Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.

doi:10.1063/1.4923254

Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

Journal Article · Tue Jul 07 04:00:00 EDT 2015 · Journal of Chemical Physics, 143(1):014101

DOI:https://doi.org/10.1063/1.4923254· OSTI ID:1221497

Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.

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 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 particles, and an analytical formula is proposed to relate the mesoscopic concentration friction 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 DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Pacific Northwest National Laboratory (PNNL), Richland, WA (US)

Sponsoring Organization:: DOE Office of Science; USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1221497

Report Number(s):: PNNL-SA-108851; KJ0401000; KJ0401000

Journal Information:: Journal of Chemical Physics, 143(1):014101, Journal Name: Journal of Chemical Physics, 143(1):014101

Country of Publication:: United States

Language:: English

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