conversation with the advisor.&lt;br /&gt;
* The [https://www.uni-due.de/gleichstellung/index.php Gender Equality Officers (GEOs)] and the [https://www.uni-due.de/prwiss/kontakt.php Personalrat (PR)] may be contacted by students or post-docs for guidance to solve &amp;lt;strong&amp;gt;problems of a non-scientific nature&amp;lt;/strong&amp;gt; with the advisor. GEOs and the PR have a broad understanding of the university, so they are good initial contact partners even for issues that you think are outside their competence; they will be able to indicate who is the best contact partner for a given issue. &lt;br /&gt;
** Both GEOs and the PR are under &amp;lt;strong&amp;gt;Schweigepflicht (strict confidentiality)&amp;lt;/strong&amp;gt;. They cannot take action or even disclose any information you give them without your explicit permission.&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=223</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=223"/>
		<updated>2023-06-26T15:40:08Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany. [[How_To_Reach_Us| &#039;&#039;&#039;Here&#039;s how to find me.&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
[[Image:Robin_pic.jpg|frameless]]&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=File:Robin_pic.jpg&amp;diff=222</id>
		<title>File:Robin pic.jpg</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=File:Robin_pic.jpg&amp;diff=222"/>
		<updated>2023-06-26T11:56:44Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=221</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=221"/>
		<updated>2023-06-19T13:26:22Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany. [[How_To_Reach_Us| &#039;&#039;&#039;Here&#039;s how to find me.&#039;&#039;&#039;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=220</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=220"/>
		<updated>2023-06-19T13:22:48Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* Campus map:&lt;br /&gt;
[[Image:HowToReachUs.png|frameless|upright=3]] &lt;br /&gt;
* By car:  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot.&lt;br /&gt;
* By train/public transportation:  Take a train to Duisburg Hbf or Mülheim Hbf, then take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;.&lt;br /&gt;
* By plane: &lt;br /&gt;
** Flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent.   &lt;br /&gt;
** Flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg Hbf also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf Hbf (&amp;quot;QDU&amp;quot; in &amp;quot;airport code notation&amp;quot;)  and Frankfurt airport.   The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Duisburg Hbf.  Unfortunately, Lufthansa and Deutsche Bahn try their absolute best to hide this information; there&#039;s no good way to check online.  However, you can go to the Deutsche Bahn customer service desk in Duisburg Hbf or FRA and just ask.   If the ICE train going between FRA and QDU also stops in Duisburg Hbf, just buy the extra ticket.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=219</id>
		<title>How To Reach Us</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=How_To_Reach_Us&amp;diff=219"/>
		<updated>2023-06-19T12:30:29Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: Created page with &amp;quot;* Campus map: frameless * How to reach us:   ** By car:  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot ** By train/public transportation:  Take a train to Duisburg HBf, then take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot; ** By plane:  *** flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent.    *** flying into Frankfurt (&amp;quot;FRA&amp;quot;),...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;* Campus map:&lt;br /&gt;
[[Image:HowToReachUs.png|frameless]]&lt;br /&gt;
* How to reach us:  &lt;br /&gt;
** By car:  &amp;quot;Carl-Benz-Strasse 201, Duisburg&amp;quot; in Google Maps will lead you to the University parking lot&lt;br /&gt;
** By train/public transportation:  Take a train to Duisburg HBf, then take Tram 901 and exit at station &amp;quot;Zoo/Uni&amp;quot;&lt;br /&gt;
** By plane: &lt;br /&gt;
*** flying to Düsseldorf (&amp;quot;DUS&amp;quot;) airport is convenient; the train connections from the airport to Duisburg Hbf are very frequent.   &lt;br /&gt;
*** flying into Frankfurt (&amp;quot;FRA&amp;quot;), and then taking an ICE train from the airport to Duisburg also works very well.  In particular, Lufthansa offers combined flight+train tickets between Düsseldorf HBf (&amp;quot;QDU&amp;quot;; NOT Düsseldorf airport!)  and Frankfurt airport.   The combined ticket is advantageous because the train part of the trip as another flight (eg., in case of delays or cancellations). Sometimes, the ICE  from Frankfurt to QDU actually continues all the way to Bochum.  Unfortunately, there’s no easy way to confirm this online; for some reason, Lufthansa and Deutsche Bahn try their absolute best to hide this information.  However, you could ask the conductor once you are actually on the train, and if it indeed goes to Bochum then you just buy the necessary extra ticket while onboard and that’s that.&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=217</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=217"/>
		<updated>2023-06-17T06:01:44Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: /* News */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=216</id>
