title: Folding kinetics of a polymer.
abstract: We present the results of computer simulations giving a kinetic insight into the liquid-to-solid transition of a homopolymer chain with short-range interactions. By calculating the absolute rates in each direction of the transition, using molecular dynamics employing the forward flux sampling scheme, we provide the phase diagram based on purely kinetic data, and compare it with the results from Monte Carlo simulations. Additionally, we present and discuss a remarkably simple and general relation between the polymer topology and the folding pathway, and show that the eigenvalue spectrum of a matrix defined by non-bonded contacts (the Laplacian matrix) provides an insight into the nonequilibrium ensembles of these trajectories. In particular, the Laplacian matrix seems to identify a large fraction of configurations on the folding pathway at the free energy maximum that have a very low probability of reaching the crystallized state. This implies that the eigenvalues of this matrix may be suitable additional reaction coordinates to describe the folding transition of chain molecules.
authors.affiliation: Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom.
authors.forename: Stěpán
authors.initials: S
authors.lastname: Růžička
authors.forename: David
authors.initials: D
authors.lastname: Quigley
authors.forename: Michael P
authors.initials: MP
authors.lastname: Allen
mesh_terms: D003460:Crystallization; D007700:Kinetics; D009010:Monte Carlo Method; D011108:Polymers / Q000737:chemistry*
chemical_list: D011108:Polymers