Nanobiomodelling: Physics for proteins and molecular modelisation

Teachers : P. Senet / A. Nicolai

The course is an introduction to the methods used to simulate proteins and other biological molecules using physics-based models.  The basics of ab initio calculations (DFT, Hartree-Fock), semi-empirical approaches (tight binding), classical molecular dynamics, and Monte Carlo methods are reviewed with applications to biosystems in mind. Coarse-grained methods and simplified models of biopolymers are briefly introduced. The simulation methods are presented and discussed in relation to current experimental techniques to probe the dynamics and folding of proteins (FRET, single molecule spectroscopies, SAXS…).  The students will apply the methods to solve simple problems (calculation of electronic properties of small molecules, conformations and IR spectra of peptides, normal modes of large proteins…) using resources of the computer center of the University.