		<title>Jobs</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=216"/>
		<updated>2023-06-17T05:59:35Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__TOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--- ==Open positions==&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
 [https://www.linkedin.com/jobs/view/2971284979  PhD position - Probing the structure and thermodynamics of solvation and of aggregation of fluorinated molecules with simulations]&lt;br /&gt;
&lt;br /&gt;
08.2022: There is an open PhD position in the group. &lt;br /&gt;
&lt;br /&gt;
---&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==How to prepare for your interview==&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
* The interview will take approximately 1h.  &lt;br /&gt;
* I must be able to clearly see you and hear you; please ensure a stable internet connection.  &lt;br /&gt;
* You should prepare a 15 to 20 min long talk about your prior research.  The talk should be supported by presentation slides. &lt;br /&gt;
# The first slide should be about you: remind me of the main points of your application (e.g., your BSc. and MSc. grades, topics of BSc. projects). Emphasize your STRONGEST points (e.g., research work initiated by you or done independently; prior expertise that matches the requirements of the position for which you are applying).  Explain unusual events in your CV (e.g., long time to complete your MSc. because of sickness; an MSc. thesis with few results because of limited computational resources).  Keep it short (&amp;lt; 3 min).&lt;br /&gt;
# Focus on ONE research topic (for PhD candidates, this would be the research you did towards you Master degree).  I encourage you to show your slides to colleagues so that they are clear and have no obvious mistakes, and also that you practice the talk in front of them.    Structure the talk so that a listener understands: &lt;br /&gt;
## What is the scientific question motivating that work;  &lt;br /&gt;
## Why is that question important;  &lt;br /&gt;
## How you approached the question (which methods you used and why are they appropriate); &lt;br /&gt;
## What are your results and what can be learned from them. &lt;br /&gt;
# Things to keep in mind: &lt;br /&gt;
## Make sure you understand the physical meaning of the observables you show, and the units in which these observables are expressed.&lt;br /&gt;
## Have the mathematical expression used to calculate the observables either in the main slide or in a support slide.  Make sure it is correct (!) and that you understand what you calculated.&lt;br /&gt;
&lt;br /&gt;
* During the talk I will interrupt you many times with questions; don&#039;t be put off by this.&lt;br /&gt;
* After the talk I will answer your questions about the project I am offering, my group, life in Duisburg, etc... &lt;br /&gt;
** I have noticed that many applicants barely ask me questions, perhaps out of shyness or out of concern they will appear rude or pushy.  To be clear:  I typically get a favorable impression about applicants that ask questions that will enable them to decide whether the project, my group, the University of Duisburg-Essen and the city of Duisburg are good fits for them.  Not asking questions is more likely to count against you than in your favor...&lt;br /&gt;
* We keep going until we are both out of questions or the time is up, whichever comes first.  By the end of it, we should both be in a position to decide whether we&#039;d work well together on the project for which you apply.&lt;br /&gt;
* I do interviews so I can assess your intellectual maturity,  your ability to communicate in English, and if your expectations and mine are a good fit so that the project can be carried out successfully. I want to get a feel for your level of understanding about fundamental knowledge from your undergraduate degree and your own prior research work, as well as your ability to think like a scientist.&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=215</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=215"/>
