
[Dr. Jayandren Rasaiah] Course Offerings  (Schedule Variable)
Chemical Simulation Methods:
(CHY 573)
(3 Credit Hours)
The course discusses Monte Carlo and Molecular Dynamics simulation methods with applications in chemistry, physics, chemical engineering, materials science and molecular biology. Students are required to complete programming assignments in the main simulations methods discussed in class. Hands on experience will be provided with model programs on Silicon Graphics(SGI) workstations in Aubert Hall which could also be accessed through the campus network with appropiate software and a password.
Fortran is the programming language used for the course. UNIX is the operating system for the SGI workstations. An introduction to basic UNIX commands will be taught simultaneously.
Prerequisites: Undergraduate Physical Chemistry CHY471 or Introductory Modern Physics PHY236, and a knowledge of Fortran)
Syllabus
 Ensembles. The Microcanonical, Canonical and Grand Canonical Ensembles. Ensemble Averages and Fluctuations. Time averages and the ergodic theorem. Time correlation functions. Density of states.
 Molecular Dynamics: Integrating schemes (Verlet algorithm, predictorcorrector methods) for the microcanonical ensemble, periodic boundary conditions. Constant temperature and constant chemical potential simulations. Simulations of argon and a simple dipolar fluid using the method of constraints. Simulation of a simple point charge (SPC) model for water using quaternions or the SHAKE algorithm. Calculations of ion solvation energy and dynamics.
 Brownian Dynamics. Langevin equation and Diffusion. Simulation of an enzyme substrate reactions.
 Monte Carlo Simulations. Importance Sampling and the Metropolis method. NonBoltzmann or Umbrella sampling. Ising model simulations. The Gibbs ensemble method for simulating phase equilibria. Simulation of vapor liquid equilibria for a simple (LennardJones) fluid.
 Quantum simulations. Path integral Monte Carlo. Split operator method for Quantum systems. Wave packet dynamics. Simulation of an electron in a simple fluid.
Texts and References
 Lecture Notes: by J. C. Rasaiah
 Computer Simulation Methods in Theoretical Physics: by D.W. Hermann, second edition; Springer Verlag. (1990).
 Computer Simulation of Liquids by J. Allen and D. J. Tildesley; Oxford Univ Press.(1987)
 Understanding Molecular Simulation, D.Frenkel and B. Smit, Academic Press (1996)
 Molecular Dynamics Simulation, Elementary methods by J. Haile; J. Wiley (1992)
 Simulation of Liquids and Solids, edited by G. Cicotti, D. Frenkel and I. R. McDonald. NorthHolland (1987).
 Computer Simulation of Biomolecular Systems, Eds. W.F. van Gunsteren, P.K.Weiner and A.J.Wilkinson, ESCOM Leiden (1993).