Accelerated molecular dynamics in studying long-timescale biomolecular events

COMP 184

Donald Hamelberg, dhamelberg@gsu.edu, Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098
Computational modeling of biomolecules presents a two-fold challenge: the large size of the system and the long timescale of the phenomenon. The advancement in computational chemistry has led to the development of an incredible amount of methodologies to circumvent these problems. These computational methodologies are fast becoming indispensible in the field as a whole. We present an accelerated MD method to study the mechanism of cis-trans isomerization of the peptide prolyl bond. We have provided detailed description of cis-trans isomerization of the free substrate and the enzyme-assisted process. We have extensively studied the reweighting step of the accelerated MD method and have provided a priori guidance for improving the accuracy and sampling of reweighting-based simulations. We also present an approach to extract the kinetics from the accelerated MD by establishing the relationship between the local energetic roughness of the energy landscape and the effective diffusion coefficient.
 

Hewlett-Packard Scholar Awards
6:00 PM-8:00 PM, Tuesday, August 18, 2009 Walter E. Washington Convention Center -- Ballroom A, Poster

Division of Computers in Chemistry

The 238th ACS National Meeting, Washington, DC, August 16-20, 2009