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A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems.
J Comput Phys 2019; 378:1-17JC

Abstract

We have developed a new algorithm which merges discrete stochastic simulation, using the spatial stochastic simulation algorithm (sSSA), with the particle based fluid dynamics simulation framework of smoothed dissipative particle dynamics (SDPD). This hybrid algorithm enables discrete stochastic simulation of spatially resolved chemically reacting systems on a mesh-free dynamic domain with a Lagrangian frame of reference. SDPD combines two popular mesoscopic techniques: smoothed particle hydrodynamics and dissipative particle dynamics (DPD), linking the macroscopic and mesoscopic hydrodynamics effects of these two methods. We have implemented discrete stochastic simulation using the reaction-diffusion master equations (RDME) formalism, and deterministic reaction-diffusion equations based on the SDPD method. We validate the new method by comparing our results to four canonical models, and demonstrate the versatility of our method by simulating a flow containing a chemical gradient past a yeast cell in a microfluidics chamber.

Authors+Show Affiliations

Department of Computer Science, University of North Carolina at Asheville, Asheville, North Carolina, 28804, USA.Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA.Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA.Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA.Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA. Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California, 93106, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31031417

Citation

Brian, Drawert, et al. "A Hybrid Smoothed Dissipative Particle Dynamics (SDPD) Spatial Stochastic Simulation Algorithm (sSSA) for Advection-diffusion-reaction Problems." Journal of Computational Physics, vol. 378, 2019, pp. 1-17.
Brian D, Bruno J, Zhen L, et al. A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems. J Comput Phys. 2019;378:1-17.
Brian, D., Bruno, J., Zhen, L., Tau-Mu, Y., & Linda, P. (2019). A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems. Journal of Computational Physics, 378, pp. 1-17. doi:10.1016/j.jcp.2018.10.043.
Brian D, et al. A Hybrid Smoothed Dissipative Particle Dynamics (SDPD) Spatial Stochastic Simulation Algorithm (sSSA) for Advection-diffusion-reaction Problems. J Comput Phys. 2019 Feb 1;378:1-17. PubMed PMID: 31031417.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems. AU - Brian,Drawert, AU - Bruno,Jacob, AU - Zhen,Li, AU - Tau-Mu,Yi, AU - Linda,Petzold, Y1 - 2018/11/05/ PY - 2019/4/30/entrez PY - 2019/4/30/pubmed PY - 2019/4/30/medline KW - Discrete Stochastic Simulation KW - Particle Based Fluid Dynamics KW - Reaction-Diffusion Master Equation SP - 1 EP - 17 JF - Journal of computational physics JO - J Comput Phys VL - 378 N2 - We have developed a new algorithm which merges discrete stochastic simulation, using the spatial stochastic simulation algorithm (sSSA), with the particle based fluid dynamics simulation framework of smoothed dissipative particle dynamics (SDPD). This hybrid algorithm enables discrete stochastic simulation of spatially resolved chemically reacting systems on a mesh-free dynamic domain with a Lagrangian frame of reference. SDPD combines two popular mesoscopic techniques: smoothed particle hydrodynamics and dissipative particle dynamics (DPD), linking the macroscopic and mesoscopic hydrodynamics effects of these two methods. We have implemented discrete stochastic simulation using the reaction-diffusion master equations (RDME) formalism, and deterministic reaction-diffusion equations based on the SDPD method. We validate the new method by comparing our results to four canonical models, and demonstrate the versatility of our method by simulating a flow containing a chemical gradient past a yeast cell in a microfluidics chamber. SN - 0021-9991 UR - https://www.unboundmedicine.com/medline/citation/31031417/A_hybrid_smoothed_dissipative_particle_dynamics__SDPD__spatial_stochastic_simulation_algorithm__sSSA__for_advection_diffusion_reaction_problems_ L2 - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31031417/ DB - PRIME DP - Unbound Medicine ER -