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Volumn 227, Issue 4, 2008, Pages 2644-2665

Stochastic Event-Driven Molecular Dynamics

Author keywords

Complex flow; DSMC; Event driven molecular dynamics; Polymer suspension

Indexed keywords

MONTE CARLO METHODS; SOLVENTS; STOCHASTIC SYSTEMS; SUSPENSIONS (FLUIDS);

EID: 38049038356     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2007.11.010     Document Type: Article
Times cited : (37)

References (57)
  • 1
    • 9744268135 scopus 로고    scopus 로고
    • Complex flows by nanohydrodynamics
    • Alley W.E., Covello P., and Alder B.J. Complex flows by nanohydrodynamics. Mol. Phys. 102 19 (2004) 0026-8976
    • (2004) Mol. Phys. , vol.102 , Issue.19 , pp. 0026-8976
    • Alley, W.E.1    Covello, P.2    Alder, B.J.3
  • 2
    • 5744225887 scopus 로고    scopus 로고
    • Low-Reynolds-number hydrodynamics of complex fluids by multi-particle-collision dynamics
    • Ripoll M., Mussawisade K., Winkler R.G., and Gompper G. Low-Reynolds-number hydrodynamics of complex fluids by multi-particle-collision dynamics. Europhys. Lett. 68 1 (2004) 106
    • (2004) Europhys. Lett. , vol.68 , Issue.1 , pp. 106
    • Ripoll, M.1    Mussawisade, K.2    Winkler, R.G.3    Gompper, G.4
  • 3
    • 24944498780 scopus 로고    scopus 로고
    • Microfluidics: fluid physics at the nanoliter scale
    • Squires T.M., and Quake S.R. Microfluidics: fluid physics at the nanoliter scale. Rev. Mod. Phys. 77 3 (2005) 977
    • (2005) Rev. Mod. Phys. , vol.77 , Issue.3 , pp. 977
    • Squires, T.M.1    Quake, S.R.2
  • 4
    • 26944443829 scopus 로고    scopus 로고
    • The dynamics of single-molecule DNA in flow
    • Shaqfeh E.S.G. The dynamics of single-molecule DNA in flow. J. Non-Newtonian Fluid Mech. 130 (2005) 1-28
    • (2005) J. Non-Newtonian Fluid Mech. , vol.130 , pp. 1-28
    • Shaqfeh, E.S.G.1
  • 6
    • 22844433770 scopus 로고    scopus 로고
    • Deformation, stretching, and relaxation of single-polymer chains: fundamentals and examples
    • Slater G.W., Gratton Y., Kenward M., McCormick L., and Tessier F. Deformation, stretching, and relaxation of single-polymer chains: fundamentals and examples. Soft Mater. 2 (2004) 155-182
    • (2004) Soft Mater. , vol.2 , pp. 155-182
    • Slater, G.W.1    Gratton, Y.2    Kenward, M.3    McCormick, L.4    Tessier, F.5
  • 7
    • 17444437323 scopus 로고    scopus 로고
    • Dynamics of a tethered polymer in shear flow
    • Doyle P.S., Ladoux B., and Viovy J.-L. Dynamics of a tethered polymer in shear flow. Phys. Rev. Lett. 84 20 (2000) 4769-4772
    • (2000) Phys. Rev. Lett. , vol.84 , Issue.20 , pp. 4769-4772
    • Doyle, P.S.1    Ladoux, B.2    Viovy, J.-L.3
  • 8
    • 3843105631 scopus 로고    scopus 로고
    • Comparison of molecular dynamics with hybrid continuum-molecular dynamics for a single tethered polymer in a solvent
    • Barsky S., Delgado-Buscalioni R., and Coveney P.V. Comparison of molecular dynamics with hybrid continuum-molecular dynamics for a single tethered polymer in a solvent. J. Chem. Phys. 121 5 (2004) 2403-2411
    • (2004) J. Chem. Phys. , vol.121 , Issue.5 , pp. 2403-2411
