CS 726 Fall 2006,

** IMPORTANT -- No seminar on November 28 **

-- Next Seminar November 14 by Prof. Jin Wang, Physics, Stony Brooks, on "Diffusion dynamics in protein folding" ** 

Tuesday  4:15-5:15, 5130 Upson Hall

Schedule

Instructor: Ron Elber ron@cs.cornell.edu

Literature survey in computational biology

Topic for this semester: Sampling methods in computational biophysics

Papers to choose from (red -- was assigned already):

1. Calculation free energy by using average force, Eric Darve

2. Parallel tempering: Theory applications and new perspectives, Michael Deem

3. Escaping free energy minima, Laio et al.

4. Performances of Wang Landau algorithms for continuous systems, Poulain et al.

5. Optimal estimates of free energies from multistate nonequilibrium data, Margakis et al. (supporting paper by Panda.)

6. Generalized-ensemble algorithms: enhanced sampling techniques for monte carlo and molecular dynamics simulations, Yuko Okamoto

7. General ensembles serve to improve the convergence of free energy simulations, Ryana Bitetti-Putzer et al.

8. Enhanced sampling of rare events, Simone Melchiome

9. Analysis of statistical errors in umbrella sampling simulation by umbrella integration, Kastner et al.

10. A temperature accelerated methods for sampling free energies and determining reaction pathways in rare events simulations,  Luca Maragliano et al.

11. Resolution exchange simulation with incremental coarsening, Daniel Zuckerman