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A Multi-Algorithm, Multi-Timescale Method for Cell Simulation (2004)
| Citations: | 55 - 5 self |
BibTeX
@MISC{Takahashi04amulti-algorithm,,
author = {Kouichi Takahashi and Kazunari Kaizu and Bin Hu and Masaru Tomita},
title = {A Multi-Algorithm, Multi-Timescale Method for Cell Simulation },
year = {2004}
}
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Abstract
Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models. Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a ‘composite ’ heat-shock response model that combines the Gillespie–Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multitimescale demonstration of coupled harmonic oscillators is also shown. Availability: An implementation of the method is available as part of E-Cell Simulation Environment Version 3 downloadable from
Keyphrases
multi-timescale method cell simulation many important problem gillespie gibson stochastic algorithm cellular process sub-cellular model new method order model simulation framework functional module hermite polynomial interpolation different timescales cell biology composite heat-shock response model dramatic improvement different algorithm large number significant accuracy drawback object-oriented simulation meta-algorithm harmonic oscillator multitimescale demonstration significant computational challenge many component e-cell simulation environment version simulation algorithm computer simulation certain subsystem dense nonlinear interaction discrete-event scheduler deterministic differential equation different type
