title: ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.
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.
authors.affiliation: Department of Mathematics, Free University of Berlin, Berlin, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Schöneberg
authors.forename: Frank
authors.initials: F
authors.lastname: Noé
mesh_terms: D000465:Algorithms; D015220:Calcium Channels / Q000737:chemistry / Q000378:metabolism; D004058:Diffusion; D006801:Humans; D007700:Kinetics; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D010316:Particle Size; D017948:Retinal Rod Photoreceptor Cells / Q000737:chemistry / Q000378:metabolism; D050600:SNARE Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software; D013572:Synaptic Vesicles / Q000737:chemistry / Q000378:metabolism; D014785:Vision, Ocular
chemical_list: D015220:Calcium Channels; D050600:SNARE Proteins
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