Fröhner, Chr. and Noé, F. (2018) Reversible interactingparticle reaction dynamics. J. Phys. Chem. B, 122 (49). pp. 1124011250.

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Official URL: https://dx.doi.org/10.1021/acs.jpcb.8b06981
Abstract
InteractingParticle Reaction Dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enable a wide range of complex reactive systems in biology and chemistry, but give rise to new questions such as how to evolve the dynamical equations in a computationally efficient and statistically correct manner. Here we consider reversible reactions such as A + B <> C with interacting particles and derive expressions for the microscopic iPRD simulation parameters such that desired values for the equilibrium constant and the dissociation rate are obtained in the dilute limit. We then introduce a MonteCarlo algorithm that ensures detailed balance in the iPRD timeevolution (iPRDDB). iPRDDB guarantees the correct thermodynamics at all concentrations and maintains the desired kinetics in the dilute limit, where chemical rates are welldefined and kinetic measurement experiments usually operate. We show that in dense particle systems, the incorporation of detailed balance is essential to obtain physically realistic solutions. iPRDDB is implemented in ReaDDy 2 (https://readdy.github.io).
Item Type:  Article 

Additional Information:  SFB1114 Preprint in arXiv:1807.07355 (https://arxiv.org/abs/1807.07355) 
Subjects:  Mathematical and Computer Sciences > Mathematics > Applied Mathematics 
Divisions:  Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group 
ID Code:  2352 
Deposited By:  Silvia Hoemke 
Deposited On:  25 Jun 2019 15:12 
Last Modified:  25 Jun 2019 15:12 
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