    • Barsky, S.1    Delgado-Buscalioni, R.2    Coveney, P.V.3
  • 9
    • 24344480454 scopus 로고    scopus 로고
    • Molecular dynamics study of tethered polymers in shear flow
    • Gratton Y., and Slater G.W. Molecular dynamics study of tethered polymers in shear flow. Euro. Phys. J. E 17 (2005) 455-465
    • (2005) Euro. Phys. J. E , vol.17 , pp. 455-465
    • Gratton, Y.1    Slater, G.W.2
  • 10
    • 33644651481 scopus 로고    scopus 로고
    • Cyclic motion of a grafted polymer under shear flow
    • Delgado-Buscalioni R. Cyclic motion of a grafted polymer under shear flow. Phys. Rev. Lett. 96 8 (2006) 088303
    • (2006) Phys. Rev. Lett. , vol.96 , Issue.8 , pp. 088303
    • Delgado-Buscalioni, R.1
  • 11
    • 33947516000 scopus 로고    scopus 로고
    • Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows
    • Wang G.M., and Sandberg W.C. Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows. Nanotechnology 18 13 (2007) 135702
    • (2007) Nanotechnology , vol.18 , Issue.13 , pp. 135702
    • Wang, G.M.1    Sandberg, W.C.2
  • 13
    • 34548807204 scopus 로고    scopus 로고
    • Dynamics of a single tethered polymer under shear flow
    • Delgado-Buscalioni R. Dynamics of a single tethered polymer under shear flow. AIP Conf. Proc. 913 1 (2007) 114-120
    • (2007) AIP Conf. Proc. , vol.913 , Issue.1 , pp. 114-120
    • Delgado-Buscalioni, R.1
  • 14
    • 0036571979 scopus 로고    scopus 로고
    • Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions
    • Jendrejack R.M., de Pablo J.J., and Graham M.D. Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions. J. Chem. Phys. 116 17 (2002) 7752-7759
    • (2002) J. Chem. Phys. , vol.116 , Issue.17 , pp. 7752-7759
    • Jendrejack, R.M.1    de Pablo, J.J.2    Graham, M.D.3
  • 15
    • 34147140456 scopus 로고    scopus 로고
    • Fast computation of many-particle hydrodynamic and electrostatic interactions in a confined geometry
    • Hernandez-Ortiz J.P., de Pablo J.J., and Graham M.D. Fast computation of many-particle hydrodynamic and electrostatic interactions in a confined geometry. Phys. Rev. Lett. 98 14 (2007) 140602
    • (2007) Phys. Rev. Lett. , vol.98 , Issue.14 , pp. 140602
    • Hernandez-Ortiz, J.P.1    de Pablo, J.J.2    Graham, M.D.3
  • 16
    • 22944485027 scopus 로고    scopus 로고
    • Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries
    • Usta O.B., Ladd A.J.C., and Butler J.E. Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries. J. Chem. Phys. 122 9 (2005) 094902
    • (2005) J. Chem. Phys. , vol.122 , Issue.9 , pp. 094902
    • Usta, O.B.1    Ladd, A.J.C.2    Butler, J.E.3
  • 17
    • 8744287596 scopus 로고    scopus 로고
    • Direct numerical simulation of the Brownian motion of particles by using fluctuating hydrodynamic equations
    • Sharma N., and Patankar N.A. Direct numerical simulation of the Brownian motion of particles by using fluctuating hydrodynamic equations. J. Comput. Phys. 201 (2004) 466-486
    • (2004) J. Comput. Phys. , vol.201 , pp. 466-486
    • Sharma, N.1    Patankar, N.A.2
  • 19
    • 34247334627 scopus 로고    scopus 로고
    • Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules
