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.
Highlights
Which molecules interact at which place and in which sequence, in order to orchestrate a specific cellular function? Understanding the detailed spatiotemporal mechanisms behind cellular processes is one of the main topics in current biology
Monte Carlo core: Implements the Markov chain Monte Carlo (MCMC) method for particle moves described in the Supporting Information
It can be stated that the performance of ReaDDy is more comparable to MD and Brownian dynamics (BD) packages, that integrate the dynamics of interacting particles using short time steps, rather than to reaction-diffusion packages,that do not involve particle interaction potentials, like e.g. Smoldyn [40]
Summary
Understanding the detailed spatiotemporal mechanisms behind cellular processes is one of the main topics in current biology This topic is driven by recent experimental advances, e.g. in superresolution microscopy, which permit proteins to be counted and individually located in a cell, and demonstrated the existence of complex multiprotein architectures [1] [2][3] [4]. Proteins occur with copy numbers between 1 and 100, sometimes with a surprisingly precise stoichiometry [8] These facts suggest, that concentration-based approaches such as ODE and PDE approaches are often inadequate [9,10], and that treating proteins and other signaling molecules as explicit particles, with a specific location in space, is both feasible and necessary
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