Abstract
Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics.
Highlights
In order for them to occur, the educts have to be in physical proximity, a situation often termed encounter complex
The overall probability of a reaction to occur depends on two parameters: 1) the frequency by which the educts form encounter complexes and 2) the transition rate of this encounter complex to the actual products
In this paper we review software tools for conducting particle-based reaction-diffusion (PBRD) simulations with respect to the level of modeling detail
Summary
A whole E-coli cytoplasm diffusion study, based on crystal structure shaped particles including their full potential energy landscape was done by Mc Guffee and Elcock [53] showing the formation of transient complexes with short lifetimes influencing the diffusion dynamics The investigation of these effects on reactions between particles on a cytoplasm scale would be an interesting future application of level 4 reaction-diffusion simulations (compare Figure 2B for an illustration). For some molecular reaction-diffusion systems, a certain amount of fine-graining might be necessary, e.g. association of elongated, thread like proteins such as Syntaxin (see Figure 2A) or protein-ligand binding involving a distinct binding pocket This pocket might be modeled as a reactive patch on an otherwise spherical particle, as it is implemented in SRSim. A comparable approach is used in ReaDDy where the protein would be modeled as a group of bonded spherical particles from which some are reactive.
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