		<updated>2023-06-17T05:54:53Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.jpg|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; Guests&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Fatemeh Mehdikhani (starting 15.05.2023)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=File:Mehdikhani.jpg&amp;diff=214</id>
		<title>File:Mehdikhani.jpg</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=File:Mehdikhani.jpg&amp;diff=214"/>
		<updated>2023-06-17T05:53:08Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=213</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=213"/>
		<updated>2023-06-17T05:52:06Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.15: Fatemeh Mehdikhani, a PhD student from the group of Prof. Ehsan Nedaaee at the Institute for Advanced Studies in Basic Sciences, is visiting us for 6 months on a RESOLV fellowship.  Welcome Fatemeh!&lt;br /&gt;
[[Image:Mehdikhani.png|frameless]]&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=212</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=212"/>
		<updated>2023-06-01T07:27:53Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=211</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=211"/>
		<updated>2023-06-01T07:17:33Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;font-size:large;&amp;quot;&lt;br /&gt;
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! 23.05.31: Hosein&#039;s paper explaining the [https://www.cell.com/biophysj/pdf/S0006-3495(23)00323-5.pdf prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins] was just published in the Biophysical Journal.&lt;br /&gt;
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* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=210</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=210"/>
		<updated>2023-06-01T07:01:11Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.31: Hosein&#039;s paper explaining the [https://www.cell.com/biophysj/pdf/S0006-3495(23)00323-5.pdf prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins] was just published in the Biophysical Journal.&lt;br /&gt;
* 23.03.01:  Our paper [https://onlinelibrary.wiley.com/doi/full/10.1002/mabi.202200563 Chain Sliding versus β-Sheet formation upon shearing single α-helical coiled coils] was published in Macromolecular Bioscience.  Through simulations by Ana Vila Verde, Single Molecule Force Spectroscopy experiments done in the group of [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Kerstin Blank] and physical insight from [https://www.mpikg.mpg.de/valleriani  Angelo Valleriani], we were able to show that the alpha-to-beta transition of protein coiled coils pulled in shear geometry is less likely for dimeric coiled coils and at low pull speeds, because chain sliding and chain dissociation preferentially occur under those conditions.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=209</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Main_Page&amp;diff=209"/>
		<updated>2023-06-01T05:27:03Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;big&amp;gt;&amp;lt;strong&amp;gt;Computational Soft Matter and Interfaces&amp;lt;/strong&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt;&amp;lt;/big&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
&#039;&#039;&#039; On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time.&#039;&#039;&#039;  You&#039;ll know I&#039;ve pulled myself together when there is enough information here to make it useful.&lt;br /&gt;
&lt;br /&gt;
[[Image:AnaVilaVerde.JPG|thumb|&amp;lt;big&amp;gt;Dr. Ana Vila Verde (she)&amp;lt;/big&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;My CV, funding, referee activities can be seen in my &#039;&#039;&#039; [https://orcid.org/0000-0003-0337-3972 ORCID record]. My [https://publons.com/researcher/1670773/ana-vila-verde/ pubIons] record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Publications:&#039;&#039;&#039; best checked in my [https://scholar.google.com/citations?user=wKC6n28AAAAJ&amp;amp;hl=en Google Scholar profile], which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Postal address&#039;&#039;&#039;&lt;br /&gt;
University of Duisburg-Essen,&lt;br /&gt;
Faculty of Physics (AG Kuiper),&lt;br /&gt;
Lotharstr. 1,&lt;br /&gt;
47057 Duisburg,&lt;br /&gt;
Germany&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Where I do my thinking:&#039;&#039;&#039; building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Email:&#039;&#039;&#039; ana.araujo-vila-verde _at_ uni-due.de&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Jobs ==&lt;br /&gt;
&lt;br /&gt;
* Post-doc positions: I have no positions available. &lt;br /&gt;
&lt;br /&gt;
