Folding Kinetics of a Polymer

Abstract

By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are different and we propose a way of quantifying the kinetic hindering. We then also observe that the top eigenvalue in the spectrum of the dynamical (contact or adjacency) matrix provides insight into the ensembles of folding and unfolding trajectories, and may be a suitable additional reaction coordinate for the folding transition of chain molecules.

4 pages, 4 figures

References in corpus (3)

• Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling
• Loop Dynamics in DNA Denaturation
• Helical structures from an isotropic homopolymer model

Cited by in corpus (7)

• Studying Rare Events using Forward-Flux Sampling: Recent Breakthroughs and Future Outlook
• Folding mechanism of a polymer chain with short-range attractions
• Homogeneous Nucleation of Sheared Liquids: Advances and Insights from Simulations and Theory
• A string reaction coordinate for the folding of a polymer chain
• Kinetic control of competing nuclei in a dimer lattice-gas model
• Folding kinetics of a polymer [corrigendum]
• Minimal energy packings of nearly flexible polymers