NDLI: An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of molecules

Content Provider	IEEE Xplore Digital Library
Author	Youfang Cao Jie Liang
Copyright Year	2007
Description	Author affiliation: Shanghai Jiaotong Univ., Shanghai (Youfang Cao)
Abstract	Stochasticity plays central role in molecular networks of small copy numbers, including those important in protein synthesis and gene regulation. The combination of copy numbers of molecular species defines the microscopic state of molecular interactions. With this formulation, nonlinear reactions can be effectively modeled through chemical master equations. However, currently little is known about the state space associated with stochastic networks, other than the defeatist admission that it is exponentially large. There is neither closed-form solution nor computational algorithm that can effectively characterize the state space of molecular networks. Such a characterization is a prerequisite for directly solving the chemical master equation. In this study, we describe an algorithm that can exhaustively characterize all possible states of a molecular networks with small copy numbers of species for a given initial condition. Our algorithm works for networks of arbitrary stoichiometry, and is optimal in both storage and time complexity. It allows the approach of solving chemical master equation to be applicable to a larger class of stochastic molecular networks. We show an example of application of our method to the MAPK cascade network.
Starting Page	4599
Ending Page	4602
File Size	650959
Page Count	4
File Format	PDF
ISBN	9781424407873
ISSN	1557170X
DOI	10.1109/IEMBS.2007.4353364
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-08-22
Publisher Place	France
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	State-space methods Stochastic processes Chemicals Nonlinear equations Proteins Network synthesis Microscopy Cellular networks Differential equations Fluctuations
Content Type	Text
Resource Type	Article
Subject	Signal Processing Biomedical Engineering Health Informatics Computer Vision and Pattern Recognition

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