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.
Sonoporation at small and large length scales: Effect of cavitation bubble collapse on membranes. Ultrasound has emerged as a promising means to effect controlled delivery of therapeutic agents through cell membranes. One possible mechanism that explains the enhanced permeability of lipid bilayers is the fast contraction of cavitation bubbles produced on the membrane surface, thereby generating large impulses, which, in turn, enhance the permeability of the bilayer to small molecules. In the present contribution, we investigate the collapse of bubbles of different diameters, using atomistic and coarse-grained molecular dynamics simulations to calculate the force exerted on the membrane. The total impulse can be computed rigorously in numerical simulations, revealing a superlinear dependence of the impulse on the radius of the bubble. The collapse affects the structure of a nearby immobilized membrane, and leads to partial membrane invagination and increased water permeation. The results of the present study are envisioned to help optimize the use of ultrasound, notably for the delivery of drugs. J. Phys. Chem. Lett., 2015.
Efficient determination of relative entropy using combined temperature and Hamiltonian replica-exchange molecular dynamics
J. Chem. Theory Comput.
2015, 11 (5), 2234-2244.
Comer, J.; Gumbart, J. C.; Hénin, J.; Lelièvre, T.; Pohorille, A.; Chipot, C.
The adaptive biasing force method: Everything you always wanted to know, but were afraid to ask
J. Phys. Chem. B
2015, 119 (3), 1129-1151.
Fu, H.; Comer, J.; Cai, W.; Chipot, C
Sonoporation at small and large length scales. Effect of cavitation bubble collapse on membranes
J. Phys. Chem. Letters
2015, 6 (3), 413-418.
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