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

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 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 themore » hydrodynamics only, which is a significant advantage over available continuum solvers.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1221497
Report Number(s):
PNNL-SA-108851
KJ0401000; KJ0401000
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Physics, 143(1):014101
Additional Journal Information:
Journal Name: Journal of Chemical Physics, 143(1):014101
Country of Publication:
United States
Language:
English
Subject:
dissipative particle dynamics; mesoscopic transport; advection- diffusion-reaction problems

Citation Formats

Zhen, Li, Yazdani, Alireza, Tartakovsky, Alexandre M., and Karniadakis, George E. Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems. United States: N. p., 2015. Web. doi:10.1063/1.4923254.
Zhen, Li, Yazdani, Alireza, Tartakovsky, Alexandre M., & Karniadakis, George E. Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems. United States. doi:10.1063/1.4923254.
Zhen, Li, Yazdani, Alireza, Tartakovsky, Alexandre M., and Karniadakis, George E. Tue . "Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems". United States. doi:10.1063/1.4923254.
@article{osti_1221497,
title = {Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems},
author = {Zhen, Li and Yazdani, Alireza and Tartakovsky, Alexandre M. and Karniadakis, George E.},
abstractNote = {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.},
doi = {10.1063/1.4923254},
journal = {Journal of Chemical Physics, 143(1):014101},
number = ,
volume = ,
place = {United States},
year = {2015},
month = {7}
}

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