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Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems.
J Chem Phys 2015; 143(1):014101JC

Abstract

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

Authors+Show Affiliations

Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA.Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA.Computational Mathematics Group, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA.

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

26156459

Citation

Li, Zhen, et al. "Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-diffusion-reaction Problems." The Journal of Chemical Physics, vol. 143, no. 1, 2015, p. 014101.
Li Z, Yazdani A, Tartakovsky A, et al. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems. J Chem Phys. 2015;143(1):014101.
Li, Z., Yazdani, A., Tartakovsky, A., & Karniadakis, G. E. (2015). Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems. The Journal of Chemical Physics, 143(1), p. 014101. doi:10.1063/1.4923254.
Li Z, et al. Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-diffusion-reaction Problems. J Chem Phys. 2015 Jul 7;143(1):014101. PubMed PMID: 26156459.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems. AU - Li,Zhen, AU - Yazdani,Alireza, AU - Tartakovsky,Alexandre, AU - Karniadakis,George Em, PY - 2015/7/10/entrez PY - 2015/7/15/pubmed PY - 2015/12/22/medline SP - 014101 EP - 014101 JF - The Journal of chemical physics JO - J Chem Phys VL - 143 IS - 1 N2 - We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. SN - 1089-7690 UR - https://www.unboundmedicine.com/medline/citation/26156459/Transport_dissipative_particle_dynamics_model_for_mesoscopic_advection_diffusion_reaction_problems_ L2 - https://dx.doi.org/10.1063/1.4923254 DB - PRIME DP - Unbound Medicine ER -