Literature DB >> 19275421

Lattice kinetic Monte Carlo simulations of convective-diffusive systems.

Matthew H Flamm1, Scott L Diamond, Talid Sinno.   

Abstract

Diverse phenomena in physical, chemical, and biological systems exhibit significant stochasticity and therefore require appropriate simulations that incorporate noise explicitly into the dynamics. We present a lattice kinetic Monte Carlo approach to simulate the trajectories of tracer particles within a system in which both diffusive and convective transports are operational. While diffusive transport is readily accounted for in a kinetic Monte Carlo simulation, we demonstrate that the inclusion of bulk convection by simply biasing the rate of diffusion with the rate of convection creates unphysical, shocklike behavior in concentrated systems due to particle pile up. We report that elimination of shocklike behavior requires the proper passing of blocked convective rates along nearest-neighbor chains to the first available particle in the direction of flow. The resulting algorithm was validated for the Taylor-Aris dispersion in parallel plate flow and multidimensional flows. This is the first generally applicable lattice kinetic Monte Carlo simulation for convection-diffusion and will allow simulations of field-driven phenomena in which drift is present in addition to diffusion.

Mesh:

Year:  2009        PMID: 19275421      PMCID: PMC2671687          DOI: 10.1063/1.3078518

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

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2.  Building reliable lattice Monte Carlo models for real drift and diffusion problems.

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Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-07-26

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4.  Coarse-grained lattice kinetic Monte Carlo simulation of systems of strongly interacting particles.

Authors:  Jianguo Dai; Warren D Seider; Talid Sinno
Journal:  J Chem Phys       Date:  2008-05-21       Impact factor: 3.488

5.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells.

Authors:  A Arkin; J Ross; H H McAdams
Journal:  Genetics       Date:  1998-08       Impact factor: 4.562

6.  Classically exact overlayer dynamics: Diffusion of rhodium clusters on Rh(100).

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Journal:  Phys Rev B Condens Matter       Date:  1986-11-15

7.  Coupled Burgers equations: A model of polydispersive sedimentation.

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Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1995-10
  7 in total
  8 in total

1.  Stochastic electrotransport selectively enhances the transport of highly electromobile molecules.

Authors:  Sung-Yon Kim; Jae Hun Cho; Evan Murray; Naveed Bakh; Heejin Choi; Kimberly Ohn; Luzdary Ruelas; Austin Hubbert; Meg McCue; Sara L Vassallo; Philipp J Keller; Kwanghun Chung
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-02       Impact factor: 11.205

2.  Simulation of aggregating particles in complex flows by the lattice kinetic Monte Carlo method.

Authors:  Matthew H Flamm; Talid Sinno; Scott L Diamond
Journal:  J Chem Phys       Date:  2011-01-21       Impact factor: 3.488

Review 3.  Multiscale systems biology and physics of thrombosis under flow.

Authors:  Mathew H Flamm; S L Diamond
Journal:  Ann Biomed Eng       Date:  2012-03-30       Impact factor: 3.934

4.  Multiscale prediction of patient-specific platelet function under flow.

Authors:  Matthew H Flamm; Thomas V Colace; Manash S Chatterjee; Huiyan Jing; Songtao Zhou; Daniel Jaeger; Lawrence F Brass; Talid Sinno; Scott L Diamond
Journal:  Blood       Date:  2012-04-18       Impact factor: 22.113

Review 5.  Systems Analysis of Thrombus Formation.

Authors:  Scott L Diamond
Journal:  Circ Res       Date:  2016-04-29       Impact factor: 17.367

6.  Multiscale simulation of thrombus growth and vessel occlusion triggered by collagen/tissue factor using a data-driven model of combinatorial platelet signalling.

Authors:  Yichen Lu; Mei Yan Lee; Shu Zhu; Talid Sinno; Scott L Diamond
Journal:  Math Med Biol       Date:  2017-12-11       Impact factor: 1.854

7.  Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli.

Authors:  Manash S Chatterjee; Jeremy E Purvis; Lawrence F Brass; Scott L Diamond
Journal:  Nat Biotechnol       Date:  2010-06-20       Impact factor: 54.908

8.  Systems biology of platelet-vessel wall interactions.

Authors:  Scott L Diamond; Jeremy Purvis; Manash Chatterjee; Matthew H Flamm
Journal:  Front Physiol       Date:  2013-08-26       Impact factor: 4.566

  8 in total

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