    • Giupponi G., De Fabritiis G., and Coveney P.V. Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules. J. Chem. Phys. 126 15 (2007) 154903
    • (2007) J. Chem. Phys. , vol.126 , Issue.15 , pp. 154903
    • Giupponi, G.1    De Fabritiis, G.2    Coveney, P.V.3
  • 20
    • 27944502464 scopus 로고    scopus 로고
    • Kinetics of the polymer collapse transition: the role of hydrodynamics
    • Kikuchi N., Ryder J.F., Pooley C.M., and Yeomans J.M. Kinetics of the polymer collapse transition: the role of hydrodynamics. Phys. Rev. E 71 6 (2005) 061804
    • (2005) Phys. Rev. E , vol.71 , Issue.6 , pp. 061804
    • Kikuchi, N.1    Ryder, J.F.2    Pooley, C.M.3    Yeomans, J.M.4
  • 21
    • 34250162803 scopus 로고    scopus 로고
    • A hard constraint algorithm to model particle interactions in DNA-laden flows
    • Trebotich D., Miller G.H., and Bybee M.D. A hard constraint algorithm to model particle interactions in DNA-laden flows. Nanoscale Microscale Thermophys. Eng. 11 1 (2007) 121-128
    • (2007) Nanoscale Microscale Thermophys. Eng. , vol.11 , Issue.1 , pp. 121-128
    • Trebotich, D.1    Miller, G.H.2    Bybee, M.D.3
  • 22
    • 26944436625 scopus 로고    scopus 로고
    • Dynamics of polymers in a particle-based mesoscopic solvent
    • Mussawisade K., Ripoll M., Winkler R.G., and Gompper G. Dynamics of polymers in a particle-based mesoscopic solvent. J. Chem. Phys. 123 14 (2005) 144905
    • (2005) J. Chem. Phys. , vol.123 , Issue.14 , pp. 144905
    • Mussawisade, K.1    Ripoll, M.2    Winkler, R.G.3    Gompper, G.4
  • 23
    • 34547853743 scopus 로고    scopus 로고
    • Mesoscopic description of solvent effects on polymer dynamics
    • Lee S.H., and Kapral R. Mesoscopic description of solvent effects on polymer dynamics. J. Chem. Phys. 124 21 (2006) 214901
    • (2006) J. Chem. Phys. , vol.124 , Issue.21 , pp. 214901
    • Lee, S.H.1    Kapral, R.2
  • 24
    • 85189842028 scopus 로고    scopus 로고
    • D. Trebotich, G.H. Miller, M.D. Bybee, A penalty method to model particle interactions in DNA-laden flows, J. Nanosci. Nanotech. in press.
  • 25
    • 0032598403 scopus 로고    scopus 로고
    • Structure and dynamics of dilute polymer solutions under shear flow via nonequilibrium molecular dynamics
    • Aust C., Kroger M., and Hess S. Structure and dynamics of dilute polymer solutions under shear flow via nonequilibrium molecular dynamics. Macromolecules 32 17 (1999) 5660-5672
    • (1999) Macromolecules , vol.32 , Issue.17 , pp. 5660-5672
    • Aust, C.1    Kroger, M.2    Hess, S.3
  • 26
    • 34547504057 scopus 로고    scopus 로고
    • Numerical methods for the stochastic Landau-Lifshitz Navier-Stokes equations
    • Bell J.B., Garcia A., and Williams S.A. Numerical methods for the stochastic Landau-Lifshitz Navier-Stokes equations. Phys. Rev. E 76 (2007) 016708
    • (2007) Phys. Rev. E , vol.76 , pp. 016708
    • Bell, J.B.1    Garcia, A.2    Williams, S.A.3
  • 27
    • 85189841008 scopus 로고    scopus 로고
    • S.A. Williams, J.B. Bell, A.L. Garcia, Algorithm refinement for fluctuating hydrodynamics, submitted for publication.
