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

Tianzhi Luo, Douglas Robinson

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)3922-3929
Number of pages8
JournalRSC Advances
Volume5
Issue number6
DOIs
StatePublished - 2015

Fingerprint

Dimers
Kinetics
Agglomeration
Oligomers
Masks
Monte Carlo simulation

ASJC Scopus subject areas

  • Chemical Engineering(all)
  • Chemistry(all)

Cite this

Kinetic Monte Carlo simulations of the assembly of filamentous biomacromolecules by the dimer addition mechanism. / Luo, Tianzhi; Robinson, Douglas.

In: RSC Advances, Vol. 5, No. 6, 2015, p. 3922-3929.

Research output: Contribution to journalArticle

@article{8c877b76dd1644d4b8fb40df3bcf7b46,
title = "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.",
author = "Tianzhi Luo and Douglas Robinson",
year = "2015",
doi = "10.1039/c4ra09189b",
language = "English (US)",
volume = "5",
pages = "3922--3929",
journal = "RSC Advances",
issn = "2046-2069",
publisher = "Royal Society of Chemistry",
number = "6",

}

TY - JOUR

T1 - Kinetic Monte Carlo simulations of the assembly of filamentous biomacromolecules by the dimer addition mechanism

AU - Luo, Tianzhi

AU - Robinson, Douglas

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84919682648&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84919682648&partnerID=8YFLogxK

U2 - 10.1039/c4ra09189b

DO - 10.1039/c4ra09189b

M3 - Article

C2 - 25574377

AN - SCOPUS:84919682648

VL - 5

SP - 3922

EP - 3929

JO - RSC Advances

JF - RSC Advances

SN - 2046-2069

IS - 6

ER -