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The Laboratoire International Associé between the Centre National de la Recherche Scientifique and the University of Illinois at Urbana-Champaign was launched at the end of 2012. Its primary objective is to develop methods for high-performance molecular simulation with the aim of understanding the function of complex biological assemblies, transcending the frontiers of traditional disciplines by uniting mathematicians, physicists, theoretical chemists and biologists on both sides of the Atlantic. In France, the major contributors are located at the Université de Lorraine, the École des Ponts ParisTech, the Institut de Biologie et Chimie des Protéines-Université Claude Bernard and the Laboratoire d'Ingénierie des Systèmes Macromoléculaires-Université d'Aix-Marseille. In the United States, the contributors belong to the NIH Resource for Macromolecular Modeling and Bioinformatics. In Nancy, the partner is a theoretical chemistry and biophysics group incepted in 2003. Its expertise lies in describing the structure and the dynamic properties of the biological membrane and elucidating the mechanisms of the cell machinery. To attain this goal, its members leverage numerical simulations over size and timescales commensurate with the biological process at hand. Over the years, the team has gleaned milestone results in such diverse research areas as membrane transport, interaction with the biological membrane, membrane protein structure and function, as well as self-organized molecular systems. They also develop original approaches in the field of free-energy calculations, as well as that of intermolecular potentials.

### Highlight

**Calculating position-dependent diffusivity in biased molecular dynamics simulations.**Calculating transition rates and other kinetic quantities from molecular simulations requires knowledge not only of the free energy along the relevant coordinate but also the diffusivity as a function of that coordinate. A variety of methods are currently used to map the free-energy landscape in molecular simulations; however, simultaneous calculation of position-dependent diffusivity is complicated by biasing forces applied with many of these methods. Here, we describe a method to calculate position-dependent diffusivities in simulations including known time-dependent biasing forces, which relies on a previously proposed Bayesian inference scheme. We first apply the method to an explicitly diffusive model, and then to an equilibrium molecular dynamics simulation of liquid water including a position-dependent thermostat, comparing the results to those of an established method. Finally, we test the method on a system of liquid water, where oscillations of the free energy along the coordinate of interest preclude sufficient sampling in an equilibrium simulation. The adaptive biasing force method permits roughly uniform sampling along this coordinate, while the method presented here gives a consistent result for the position-dependent diffusivity, even in a short simulation where the adaptive biasing force is only partially converged.

*J. Chem. Theor. Comput.*

**2013**.

### Recent publications

**Comer, J.; Schulten, K.; Chipot, C.**

Calculation of lipid-bilayer permeabilities using an average force

J.Chem. Theory Comput.2014, 10 (2), 554-564.

Calculation of lipid-bilayer permeabilities using an average force

J.Chem. Theory Comput.

dx.doi.org

**Marquardt, R.; Hénin, J.; Dehez, F.; Chipot, C.,**

Dynamiques moléculaires quantiques et classiques

L’Actualité Chimique2014, (382-383), 56-62.

Dynamiques moléculaires quantiques et classiques

L’Actualité Chimique

**Comer, J.; Roux, B.; Chipot, C.;**

Achieving ergodic sampling using replica-exchange free-energy calculations

Mol. Sim.2014, 40 (1-3), 218-228.

Achieving ergodic sampling using replica-exchange free-energy calculations

Mol. Sim.

dx.doi.org

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### Contact

**Laboratoire International Associé**

**CNRS-UIUC**

**Unité mixte de recherche n°7565 Université de Lorraine, B.P. 7023954506 Vandoeuvre-lès-Nancy Cedex, France**

Phone: +33.(0)3.83.68.40.97Fax: +33.(0)3.83.68.43.87 How to reach us