 PhD students in their last year or who very recently graduated, with excellent writing skills and who wish to develop a research idea that fits well in my group, are welcome to contact me to develop an application for the [https://www.dfg.de/en/research_funding/programmes/individual/walter_benjamin/index.html Walter Benjamin program], which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.&lt;br /&gt;
&lt;br /&gt;
* PhD positions &lt;br /&gt;
&lt;br /&gt;
 The [https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?status=&amp;amp;origin=&amp;amp;subjectGrps=&amp;amp;daad=&amp;amp;intention=&amp;amp;q=&amp;amp;page=1&amp;amp;detail=57135739 DAAD] accepts applications from students of some developing countries to do their PhD in Germany.   Students who are in the last year of an MSc. in Physics or Chemistry or who have recently completed their MSc., who have excellent writing skills and top grades (minimum average A, or 80%) in their MSc. and BSc., and who want to develop a research idea that fits well in my group, are welcome to contact me to develop an application.  &lt;br /&gt;
&lt;br /&gt;
*  [[Jobs | How to interview for a PhD or post-doc position]]&lt;br /&gt;
&lt;br /&gt;
== News ==&lt;br /&gt;
* 23.05.31: Hosein&#039;s paper explaining the [https://www.cell.com/biophysj/pdf/S0006-3495(23)00323-5.pdf prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins] was just published in the Biophysical Journal.&lt;br /&gt;
* 23.01.15:  Robin Singh has joined us for 3 years as PhD student.  Welcome Robin!&lt;br /&gt;
* 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!&lt;br /&gt;
[[Image:Elio.png|frameless]]&lt;br /&gt;
* Congratulations to Hosein Geraili for defending his PhD Thesis &#039;&#039;The role of acidic amino acids in the hydration and stabilization of halophilic proteins&#039;&#039;!&lt;br /&gt;
[[Image:ForWebpage.png|frameless]]&lt;br /&gt;
* Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the [https://doi.org/10.1016/j.bpj.2021.05.015 Biophysical Journal], &lt;br /&gt;
* Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in [https://doi.org/10.1039/D0SM01166E PCCP]. &lt;br /&gt;
* João Robalo shows that features of the hydration shell of  CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are fundamentally different from those around CH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; in his paper in [https://doi.org/10.1021/jacs.9b06862 JACS].&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Topics == &lt;br /&gt;
&#039;&#039;(For now, just a few place holders.  &amp;quot;Soon&amp;quot; I&#039;ll write something that conveys how excited I am about what I do -  hint: I like doing the work more than I like writing my webpage.)&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
We use particle-based simulation methods to investigate the structure and dynamics of soft matter and of interfaces, both biological and inorganic. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom,  coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.&lt;br /&gt;
&lt;br /&gt;
* Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations &lt;br /&gt;
* Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation&lt;br /&gt;
* Mechanical response of proteins to applied force&lt;br /&gt;
* Hydration of inorganic and organic ions; ion-ion interactions&lt;br /&gt;
* [[#Force field development|Force field development]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Members ==&lt;br /&gt;
&#039;&#039;&#039; Post-docs&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=jT0cwvYAAAAJ&amp;amp;hl=en Dr. Hosein Geraili], who completed his PhD in the group and continued his project as a post-doc.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039; PhD students&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
* Robin Singh (starting 15.01.2023)&lt;br /&gt;
&lt;br /&gt;
* Elio Casalini (starting 15.06.2022)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Former Members&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
I have been fortunate to work with some wonderful students and post-docs.  Here they are:&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?user=htxC8PUAAAAJ&amp;amp;hl=en Dr. Ana Elisa Bergues-Pupo], currently a Bioinformatics Scientist at Targenomix GmbH, in Berlin.&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.es/citations?hl=en&amp;amp;user=ge4yXdAAAAAJ Dr. João Robalo]&amp;lt;!--, currently at the Max Planck Institute for Colloids and Interfaces, Golm, Germany. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
* [https://scholar.google.com/citations?user=EfHrGvkAAAAJ&amp;amp;hl=en Dr. Sadra Kashefolgheta], currently at the R&amp;amp;D Pharmaceuticals department of Bayer, Wuppertal, Germany. &lt;br /&gt;
&lt;br /&gt;
