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

Publikation: Beitrag in FachzeitschriftForschungsartikelBeigetragenBegutachtung

Beitragende

  • Jo A. Helmuth - , ETH Zurich (Autor:in)
  • Sylvain Reboux - , ETH Zurich (Autor:in)
  • Ivo F. Sbalzarini - , ETH Zurich (Autor:in)

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.

Details

OriginalspracheEnglisch
Seiten (von - bis)324-334
Seitenumfang11
FachzeitschriftJournal of Computational Science
Jahrgang2
Ausgabenummer4
PublikationsstatusVeröffentlicht - Dez. 2011
Peer-Review-StatusJa
Extern publiziertJa

Externe IDs

ORCID /0000-0003-4414-4340/work/159608307

Schlagworte

Schlagwörter

  • Hybrid continuous-discrete simulation, Hybrid stochastic-deterministic model, Intra-cellular transport, Motor proteins, Stochastic simulation algorithm