Atomisitc Modeling and Computation

The development of high-speed computers in recent years has made possible numerical simulations of many physical processes at the atomistic scale. This course will cover various topics in the area of atomistic modeling and computation of materials with an emphasis on biomolecules and fluid systems. Topics to be covered include empirical force fields for the modeling of fluids and biomolecules, symplectic integrators for Hamiltonian systems, molecular dynamics simulation in various ensembles, Monte Carlo and kinetic Monte Carlo method. More advanced topics such as constrained molecular dynamics simulations, free energy calculations and methods for treating barrier-crossing events will also be discussed.