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The computational approach, called "molecular dynamics" (MD), is central to our work. It consists of constructing detailed atomic models of the macromolecular system and, having described the microscopic forces with a potential function, using Newton's classical equation, F=MA, to simulate the dynamical motions of all the atoms as a function of time. The calculated trajectory, though an approximation to the real world, provides detailed information about the time course of the atomic motions, which is nearly impossible to access experimentally. We use such all-atom MD simulations to rigorously compute conformational free energies, and binding free energies. We are particularly interested in understanding the function of biomolecular systems. We are also developing new computational approaches (polarizable force field, solvent boundary potentials, efficient sampling methods) for studying biological macromolecular systems. Here are a few area of active research in my group.
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JOURNAL OF CHEMICAL INFORMATION AND MODELINGno. 3 (2024): 1081-1091
The journal of physical chemistry lettersno. 14 (2024): 3796-3804
Journal of Chemical Information and Modeling (2024)
JOURNAL OF PHYSICAL CHEMISTRY Bno. 3 (2024): 795-811
JOURNAL OF CHEMICAL INFORMATION AND MODELINGno. 8 (2024): 3488-3502
Werner Treptow,Yichen Liu, Carlos A. Z. Bassetto Jr,Bernardo I. Pinto, João Alves,Christophe Chipot,Francisco Bezanilla,Benoît Roux
arxiv(2024)
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Nature Communicationsno. 1 (2024): 1-13
Cell reportsno. 10 (2023): 113190-113190
JOURNAL OF CHEMICAL THEORY AND COMPUTATIONno. 24 (2023): 9077-9092
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