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Multi-Algorithm Particle Simulations with Spatiocyte

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Protein Function Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1611))

Abstract

As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle simulator for biochemical reaction and diffusion processes. Simulations can be performed at single molecule and compartment spatial scales simultaneously. Molecules can diffuse and react in 1D (filament), 2D (membrane), and 3D (cytosol) compartments. The implications of crowded regions in the cell can be investigated because each diffusing molecule has spatial dimensions. Spatiocyte adopts multi-algorithm and multi-timescale frameworks to simulate models that simultaneously employ deterministic, stochastic, and particle reaction-diffusion algorithms. Comparison of light microscopy images to simulation snapshots is supported by Spatiocyte microscopy visualization and molecule tagging features. Spatiocyte is open-source software and is freely available at http://spatiocyte.org .

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Acknowledgment

We thank Masaki Watabe, Hanae Shimo, and Kaizu Kazunari for discussions that led to the improvement of Spatiocyte usage. We also appreciate Kozo Nishida for Spatiocyte software packaging, installation, and documentation assistance.

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Authors and Affiliations

  1. Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan

    Satya N. V. Arjunan & Koichi Takahashi

Authors
  1. Satya N. V. Arjunan
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  2. Koichi Takahashi
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Corresponding authors

Correspondence to Satya N. V. Arjunan or Koichi Takahashi .

Editor information

Editors and Affiliations

  1. Department of Biological Sciences and Computer Science, Purdue University, West Lafayette, Indiana, USA

    Daisuke Kihara

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Arjunan, S.N.V., Takahashi, K. (2017). Multi-Algorithm Particle Simulations with Spatiocyte. In: Kihara, D. (eds) Protein Function Prediction. Methods in Molecular Biology, vol 1611. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7015-5_16

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  • DOI: https://doi.org/10.1007/978-1-4939-7015-5_16

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7013-1

  • Online ISBN: 978-1-4939-7015-5

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