MWF 11:30-12:20, Lawson B134

Concerning "Consent of Department Required."
   Got to Lawson 1137; consent is almost always granted.

Instructor Robert Skeel

Purpose of course:
to explain how to do simulations and computations. The course describes the use of simulation packages and discusses the methodology and selected details of algorithms.

Prerequisites:
* mathematical knowledge and maturity of an MS student in the physical or chemical sciences or engineering. In particular, some probability, dif eqs, and matrix algebra, including use of multidimensional integrals to represent probability.
* programming experience in a simple language and commensurate computer skills.
* freshman course in physics.

Following are tentative plans.

Textbook:
Instructor's notes (contents)   supplemented by tutorial material from http://www.ks.uiuc.edu/Training/
Recommended:
Book by D. Frenkel and B. Smit.
Understanding Molecular Simulation: From Algorithms to Applications,
2nd edition, Academic Press, 2002.

topic outline
* getting started (visualization and simulation software)
    Scripting Biomolecular Simulation with Tcl.ppt     PDF
    ubq.tcl
* tasks (structure, free energies, kinetics)
* models (atomistic, coarse-grained)
* MC and MD sampling techniques
* methods for free energies, structure, kinetics
* minimization
* integrators
* fast force evalution and implementation issues
* references PDF

assignments
* several homework sets, including hands-on experience
* a project, either entirely written or involving computing, which gives student chance to explore subject of interest to them

Good references:
M.P. Allen and D.J. Tildesley.
Computer Simulation of Liquids,
Clarendon Press, Oxford, New York, 1987,
Reprinted in paperback in 1989 with corrections.
 
A.R. Leach.
Molecular Modelling: Principles and Applications, 2nd edition
Prentice Hall, Englewood Cliffs, N.J., February 2001,
 
T. Schlick.
Molecular Modeling and Simulation: An Interdisciplinary Guide,
volume 21 of Springer Series in Interdisciplinary Applied Mathematics.
Springer-Verlag, New York, 2002.

  Last updated 2009-3-10