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ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units.

Johann Biedermann1, Alexander Ullrich1, Johannes Schöneberg1

  • 1Department of Mathematics, Computer Science and Bioinformatics, Free University of Berlin, Berlin, Germany.

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We present a faster ReaDDy particle simulation package using graphical processing units (GPUs). This acceleration enables multi-second simulations of cellular processes, resolving individual protein molecules.

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Area of Science:

  • Computational biology
  • Biophysics
  • Molecular dynamics

Background:

  • ReaDDy is a particle simulation package for off-lattice reaction kinetics and particle interactions.
  • Simulating complex biological systems requires efficient computational methods.

Purpose of the Study:

  • To implement ReaDDy on graphical processing units (GPUs) for enhanced performance.
  • To enable simulations of cellular signal transduction pathways at the molecular level.

Main Methods:

  • Utilized the OpenMM package for GPU implementation of ReaDDy.
  • Combined off-lattice reaction kinetics with particle interaction forces.
  • Performed simulations on single GPUs.

Main Results:

  • Achieved a speedup of up to two orders of magnitude compared to previous implementations.
  • Enabled simulations spanning multiple seconds on single GPUs.
  • Facilitated the resolution of all protein copies in simulated systems.

Conclusions:

  • The GPU implementation of ReaDDy significantly accelerates particle simulations.
  • This advancement allows for the study of cellular signal transduction with high molecular resolution.
  • The enhanced ReaDDy package opens new possibilities in computational systems biology.