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Abstract
The reactiondiffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are pointlike. Here, we introduce the excluded volume reactiondiffusion master equation (vRDME) which takes into account volume exclusion effects on stochastic kinetics due to a finite molecular radius. We obtain an exact closed form solution of the RDME and of the vRDME for a general chemical system in equilibrium conditions. The difference between the two solutions increases with the ratio of molecular diameter to the compartment length scale. We show that an increase in the fraction of excluded space can (i) lead to deviations from the classical inverse square root law for the noisestrength, (ii) flip the skewness of the probability distribution from right to leftskewed, (iii) shift the equilibrium of bimolecular reactions so that more product molecules are formed, and (iv) strongly modulate the Fano factors and coefficients of variation. These volume exclusion effects are found to be particularly pronounced for chemical species not involved in chemical conservation laws. Finally, we show that statistics obtained using the vRDME are in good agreement with those obtained from Brownian dynamics with excluded volume interactions.
Original language  English 

Article number  084101 
Journal  The Journal of Chemical Physics 
Volume  144 
Issue number  8 
DOIs  
Publication status  Published  28 Feb 2016 
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Dive into the research topics of 'Molecular finitesize effects in stochastic models of equilibrium chemical systems'. Together they form a unique fingerprint.Projects
 1 Finished

Pushing the frontiers of stochastic modelling in biology:intrinsic noise in nondilute conditions
17/03/14 → 30/09/16
Project: Research