title: Temperature-Dependent Probabilistic Roadmap Algorithm for Calculating Variationally Optimized Conformational Transition Pathways.
abstract: 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 [Formula: see text] the Müller potential, the three-hole potential, alanine dipeptide, and the folding of β-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.
authors.affiliation: Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610.
authors.forename: Haijun
authors.initials: H
authors.lastname: Yang
authors.affiliation: Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610.
authors.forename: Hao
authors.initials: H
authors.lastname: Wu
authors.affiliation: Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610.
authors.forename: Dawei
authors.initials: D
authors.lastname: Li
authors.affiliation: Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610.
authors.forename: Li
authors.initials: L
authors.lastname: Han
authors.affiliation: Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610.
authors.forename: Shuanghong
authors.initials: S
authors.lastname: Huo