Time: 3:30 - 4:45 Tu/Th
Place: 1304 Siebel Center
Instructor: Stephen Bond
Office: 4318 Siebel Center
Email: sdbond«at»uiuc«dot»edu
Phone: (217) 244-5975
Semester: Fall 2004
CRN: 36022
Description:
This course surveys current numerical methods used in biomolecular simulation, including both Molecular Dynamics and Monte Carlo. Techniques for extracting important macroscopic (thermodynamic) properties from microscopic (molecular) simulations are presented. Special attention is given to analytical tools from Statistical Physics and Numerical Analysis. A basic understanding of ODEs, probability, statistics, and a programming language is recommended.
Prerequisites: CS 450 or Consent of the Instructor
Credit: 1 Unit
Textbook: Suggested Reading List will be provided
Selected Topics: Molecular Dynamics, Force Fields, Electrostatic Computation, Minimization, Classical Monte Carlo, Constrained MD, Alternative Ensembles, Geometric Integration, Brownian Dynamics, Langevin Dynamics, Quantum Monte Carlo, Essential Dynamics.
Course Policies:
The material for this course is drawn from both books and literature on Molecular and Biomolecular simulation. Students are required to read articles on various topics in this field, and give presentations during the class period. The format and subject matter for the presentation is flexible, and should be discussed with the instructor prior to the assigned presentation date.
"To insure that disability-related concerns are properly addressed from the beginning, students with disabilities who require assistance to participate in this class are asked to see me as soon as possible." [DRES]
Grading:
70% In Class Presentations
25% Computer Project
5% Daily Participation
Suggested Reading List:
1. T. Schlick. Molecular Modeling and Simulation: An Interdisciplinary Guide. Springer (2002).
2. D. Frenkel and B. Smit. Understanding Molecular Simulation: From Algorithms to Applications. Academic Press (1986).
3. M.P. Allen and D.J. Tildesley. Computer Simulation of Liquids. Oxford University Press (1987).
4. J.A. McCammon and S.C. Harvey. Dynamics of Proteins and Nucleic Acids. Cambridge University Press (1987).
5. D.C. Rapaport. The Art of Molecular Simulation. Cambridge University Press (1995).