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Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors


Helmuth, Jo A; Reboux, Sylvain; Sbalzarini, Ivo F (2011). Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors. Journal of Computer Science, 2(4):324-334.

Abstract

Numerous processes in live cells depend on active, motor-driven transport of cargo and organelles along the filaments of the cytoskeleton. Understanding the resulting dynamics and the underlying biophysical and biochemical processes critically depends on computational models of intra-cellular transport. A number of motor{cargo models have hence been developed to reproduce experimentally observed transport dynamics on various levels of detail. Computer simulations of these models have so far exclusively relied on approximate time-discretization methods. Using a consensus motor{cargo model that unites several existing models from the literature we demonstrate that this simulation approach is not correct. The numerical errors do not vanish even for arbitrarily small time steps, rendering the algorithm inconsistent. We propose a novel exact simulation algorithm for intra-cellular transport models that is also computationally more efficient than the approximate one. Furthermore, we introduce a robust way of analyzing the different time scales in the model dynamics using velocity autocorrelation functions.

Abstract

Numerous processes in live cells depend on active, motor-driven transport of cargo and organelles along the filaments of the cytoskeleton. Understanding the resulting dynamics and the underlying biophysical and biochemical processes critically depends on computational models of intra-cellular transport. A number of motor{cargo models have hence been developed to reproduce experimentally observed transport dynamics on various levels of detail. Computer simulations of these models have so far exclusively relied on approximate time-discretization methods. Using a consensus motor{cargo model that unites several existing models from the literature we demonstrate that this simulation approach is not correct. The numerical errors do not vanish even for arbitrarily small time steps, rendering the algorithm inconsistent. We propose a novel exact simulation algorithm for intra-cellular transport models that is also computationally more efficient than the approximate one. Furthermore, we introduce a robust way of analyzing the different time scales in the model dynamics using velocity autocorrelation functions.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > LipidX
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2011
Deposited On:05 Jul 2013 12:21
Last Modified:07 Dec 2017 21:38
Publisher:Science Publications
ISSN:1549-3636
Publisher DOI:https://doi.org/10.1016/j.jocs.2011.08.006

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