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

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 motorcargo 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 motorcargo 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. DOI: https://doi.org/10.1016/j.jocs.2011.08.006 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-79220 Originally published at: 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. DOI: https://doi.org/10.1016/j.jocs.2011.08.006 Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors Jo A. Helmuth, Sylvain Reboux, Ivo F. Sbalzarini∗ Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092 Zürich, Switzerland