* Dr. Chuanfu Luo &amp;lt;!--, currently at the State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Collaborators ==&lt;br /&gt;
* [https://sites.psu.edu/cremer/ Prof. Paul Cremer ], Penn State University, State College, Pennsylvania, USA.&lt;br /&gt;
* [https://ccb.tu-dortmund.de/en/professorships/pc/linser/ Prof. Dr. Rasmus Linser ], Technische Universität Dortmund, Dortmund, Germany.&lt;br /&gt;
* [https://www.ruhr-uni-bochum.de/pc2/petersen/ Prof. Dr. Poul Petersen ], Ruhr-Universität Bochum, Bochum, Germany.&lt;br /&gt;
* [https://www.jku.at/en/institute-of-experimental-physics/biomolecular-selforganizing-matter/about-us/ Univ.-Prof. Dr. Kerstin Blank ], Johannes Kepler University Linz, Linz, Austria.&lt;br /&gt;
* [https://www.mpikg.mpg.de/valleriani  Dr. Angelo Valleriani], Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.&lt;br /&gt;
* [https://www.chem.purdue.edu/bendor/ Prof. Dr. Dor Ben-Amotz ], Dept. Chemistry, Purdue University, USA.&lt;br /&gt;
* [https://www.bcp.fu-berlin.de/en/chemie/chemie/forschung/OrgChem/koksch/index.html  Prof. Dr. Beate Koksch], Department of Biology, Chemistry, Pharmacy/, Free University of Berlin, Germany.&lt;br /&gt;
* [https://www.chemistry.nat.fau.eu/person/petra-imhof/ Prof. Dr. Petra Imhof], Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg, Germany.&lt;br /&gt;
* [https://www.desy.de/about_desy/lead_scientists/melanie_schnell/index_eng.html Prof. Dr. Melanie Schnell], Christian-Albrechts-Universität zu Kiel, Germany.&lt;br /&gt;
* [https://www.uni-goettingen.de/de/642624.html J. Prof. Dr. Dan Obenchain], Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Germany.&lt;br /&gt;
&lt;br /&gt;
== Force field development ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Optimized parameters for ions in the AMBER/GAFF force field:  AMBER-ready input files [https://ars.els-cdn.com/content/image/1-s2.0-S0006349521004446-mmc2.zip here]; Gromacs-ready input files [https://www.rsc.org/suppdata/c7/cp/c7cp02557b/c7cp02557b3.zip?_ga=2.148149042.489513478.1629728775-1557646847.1629452218 here]&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
The Amber/GAFF suite of force fields is widely used by the molecular simulation community.  We have recently developed Lennard-Jones parameters (see the SI of [https://doi.org/10.1039/C7CP02557B] and of [https://doi.org/10.1016/j.bpj.2021.05.015]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF.  We provide improved parameters for the interaction of anions (&#039;&#039;&#039;carboxylates, sulfates, sulfonates, phosphates&#039;&#039;&#039;) with &#039;&#039;&#039;TIP3P&#039;&#039;&#039; water and with important cations (&#039;&#039;&#039;sodium&#039;&#039;&#039;, &#039;&#039;&#039;potassium&#039;&#039;&#039;, &#039;&#039;&#039;ammonium&#039;&#039;&#039; and &#039;&#039;&#039;primary amines&#039;&#039;&#039;).  We &#039;&#039;strongly&#039;&#039; recommend using these parameters to adequately describe, e.g., salt bridges between &#039;&#039;&#039;acidic amino acids&#039;&#039;&#039; and &#039;&#039;&#039;lysine&#039;&#039;&#039;, and protein solvation at high &#039;&#039;&#039;NaCl&#039;&#039;&#039; and &#039;&#039;&#039;KCl&#039;&#039;&#039; concentrations.  Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Force fields for fluorinated amino acids: &#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
AMBER-ready input files to simulate amino acids with CF&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; groups are in the SI of [https://doi.org/10.1016/j.chempr.2017.09.012 this paper], and for those with CF and CF&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups are [https://doi.org/10.1039/C8CP07025C here]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;DIY: Modifying Lennard-Jones parameters in the Amber force field&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Should you ever need to do it yourself, [[Media:Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf|this tutorial]]  explains how to: &lt;br /&gt;
*  Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins. &lt;br /&gt;
*  Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.&lt;br /&gt;
&lt;br /&gt;
== Useful information ==&lt;br /&gt;
* [https://udue.de/acluster Group cluster]&lt;br /&gt;
* [[lbox-hints| Roadmap to get started in the group]]&lt;br /&gt;
&lt;br /&gt;
== Research affiliations and funding ==&lt;br /&gt;
&amp;lt;gallery widths=&amp;quot;250px&amp;quot; &amp;gt;&lt;br /&gt;
File:RESOLVlogo.png|link=https://www.solvation.de&lt;br /&gt;
File:DFGlogo.jpg|link=https://www.dfg.de/foerderung/programme/index.html&lt;br /&gt;
File:LogoSPP1807.png|link=https://www.uni-giessen.de/fbz/fb08/dispersion/ssp1807projects&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=208</id>
