6.971 Introduction to Molecular Simulations (H)

L MW 10-11:30, room 34-302
Professor Colin Stultz, cmstultz@csail.mit.edu
Prereq.: 6.581J or 7.91J or 18.417 or permission of instructor
3-0-9

This subject qualifies as an bioelectrical engineering concentration subject.

An introduction to the basic concepts underlying the dynamical simulations of proteins and nucleic acids. Topics covered include classical statistical mechanics (as it relates to the calculation of macroscopic observables), normal mode analyses of protein dynamics, and thermodynamic perturbation theory. Emphasis is placed on the actual techniques, and algorithms, used for such calculations. The final assignment integrates these concepts in a project designed to address a problem of biological importance using existing molecular mechanics software packages.

Perquisite: Permission of instructor

Lectures

1. Introduction to protein structure 1 (the 20 amino acids and basic protein structural motifs)

2. Introduction to protein structure 2 (introduction to x-ray crystallography – examples of protein structures)

3. Potential functions

4. Energy minimization

5. Molecular dynamics simulations “nuts and bolts” (algorithms, treatment of electrostatics)

6. Introduction to classical statistical thermodynamics I

7. Classical statistical thermo II – Derivation of the Boltzmann distribution

8. Classical statistical thermo III – The canonical ensemble

9. MD simulations with a heat bath

10. MD simulations with explicit solvent (Boundary conditions - stochastic boundary, periodic boundary, etc.)

11. Free energy simulations

12. Umbrella sampling

13. Normal mode analyses

14. Implicit models of solvent – an overview

15. Protein unfolding with molecular simulations

16. Protein folding with molecular simulations

17. Pulling forces and single molecule experiments

18. Targeted molecular dynamics and localized conformational transitions