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Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell (2001)

Schaff, James C. ; Slepchenko, Boris M.

Woodbury, NY : American Institute of Physics (AIP)

Chaos 11 (2001), S. 115-131

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ISSN: 1089-7682

Source: AIP Digital Archive

Topics: Physics

Notes: The Virtual Cell is a modeling tool that allows biologists and theorists alike to specify and simulate cell-biophysical models on arbitrarily complex geometries. The framework combines an intuitive, front-end graphical user interface that runs in a web browser, sophisticated server-side numerical algorithms, a database for storage of models and simulation results, and flexible visualization capabilities. In this paper, we present an overview of the capabilities of the Virtual Cell, and, for the first time, the detailed mathematical formulation used as the basis for spatial computations. We also present summaries of two rather typical modeling projects, in order to illustrate the principal capabilities of the Virtual Cell. © 2001 American Institute of Physics.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1063/1.1350404

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COMPUTATIONAL CELL BIOLOGY: Spatiotemporal Simulation of Cellular Events (2002)

Slepchenko, Boris M. ; Schaff, James C. ; Carson, John H. ; [et al.]

Palo Alto, Calif. : Annual Reviews

Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 423-441

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ISSN: 1056-8700

Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff

Topics: Biology , Physics

Notes: Abstract The field of computational cell biology has emerged within the past 5 years because of the need to apply disciplined computational approaches to build and test complex hypotheses on the interacting structural, physical, and chemical features that underlie intracellular processes. To meet this need, newly developed software tools allow cell biologists and biophysicists to build models and generate simulations from them. The construction of general-purpose computational approaches is especially challenging if the spatial complexity of cellular systems is to be explicitly treated. This review surveys some of the existing efforts in this field with special emphasis on a system being developed in the authors' laboratory, Virtual Cell. The theories behind both stochastic and deterministic simulations are discussed. Examples of respective applications to cell biological problems in RNA trafficking and neuronal calcium dynamics are provided to illustrate these ideas.