  • 29
    • 33745603699 scopus 로고    scopus 로고
    • Simulating flow of DNA suspension using dissipative particle dynamics
    • Xijunand F., Phan-Thien N., Chen S., Wu X., and Ng T.Y. Simulating flow of DNA suspension using dissipative particle dynamics. Phys. Fluids 18 6 (2006) 063102
    • (2006) Phys. Fluids , vol.18 , Issue.6 , pp. 063102
    • Xijunand, F.1    Phan-Thien, N.2    Chen, S.3    Wu, X.4    Ng, T.Y.5
  • 30
    • 0000503233 scopus 로고    scopus 로고
    • The direct simulation Monte Carlo method
    • Alexander F.J., and Garcia A.L. The direct simulation Monte Carlo method. Comput. Phys. 11 6 (1997) 588-593
    • (1997) Comput. Phys. , vol.11 , Issue.6 , pp. 588-593
    • Alexander, F.J.1    Garcia, A.L.2
  • 31
    • 34447107488 scopus 로고
    • Microscopic simulation of dilute gases with adjustable transport coefficients
    • Baras F., Malek Mansour M., and Garcia A.L. Microscopic simulation of dilute gases with adjustable transport coefficients. Phys. Rev. E 49 4 (1994) 3512-3515
    • (1994) Phys. Rev. E , vol.49 , Issue.4 , pp. 3512-3515
    • Baras, F.1    Malek Mansour, M.2    Garcia, A.L.3
  • 33
    • 0034549101 scopus 로고    scopus 로고
    • The limiting kinetic equation of the consistent Boltzmann algorithm for dense gases
    • Garcia A.L., and Wagner W. The limiting kinetic equation of the consistent Boltzmann algorithm for dense gases. J. Stat. Phys. 101 (2000) 1065-1086
    • (2000) J. Stat. Phys. , vol.101 , pp. 1065-1086
    • Garcia, A.L.1    Wagner, W.2
  • 34
    • 33845313012 scopus 로고    scopus 로고
    • Shear thinning in dilute polymer solutions
    • Ryder J.F., and Yeomans J.M. Shear thinning in dilute polymer solutions. J. Chem. Phys. 125 19 (2006) 194906
    • (2006) J. Chem. Phys. , vol.125 , Issue.19 , pp. 194906
    • Ryder, J.F.1    Yeomans, J.M.2
  • 35
    • 0030774828 scopus 로고    scopus 로고
    • Simulation of the Enskog equation [a-grave] la Bird
    • Montanero J.M., and Santos A. Simulation of the Enskog equation [a-grave] la Bird. Phys. Fluids 9 7 (1997) 2057-2060
    • (1997) Phys. Fluids , vol.9 , Issue.7 , pp. 2057-2060
    • Montanero, J.M.1    Santos, A.2
  • 36
    • 0030813047 scopus 로고    scopus 로고
    • A particle scheme for the numerical solution of the Enskog equation
    • Frezzotti A. A particle scheme for the numerical solution of the Enskog equation. Phys. Fluids 9 5 (1997) 1329-1335
    • (1997) Phys. Fluids , vol.9 , Issue.5 , pp. 1329-1335
    • Frezzotti, A.1
  • 37
    • 33644968108 scopus 로고    scopus 로고
    • Consistent particle-based algorithm with a non-ideal equation of state
    • Ihle T., Tnzel E., and Kroll D.M. Consistent particle-based algorithm with a non-ideal equation of state. Europhys. Lett. 73 (2006) 664-670
    • (2006) Europhys. Lett. , vol.73 , pp. 664-670
    • Ihle, T.1    Tnzel, E.2    Kroll, D.M.3
  • 38
    • 36849126204 scopus 로고
    • Studies in molecular dynamics. I. General method
    • Alder B.J., and Wainwright T.E. Studies in molecular dynamics. I. General method. J. Chem. Phys. 31 (1959) 459
    • (1959) J. Chem. Phys. , vol.31 , pp. 459
    • Alder, B.J.1    Wainwright, T.E.2
  • 39
    • 10244220980 scopus 로고    scopus 로고
