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Lattice Kinetic Monte-Carlo Method for Simulating Chromosomal Dynamics and other (Non-)Equilibrium Bio-Assemblies

Abstract

Biological assemblies in living cells such as chromosomes constitute large many-body systems that operate in a fluctuating, out-of-equilibrium environment. Since a brute-force simulation of that many degrees of freedom is currently computationally unfeasible, it is necessary to perform coarse-grained stochastic simulations. Here, we develop all tools necessary to write a Lattice Kinetic Monte-Carlo (LKMC) algorithm capable of such simulations. We discuss the validity and limits of this approach by testing the results of the simulation method in simple settings. Importantly, we illustrate how at large external forces Metropolis-Hastings kinetics violate the fluctuation-dissipation and steady-state fluctuation theorems, and discuss better alternatives. Although this simulation framework is rather general, we demonstrate our approach using a DNA polymer with interacting SMC condensin loop-extruding enzymes. Specifically, we show that the scaling behavior of the loop-size distributions that we obtain in our LKMC simulations of this SMC-DNA system is consistent with other studies using Brownian dynamics simulations and analytic approaches. Moreover, we find that the irreversible dynamics of these enzymes under certain conditions result in frozen, sterically jammed polymer configurations, highlighting a potential pitfall of this approach.

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Supplementary files

Publication details

The article was received on 11 Sep 2019, accepted on 18 Nov 2019 and first published on 22 Nov 2019


Article type: Paper
DOI: 10.1039/C9SM01835B
Soft Matter, 2019, Accepted Manuscript

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    Lattice Kinetic Monte-Carlo Method for Simulating Chromosomal Dynamics and other (Non-)Equilibrium Bio-Assemblies

    C. A. Miermans and C. P. Broedersz, Soft Matter, 2019, Accepted Manuscript , DOI: 10.1039/C9SM01835B

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