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Folding kinetics of a polymer.

Stěpán Růžička1, David Quigley, Michael P Allen

  • 1Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom.

Physical Chemistry Chemical Physics : PCCP
|March 28, 2012
PubMed
Summary

Computer simulations reveal a simple relation between polymer topology and folding pathways. The Laplacian matrix eigenvalues offer insights into crystallization, identifying configurations with low crystallization probability.

Area of Science:

  • Computational physics
  • Polymer science
  • Chemical kinetics

Background:

  • Understanding the liquid-to-solid transition in polymers is crucial for materials science.
  • Existing models often lack detailed kinetic insights into the transition process.

Purpose of the Study:

  • To provide a kinetic perspective on the liquid-to-solid transition of homopolymer chains.
  • To develop a phase diagram based on kinetic data and explore the relationship between polymer topology and folding.
  • To investigate the utility of the Laplacian matrix in characterizing polymer folding pathways.

Main Methods:

  • Utilizing molecular dynamics with the forward flux sampling scheme to calculate transition rates.
  • Comparing simulation results with Monte Carlo simulations.

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  • Analyzing the eigenvalue spectrum of the Laplacian matrix derived from non-bonded contacts.

    • Main Results:

    • A phase diagram based purely on kinetic data was generated.
    • A general and simple relationship between polymer topology and folding pathways was identified.
    • The Laplacian matrix eigenvalue spectrum provided insights into nonequilibrium ensembles, identifying configurations with low crystallization probability.

    Conclusions:

    • The study offers a kinetic understanding of polymer liquid-to-solid transitions.
    • Polymer topology significantly influences folding pathways.
    • Laplacian matrix eigenvalues can serve as effective reaction coordinates for describing polymer folding transitions.