Multi-Algorithm Particle Simulations with Spatiocyte

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 .

Diffusion-influenced reaction rates in the presence of pair interactions

“…Stochastic particle-based reaction diffusion simulations have become increasingly popular in the past decade [36][37][38][39][40][41][42][43][44][45][46] . Such simulation methods and frameworks evolve the reaction-diffusion processes microscopically and have experienced advancements both in accuracy and computational a) Equal contributions b) Electronic mail: frank.noe@fu-berlin.de c) Electronic mail: f.hoefling@fu-berlin.de performance [47][48][49][50][51] .…”

Stochastic simulation algorithms for Interacting Particle Systems

“…This approach does allow for volume exclusion but due to the nature of Brownian motion is numerically intensive. Both Spatiocyte and our approach address this problem by restricting particles to diffuse across a lattice [ 13 , 15 , 36 ]. The software package Spatiocyte is generally similar to what we present here; particles diffuse and react across a lattice obeying volume exclusion.…”

“…Numerical approaches are computationally prohibitive, leaving direct simulation as the first and frequently only line of attack. The recent IPS simulation package Spatiocyte [ 13 ] and its numerous extensions address simulation biases generated under a lattice-based spatial structure [ 14 ] and parallelize the original simulation code [ 15 ]. We provide a more detailed description of the differences between our approach and Spatiocyte in the section “Availability and Future Directions.”…”