Paper Info
Title
Hybrid Method for Simulating Small-Number Molecular Systems
Abstract
Computational devices such as the toggle switch or the oscillator have recently been used in artificial or biological cells in which the number of molecular species is very small. To simulate their behavior, the stochastic simulation algorithm by Gillespie and the "tau-leap" method, also proposed by Gillespie to reduce simulation tithe, are widely used. In this paper, we discuss groups of cells that interact with the environment by exchanging molecules through their membranes. The stochastic simulation algorithm or even the "tau-leap" method requires a large amount of computation tithe because all the cells in the group and the environment need to be stochastically simulated. In this paper, we propose a hybrid simulation method in which molecular species in the environment are treated based on their concentration, and their time evolution is obtained by solving ordinary differential equations. The behavior of the cell group is then estimated by stochastically simulating some sampled cells. If the state of cells influences the environment, the whole simulation process is iterated until the tithe evolution of the environment becomes invariant. If the simulation ends after a few iterations, then the overall simulation tithe greatly decreases.
Year
DOI
Venue
2009
10.1007/978-3-540-88869-7_29
ALGORITHMIC BIOPROCESSES
Keywords
Field
DocType
stochastic simulation,oscillations,ordinary differential equation
Small number,Stochastic simulation,Ordinary differential equation,Biological system,Computer science,Computational science,Time evolution,Invariant (mathematics),Iterated function,Hybrid system,Computation
Conference
ISSN
Citations 
PageRank 
1619-7127
0
0.34
References 
Authors
0
2
Name
Order
Citations
PageRank
Kazufumi Mizunuma100.34
Masami Hagiya2649102.85