    • Neighbor list collision-driven molecular dynamics simulation for nonspherical particles: I. Algorithmic details II. Applications to ellipses and ellipsoids
    • 765-793
    • Donev A., Torquato S., and Stillinger F.H. Neighbor list collision-driven molecular dynamics simulation for nonspherical particles: I. Algorithmic details II. Applications to ellipses and ellipsoids. J. Comput. Phys. 202 2 (2005) 737-764 765-793
    • (2005) J. Comput. Phys. , vol.202 , Issue.2 , pp. 737-764
    • Donev, A.1    Torquato, S.2    Stillinger, F.H.3
  • 40
    • 0031161658 scopus 로고    scopus 로고
    • Molecular dynamics for polymeric fluids using discontinuous potentials
    • Smith S.W., Hall C.K., and Freeman B.D. Molecular dynamics for polymeric fluids using discontinuous potentials. J. Comput. Phys. 134 1 (1997) 16-30
    • (1997) J. Comput. Phys. , vol.134 , Issue.1 , pp. 16-30
    • Smith, S.W.1    Hall, C.K.2    Freeman, B.D.3
  • 41
    • 33845318898 scopus 로고    scopus 로고
    • Discontinuous molecular dynamics simulation study of polymer collapse
    • Opps S.B., Polson J.M., and Risk N.A. Discontinuous molecular dynamics simulation study of polymer collapse. J. Chem. Phys. 125 19 (2006) 194904
    • (2006) J. Chem. Phys. , vol.125 , Issue.19 , pp. 194904
    • Opps, S.B.1    Polson, J.M.2    Risk, N.A.3
  • 43
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of fibril formation by random coil peptides
    • Nguyen H.D., and Hall C.K. Molecular dynamics simulations of fibril formation by random coil peptides. Proc. Natl. Acad. Sci. USA 101 (2004) 16180
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 16180
    • Nguyen, H.D.1    Hall, C.K.2
  • 44
    • 85189839860 scopus 로고    scopus 로고
    • A. Donev, Asynchronous event-driven particle algorithms. in: PADS'07: Proceedings of the 21st International Workshop on Principles of Advanced and Distributed Simulation, IEEE Computer Society, Washington, DC, USA, 2007, pp. 83-92.
  • 45
    • 0034306828 scopus 로고    scopus 로고
    • Time step truncation error in direct simulation Monte Carlo
    • Garcia A.L., and Wagner W. Time step truncation error in direct simulation Monte Carlo. Phys. Fluids 12 (2000) 2621-2633
    • (2000) Phys. Fluids , vol.12 , pp. 2621-2633
    • Garcia, A.L.1    Wagner, W.2
  • 46
    • 33748524517 scopus 로고    scopus 로고
    • Generation of the Maxwellian Inflow Distribution
    • Garcia A.L., and Wagner W. Generation of the Maxwellian Inflow Distribution. J. Comput. Phys. 217 (2006) 693-708
    • (2006) J. Comput. Phys. , vol.217 , pp. 693-708
    • Garcia, A.L.1    Wagner, W.2
  • 47
    • 0000383154 scopus 로고    scopus 로고
    • Adaptive mesh and algorithm refinement using direct simulation Monte Carlo
    • Garcia A.L., Bell J., Crutchfield Wm.Y., and Alder B.J. Adaptive mesh and algorithm refinement using direct simulation Monte Carlo. J. Comput. Phys. 154 (1999) 134-155
    • (1999) J. Comput. Phys. , vol.154 , pp. 134-155
    • Garcia, A.L.1    Bell, J.2    Crutchfield, Wm.Y.3    Alder, B.J.4
  • 48
    • 11144347132 scopus 로고    scopus 로고
    • Three-dimensional hybrid continuum-atomistic simulations for multiscale hydrodynamics