		<title>Jobs</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=Jobs&amp;diff=208"/>
		<updated>2023-03-24T08:24:28Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: &lt;/p&gt;
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&lt;div&gt;__TOC__&lt;br /&gt;
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&amp;lt;!--- ==Open positions==&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
 [https://www.linkedin.com/jobs/view/2971284979  PhD position - Probing the structure and thermodynamics of solvation and of aggregation of fluorinated molecules with simulations]&lt;br /&gt;
&lt;br /&gt;
08.2022: There is an open PhD position in the group. &lt;br /&gt;
&lt;br /&gt;
---&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==How to prepare for your interview==&lt;br /&gt;
&amp;lt;big&amp;gt;&lt;br /&gt;
* The interview will take approximately 1h.  &lt;br /&gt;
* I must be able to clearly see you and hear you; please ensure a stable internet connection.  &lt;br /&gt;
* You should prepare a 15 to 20 min long talk about your prior research.  The talk should be supported by presentation slides. &lt;br /&gt;
# The first slide should be about you: remind me of the main points of your application (e.g., your BSc. and MSc. grades, topics of BSc. projects). Emphasize your STRONGEST points (e.g., research work initiated by you or done independently; prior expertise that matches the requirements of the position for which you are applying).  Explain unusual events in your CV (e.g., long time to complete your MSc. because of sickness; an MSc. thesis with few results because of limited computational resources).  Keep it short (&amp;lt; 3 min).&lt;br /&gt;
# Focus on ONE research topic (for PhD candidates, this would be the research you did towards you Master degree).  I encourage you to show your slides to colleagues so that they are clear and have no obvious mistakes, and also that you practice the talk in front of them.    Structure the talk so that a listener understands: &lt;br /&gt;
## What is the scientific question motivating that work;  &lt;br /&gt;
## Why is that question important;  &lt;br /&gt;
## How you approached the question (which methods you used and why are they appropriate); &lt;br /&gt;
## What are your results and what can be learned from them. &lt;br /&gt;
# Make sure you understand: &lt;br /&gt;
## The physical meaning of the observables you show, and the units in which these observables are expressed.&lt;br /&gt;
## Have the mathematical expression used to calculate the observables either in the main slide or in a support slide.  Make sure it is correct (!) and that you understand what you calculated.&lt;br /&gt;
&lt;br /&gt;
* During the talk I will interrupt you many times with questions; don&#039;t be put off by this.&lt;br /&gt;
* After the talk I will answer your questions about the project I am offering, my group, life in Duisburg, etc... &lt;br /&gt;
** I have noticed that many applicants barely ask me questions, perhaps out of shyness or out of concern they will appear rude or pushy.  To be clear:  I typically get a favorable impression about applicants that ask questions that will enable them to decide whether the project, my group, the University of Duisburg-Essen and the city of Duisburg are good fits for them.  Not asking questions is more likely to count against you than in your favor...&lt;br /&gt;
* We keep going until we are both out of questions or the time is up, whichever comes first.  By the end of it, we should both be in a position to decide whether we&#039;d work well together on the project for which you apply.&lt;br /&gt;
* I do interviews so I can assess your intellectual maturity,  your ability to communicate in English, and if your expectations and mine are a good fit so that the project can be carried out successfully. I want to get a feel for your level of understanding about fundamental knowledge from your undergraduate degree and your own prior research work, as well as your ability to think like a scientist.&lt;br /&gt;
&amp;lt;/big&amp;gt;&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
	</entry>
	<entry>
		<id>https://wiki.uni-due.de/vilaverde/index.php?title=File:Logo.png&amp;diff=207</id>
		<title>File:Logo.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.uni-due.de/vilaverde/index.php?title=File:Logo.png&amp;diff=207"/>
		<updated>2023-03-22T10:31:21Z</updated>

		<summary type="html">&lt;p&gt;Vilaverde: Vilaverde uploaded a new version of File:Logo.png&lt;/p&gt;
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&lt;div&gt;== Summary ==&lt;br /&gt;
Logo&lt;/div&gt;</summary>
		<author><name>Vilaverde</name></author>
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