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ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

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  • Johannes Schöneberg
  • Frank Noé

Abstract

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.

Suggested Citation

  • Johannes Schöneberg & Frank Noé, 2013. "ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-14, September.
    • Handle: RePEc:plo:pone00:0074261
    DOI: 10.1371/journal.pone.0074261
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    References listed on IDEAS

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    1. Dimitrios Fotiadis & Yan Liang & Slawomir Filipek & David A. Saperstein & Andreas Engel & Krzysztof Palczewski, 2003. "Rhodopsin dimers in native disc membranes," Nature, Nature, vol. 421(6919), pages 127-128, January.
    2. Steven S Andrews & Nathan J Addy & Roger Brent & Adam P Arkin, 2010. "Detailed Simulations of Cell Biology with Smoldyn 2.1," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-10, March.
    3. Elijah Roberts & Andrew Magis & Julio O Ortiz & Wolfgang Baumeister & Zaida Luthey-Schulten, 2011. "Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study," PLOS Computational Biology, Public Library of Science, vol. 7(3), pages 1-21, March.
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    Cited by:

    1. Albert Solernou & Benjamin S Hanson & Robin A Richardson & Robert Welch & Daniel J Read & Oliver G Harlen & Sarah A Harris, 2018. "Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules," PLOS Computational Biology, Public Library of Science, vol. 14(3), pages 1-29, March.

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