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Deterministic Reaction-Diffusion Simulators

Encyclopedia of Computational Neuroscience

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Definition

A deterministic reaction–diffusion simulator is software designed to approximate the dynamics of a system governed by the diffusion and interaction of species within a domain in a deterministic fashion.

Detailed Description

In neuroscience, these species can be one of many classes of molecules: ions, enzymes, polypeptides, globular proteins, microRNAs, etc. The interactions are chemical reactions, such as phosphorylation or binding, the synthesis of a new molecule out of substrates, or the breakdown of a molecule. Unlike stochastic simulators, which approximate these dynamics using pseudorandom processes, deterministic simulators solve a system of partial differential equations (PDEs). Thus, while stochastic simulators need to be run many times to identify the range of likely outcomes, deterministic simulators need only be run once, as the result is unique.

Theory

Deterministic simulators are most appropriate when they can rely on the law of large numbers (Kotelenez 1986),...

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Acknowledgment

This work was partially supported by NIH R01MH086638 and NIH 2T15LM007056.

Author information

Authors and Affiliations

  1. Department of Physiology and Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, USA

    William W. Lytton

  2. Department of Neurobiology, Yale University, 208001, New Haven, CT, 06520-8001, USA

    Robert A. McDougal Ph.D.

Authors
  1. William W. Lytton
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  2. Robert A. McDougal Ph.D.
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Corresponding author

Correspondence to William W. Lytton .

Editor information

Editors and Affiliations

  1. Atlanta, Georgia, USA

    Dieter Jaeger

  2. Department of Biomedical Engineering, Florida International University, Miami, Florida, USA

    Ranu Jung

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© 2013 Springer Science+Business Media New York

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Lytton, W.W., McDougal, R.A. (2013). Deterministic Reaction-Diffusion Simulators. In: Jaeger, D., Jung, R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7320-6_185-2

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  • DOI: https://doi.org/10.1007/978-1-4614-7320-6_185-2

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  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-7320-6

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

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Chapter history

  1. Latest

    Deterministic Reaction-Diffusion Simulators
    Published:
    11 December 2019

    DOI: https://doi.org/10.1007/978-1-4614-7320-6_185-3

  2. Original

    Deterministic Reaction-Diffusion Simulators
    Published:
    20 February 2014

    DOI: https://doi.org/10.1007/978-1-4614-7320-6_185-2

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