Michigan Technological University
Department of Physics

is pleased to announce a colloquium

with

Ruhong Zhou

Computational Biology Center
IBM Thomas J. Watson Research Center
1101 Kitchawan Road
Yorktown Heights, NY 10598

Tel: (914) 945-3591, Fax: (914) 945-4104
http://www.research.ibm.com/people/r/ruhong

Adjunct Professor
Department of Chemistry,
Columbia University
New York, NY 10027

Protein Folding with Molecular Dynamics

"How does a protein fold?" still remains a mystery in molecular biology.

In this talk, I will talk about methods and algorithms developed recently for efficient sampling of the free energy landscape of protein folding. Particularly, I will describe a highly parallel Replica Exchange Method (REM), which combines with a newly developed molecular dynamics algorithm P3ME/RESPA. The combined algorithm REM-P3ME/RESPA will be applied to the folding free energy landscape of several protein systems. These large-scale simulations reveal detailed results on the folding mechanisms, thermodynamic properties, and temperature dependences. Moreover, detailed comparisons on folding landscapes with both explicit and implicit water models will be described to address the question on how good these continuum solvent models are. Surprisingly, severe deficiencies are found for some widely used implicit solvent models. This talk will also briefly describe the IBM Blue Gene project, including its hardware design and protein science programs.

Thursday, October 30, 2003

4:00 p.m., Fisher 139

Refreshments will be served

MTU | Physics | Colloquium