Temperature-dependent probabilistic roadmap: Algorithm for calculating variationally optimized conformational transition pathways

PHYS 462

Haijun Yang, hyang@clarku.edu1, Hao Wu1, Dawi Li1, Li Han2, and Shuanghong Huo, shuo@clarku.edu1. (1) Department of Chemistry, clark university, 950 main st, worcester, MA 01610, (2) Department of computer science, clark university, 950 main st, worcester, MA 01610
In this paper we present a method to calculate a temperature-dependent optimized conformational transition pathways. This method is based on the maximization of the flux derived from the Smoluchowski equation and is implemented with a probabilistic roadmap algorithm. We have tested the algorithm on four systems-the Müller potential, the three-hole potential, alanine dipeptide, and the folding of -hairpin. Comparison is made with existing algorithms designed for the calculation of protein conformational transition and folding pathways. The applications demonstrate the ability of the algorithm to isolate a temperature-dependent optimal reaction path with improved sampling and efficiency.
 

Physical Chemistry Poster Session
7:00 PM-9:00 PM, Wednesday, August 22, 2007 BCEC -- Exhibit Hall - B2, Poster

Sci-Mix
8:00 PM-10:00 PM, Monday, August 20, 2007 BCEC -- Exhibit Hall - B2, Sci-Mix

Division of Physical Chemistry

The 234th ACS National Meeting, Boston, MA, August 19-23, 2007