Molecular Dynamics Modeling

Welcome to CSI 786

Wednesdays 4:30-7:10 PM, R1, room 301

Instructor: Estela Blaisten-Barojas

SPRING 2011

The course is part of the Computational Materials and Chemical Sciences and of the Computational Physics components of the doctoral program in Computational Sciences and Informatics and counts as one of the core science courses in this doctoral degree. The course is one of the computational science courses in the masters in Computational Science and is an elective topics course in the PhDs in Chemistry (register in CHEM 579) and Physics and Astronomy (register in PHYS 780).

Theme of the course: Molecular Dynamics Simulation

Molecular dynamics and Monte Carlo methods are now orthodox means for simulating molecular-scale models of matter. The methods were originally devised in the 1950's, began to receive widespread attention in the mid-1970's, and are today a fundamental scientific approach to design nano, macro, supra molecular systems, as well as bulk materials, glasses, polymers, surfaces, and interfaces. The methodology has been adopted by computational biologists, and is today an essential element of bio-oriented research. Molecular dynamics methods solve numerically the N-body problem of classical mechanics. Its importance shows when studying how atoms self-assemble into ordered or disordered solid materials, how molecules in solution self-assemble into structures such as micelles, how fluid around an object produces a turbulent wake, how a local disturbance on a few molecules propagates throughout a system in the condensed phases, among other important natural phenomena. This server will expand as the semester progresses.

Textbooks and Course Materials

The textbook for this course is:

  • Molecular Dynamics Simulation , by J. M. Haile, John Wiley, 1992.

    A suplemental textbook is:

  • Understanding Molecular Simulation, by Daan Frenkel and Berend Smit, Academic Press, 2nd edition 2004.

    Other relevant material will be taken from:

  • Computer Simulation of Liquids by M. P. Allen and D. J. Tildesley
  • StatisticalMechanics by Donald McQuarrie
  • Monte Carlo Methods in Statistical Physics by K. Binder
  • Classical Dynamics by J. B. Marion
  • Numerical Recipes by W.H. Press, B.R. Flannery, S.A. Teukolsky, and W.T. Vettering
    • The grade for this class will be based on your performance, on your semester     project, and your class presentations on the material and examples based on the textbook. You will choose the subject of the research project (to my approval concerning its feasibility). The final project will undergo two stages. In the first a "hand-in" draft will be produced, for reviewing by two referees: one of your classmates and myself. The second stage will consist of a final written project report and a final presentation in the form of a scientific conference oral paper.

    Estela Blaisten-Barojas, blaisten-at-gmu.edu