    • Wijesinghe S., Hornung R., Garcia A.L., and Hadjiconstantinou N. Three-dimensional hybrid continuum-atomistic simulations for multiscale hydrodynamics. J. Fluids Eng. 126 (2004) 768-777
    • (2004) J. Fluids Eng. , vol.126 , pp. 768-777
    • Wijesinghe, S.1    Hornung, R.2    Garcia, A.L.3    Hadjiconstantinou, N.4
  • 49
    • 0035498141 scopus 로고    scopus 로고
    • Multi-particle collision dynamics: flow around a circular and a square cylinder
    • Lamura A., Gompper G., Ihle T., and Kroll D.M. Multi-particle collision dynamics: flow around a circular and a square cylinder. Europhys. Lett. 56 3 (2001) 319-325
    • (2001) Europhys. Lett. , vol.56 , Issue.3 , pp. 319-325
    • Lamura, A.1    Gompper, G.2    Ihle, T.3    Kroll, D.M.4
  • 50
    • 0036103074 scopus 로고    scopus 로고
    • Development of a simulation model for solid objects suspended in a fluctuating fluid
    • Inoue Y., Chen Y., and Ohashi H. Development of a simulation model for solid objects suspended in a fluctuating fluid. J. Stat. Phys. 107 112 (2002) 85-100
    • (2002) J. Stat. Phys. , vol.107 , Issue.112 , pp. 85-100
    • Inoue, Y.1    Chen, Y.2    Ohashi, H.3
  • 51
    • 0000981411 scopus 로고    scopus 로고
    • Burnett description for plane poiseuille flow
    • Uribe F.J., and Garcia A.L. Burnett description for plane poiseuille flow. Phys. Rev. E 60 4 (1999) 4063-4078
    • (1999) Phys. Rev. E , vol.60 , Issue.4 , pp. 4063-4078
    • Uribe, F.J.1    Garcia, A.L.2
  • 52
    • 0000907376 scopus 로고    scopus 로고
    • Cell size dependence of transport coefficients in stochastic particle algorithms
    • (Erratum: Phys. Fluids 12 (2000) 731)
    • Alexander F., Garcia A.L., and Alder B.J. Cell size dependence of transport coefficients in stochastic particle algorithms. Phys. Fluids 10 (1998) 1540 (Erratum: Phys. Fluids 12 (2000) 731)
    • (1998) Phys. Fluids , vol.10 , pp. 1540
    • Alexander, F.1    Garcia, A.L.2    Alder, B.J.3
  • 53
    • 85189836918 scopus 로고    scopus 로고
    • T. Bartel, T. Sterk, J. Payne, B. Preppernau. DSMC simulation of nozzle expansion flow fields. AIAA Paper No. 94-2047, 1994.
  • 54
    • 32644474588 scopus 로고    scopus 로고
    • Statistics of tumbling of a single polymer molecule in shear flow
    • Gerashchenko S., and Steinberg V. Statistics of tumbling of a single polymer molecule in shear flow. Phys. Rev. Lett. 96 3 (2006) 038304
    • (2006) Phys. Rev. Lett. , vol.96 , Issue.3 , pp. 038304
    • Gerashchenko, S.1    Steinberg, V.2
  • 55
  • 56
    • 0018964750 scopus 로고
    • Direct simulation methods for compressible inviscid ideal-gas flow
    • Pullin D.I. Direct simulation methods for compressible inviscid ideal-gas flow. J. Comput. Phys. 34 (1980) 231-244
    • (1980) J. Comput. Phys. , vol.34 , pp. 231-244
    • Pullin, D.I.1
  • 57
    • 22244433533 scopus 로고    scopus 로고
    • Numerical solution of the Boltzmann equation by time relaxed Monte Carlo (TRMC) methods
    • Pareschi L., and Trazzi S. Numerical solution of the Boltzmann equation by time relaxed Monte Carlo (TRMC) methods. Int. J. Numer. Meth. Fluids 48 (2005) 947-983
    • (2005) Int. J. Numer. Meth. Fluids , vol.48 , pp. 947-983
    • Pareschi, L.1    Trazzi, S.2


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