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Computational Soft Matter and Interfaces

On-going effort to tell you how I (Ana Vila Verde) and my research group spend our time. You'll know I've pulled myself together when there is enough information here to make it useful.

Dr. Ana Vila Verde (she)

My CV, funding, referee activities can be seen in my ORCID record. My pubIons record is also reasonably informative (my referee activities are incomplete, though); my Scopus record is out-of-date.

Publications: best checked in my Google Scholar profile, which I keep tidy and up-to-date (mostly), or using my ResearcherID (H-7805-2013) in Web of Science.

Postal address University of Duisburg-Essen, Faculty of Physics (AG Kuiper), Lotharstr. 1, 47057 Duisburg, Germany

Where I do my thinking: building MF, office 246 (2nd floor), Lotharstr. 1, 47057 Duisburg, Germany

Email: ana.araujo-vila-verde _at_ uni-due.de

Jobs

• Post-doc positions: I have no positions available.
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 Walter Benjamin program, which currently has high success rates.  The whole procedure takes about 9 months.  The program has no nationality restrictions.

• PhD positions
The 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.


News

• 23.01.15: Robin Singh has joined us for 3 years as PhD student. Welcome Robin!
• 22.05.09: From June 15 onwards, Elio Casalini will join us for three years as a PhD student. Welcome Elio!

• Congratulations to Hosein Geraili for defending his PhD Thesis The role of acidic amino acids in the hydration and stabilization of halophilic proteins!

• Hosein Geraili shows that acidic amino acids are not necessary to keep proteins hydrated at high concentrations of KCl in his article in the Biophysical Journal,
• Ana Bergues clarifies the mechanisms governing the deformation of peptide alpha helices pulled in tension in her article in PCCP.
• João Robalo shows that features of the hydration shell of CF3 groups are fundamentally different from those around CH3 in his paper in JACS.

Topics

(For now, just a few place holders. "Soon" I'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.)

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.

• Halophilic proteins: understanding the origin of their surprising functionality at high salt concentrations
• Fluorinated (bio)molecules: how fluorination impacts the structure, dynamics and thermodynamics of hydration, the hydrophobic effect, and protein stability and conformation
• Mechanical response of proteins to applied force
• Hydration of inorganic and organic ions; ion-ion interactions
• Force field development

Members

Post-docs

• Dr. Hosein Geraili, who completed his PhD in the group and continued his project as a post-doc.

PhD students

• Robin Singh (starting 15.01.2023)
• Elio Casalini (starting 15.06.2022)

Former Members

I have been fortunate to work with some wonderful students and post-docs. Here they are:

• Dr. Chuanfu Luo

Force field development

Optimized parameters for ions in the AMBER/GAFF force field: AMBER-ready input files here; Gromacs-ready input files here

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 [1] and of [2]) that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF. We provide improved parameters for the interaction of anions (carboxylates, sulfates, sulfonates, phosphates) with TIP3P water and with important cations (sodium, potassium, ammonium and primary amines). We strongly recommend using these parameters to adequately describe, e.g., salt bridges between acidic amino acids and lysine, and protein solvation at high NaCl and KCl 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.

Force fields for fluorinated amino acids:

AMBER-ready input files to simulate amino acids with CF3 groups are in the SI of this paper, and for those with CF and CF2 groups are here

DIY: Modifying Lennard-Jones parameters in the Amber force field

Should you ever need to do it yourself, this tutorial explains how to:

• Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins.
• Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.