Benoit Roux, University of Chicago.
September 28, 2021. 3:35 – 4:50 pm.
A Joint Virtual Seminar with IIT’s Chemistry Colloquium on Zoom.
Classical molecular dynamics simulations based on atomic models play an increasingly important role in a wide range of applications in physics, biology and chemistry. The approach 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 literally “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 impossible to access experimentally. Specialized free energy simulations are also an important route to establish a strong connection to experiments. The development of efficient methods for simulating slow conformational transitions is another subject of great interest in computational studies of biomolecular system. A powerful paradigm for mapping the conformational landscape of biomolecular systems is to combine free energy methods, transition pathway techniques and stochastic Markov State Model based massively distributed simulations. These concepts will be illustrated with a few recent computational studies of Src tyrosine kinases, K+ channels, and the P-type ion pumps.