Issue 6, 2015

Kinetic Monte Carlo simulations of the assembly of filamentous biomacromolecules by the dimer addition mechanism

Abstract

In cells, several important biomacromolecules form oligomers through a dimer addition mechanism. Rate equations based on mean field approximations are usually employed to describe the assembly process. However, such equations often require multiple assumptions that mask some detailed changes of the biomolecular configurations during aggregations. Here, we present a kinetic Monte Carlo simulation scheme to account for the diffusion and rotation of dimers on two-dimensional hexagonal lattices while naturally including the stochastic features. We investigate the effects of the interaction energy between dimers, the diffusion coefficient and the concentration of dimers on the aggregation by dimer addition mechanism. Our simulations identified unusual double-S shape evolutions of aggregation kinetics, which are probably associated with the formation of metastable clusters.

Graphical abstract: Kinetic Monte Carlo simulations of the assembly of filamentous biomacromolecules by the dimer addition mechanism

Supplementary files

Article information

Article type
Paper
Submitted
24 Aug 2014
Accepted
04 Dec 2014
First published
05 Dec 2014

RSC Adv., 2015,5, 3922-3929

Author version available

Kinetic Monte Carlo simulations of the assembly of filamentous biomacromolecules by the dimer addition mechanism

T. Luo and D. N. Robinson, RSC Adv., 2015, 5, 3922 DOI: 10.1039/C4RA09189B

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