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Reactive multi-particle collision dynamics with reactive boundary conditions.
Phys Biol 2018; 15(4):046007PB

Abstract

In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics. The main advantages of the RMPC compared to other molecular based methods are less computational cost as well as conservation of mass, energy and momentum in the collision and free streaming steps. The proposed approach is tested on three reaction-diffusion systems and very good agreement with the solutions to their corresponding partial differential equations is observed.

Authors+Show Affiliations

Author to whom any correspondence should be addressed.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29624185

Citation

Sayyidmousavi, Alireza, and Katrin Rohlf. "Reactive Multi-particle Collision Dynamics With Reactive Boundary Conditions." Physical Biology, vol. 15, no. 4, 2018, p. 046007.
Sayyidmousavi A, Rohlf K. Reactive multi-particle collision dynamics with reactive boundary conditions. Phys Biol. 2018;15(4):046007.
Sayyidmousavi, A., & Rohlf, K. (2018). Reactive multi-particle collision dynamics with reactive boundary conditions. Physical Biology, 15(4), p. 046007. doi:10.1088/1478-3975/aabc35.
Sayyidmousavi A, Rohlf K. Reactive Multi-particle Collision Dynamics With Reactive Boundary Conditions. Phys Biol. 2018 05 9;15(4):046007. PubMed PMID: 29624185.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Reactive multi-particle collision dynamics with reactive boundary conditions. AU - Sayyidmousavi,Alireza, AU - Rohlf,Katrin, Y1 - 2018/05/09/ PY - 2018/4/7/pubmed PY - 2019/1/3/medline PY - 2018/4/7/entrez SP - 046007 EP - 046007 JF - Physical biology JO - Phys Biol VL - 15 IS - 4 N2 - In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics. The main advantages of the RMPC compared to other molecular based methods are less computational cost as well as conservation of mass, energy and momentum in the collision and free streaming steps. The proposed approach is tested on three reaction-diffusion systems and very good agreement with the solutions to their corresponding partial differential equations is observed. SN - 1478-3975 UR - https://www.unboundmedicine.com/medline/citation/29624185/Reactive_multi_particle_collision_dynamics_with_reactive_boundary_conditions_ L2 - https://doi.org/10.1088/1478-3975/aabc35 DB - PRIME DP - Unbound Medicine ER -