NDLI: Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology

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Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology

Content Provider	Springer Nature Link
Author	Byrne, Michael J. Waxham, M. Neal Kubota, Yoshihisa
Copyright Year	2010
Abstract	In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.
Starting Page	63
Ending Page	82
Page Count	20
File Format	PDF
ISSN	15392791
Journal	Neuroinformatics
Volume Number	8
Issue Number	2
e-ISSN	15590089
Language	English
Publisher	Humana Press Inc
Publisher Date	2010-04-02
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Event driven algorithm Molecular dynamics Simulator Molecular simulation Monte Carlo Stochastic simulation Computational Biology/Bioinformatics Biotechnology Neurology Computer Application in Life Sciences Neurosciences
Content Type	Text
Resource Type	Article
Subject	Neuroscience Information Systems Software

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