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Volumn 4, Issue 1, 2011, Pages

Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package

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EID: 80052401968     PISSN: 20461682     EISSN: None     Source Type: Journal    
DOI: 10.1186/2046-1682-4-7     Document Type: Article
Times cited : (32)

References (52)
  • 1
    • 84977586068 scopus 로고
    • Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen
    • Einstein A. Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen. Ann Phys 1905, 17:549-560.
    • (1905) Ann Phys , vol.17 , pp. 549-560
    • Einstein, A.1
  • 2
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak DL, McCammon JA. Brownian dynamics with hydrodynamic interactions. J Chem Phys 1978, 69:1352-1360.
    • (1978) J Chem Phys , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 3
    • 0344500752 scopus 로고    scopus 로고
    • Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin
    • 10.1006/jmbi.1999.2919, 10438612
    • Elcock AH, Gabdoulline RR, Wade RC, McCammon JA. Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin. J Mol Biol 1999, 291:149-162. 10.1006/jmbi.1999.2919, 10438612.
    • (1999) J Mol Biol , vol.291 , pp. 149-162
    • Elcock, A.H.1    Gabdoulline, R.R.2    Wade, R.C.3    McCammon, J.A.4
  • 4
    • 0036536396 scopus 로고    scopus 로고
    • Biomolecular diffusional association
    • 10.1016/S0959-440X(02)00311-1, 11959498
    • Gabdoulline RR, Wade RC. Biomolecular diffusional association. Curr Opin Struct Biol 2002, 12:204-213. 10.1016/S0959-440X(02)00311-1, 11959498.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 204-213
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 5
    • 65549085321 scopus 로고    scopus 로고
    • Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution
    • 10.1016/j.bpj.2008.11.052, 2717263, 19254533
    • Spaar A, Floeck D, Helms V. Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution. Biophys J 2009, 96:1721-1732. 10.1016/j.bpj.2008.11.052, 2717263, 19254533.
    • (2009) Biophys J , vol.96 , pp. 1721-1732
    • Spaar, A.1    Floeck, D.2    Helms, V.3
  • 6
    • 68049142311 scopus 로고    scopus 로고
    • Fruitful and futile encounters along the association reaction between proteins
    • 10.1016/j.bpj.2009.02.054, 2712199, 19450494
    • Harel M, Spaar A, Schreiber G. Fruitful and futile encounters along the association reaction between proteins. Biophys J 2009, 96:4237-4248. 10.1016/j.bpj.2009.02.054, 2712199, 19450494.
    • (2009) Biophys J , vol.96 , pp. 4237-4248
    • Harel, M.1    Spaar, A.2    Schreiber, G.3
  • 7
    • 0037043423 scopus 로고    scopus 로고
    • Corrections to scaling in the hydrodynamic properties of dilute polymer solutions
    • Dünweg B, Reith D, Steinhauser M, Kremer K. Corrections to scaling in the hydrodynamic properties of dilute polymer solutions. J Chem Phys 2002, 117:914-924.
    • (2002) J Chem Phys , vol.117 , pp. 914-924
    • Dünweg, B.1    Reith, D.2    Steinhauser, M.3    Kremer, K.4
  • 8
    • 42549173430 scopus 로고
    • Mean-field hydrodynamics Brownian dynamics simulations of viscosity and self-diffusion of near-hard-sphere colloidal liquids
    • Heyes DM. Mean-field hydrodynamics Brownian dynamics simulations of viscosity and self-diffusion of near-hard-sphere colloidal liquids. J Phys: Condens Matter 1995, 7:8857-8865.
    • (1995) J Phys: Condens Matter , vol.7 , pp. 8857-8865
    • Heyes, D.M.1
  • 9
    • 77950792003 scopus 로고    scopus 로고
    • Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm
    • 10.1371/journal.pcbi.1000694, 2832674, 20221255
    • McGuffee SR, Elcock AH. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 2010, 6:e1000694. 10.1371/journal.pcbi.1000694, 2832674, 20221255.
    • (2010) PLoS Comput Biol , vol.6
    • McGuffee, S.R.1    Elcock, A.H.2
  • 10
    • 1842497695 scopus 로고    scopus 로고
    • Diffusional dynamics of cytochrome c molecules in the presence of a charged surface
    • Gorba C, Helms V. Diffusional dynamics of cytochrome c molecules in the presence of a charged surface. Soft Materials 2003, 1:187-204.
    • (2003) Soft Materials , vol.1 , pp. 187-204
    • Gorba, C.1    Helms, V.2
  • 11
    • 3142735054 scopus 로고    scopus 로고
    • Brownian dynamics simulations of simplified cytochrome c molecules in the presence of a charged membrane
    • 10.1063/1.1755668, 15260567
    • Gorba C, Geyer T, Helms V. Brownian dynamics simulations of simplified cytochrome c molecules in the presence of a charged membrane. J Chem Phys 2004, 121:457-464. 10.1063/1.1755668, 15260567.
    • (2004) J Chem Phys , vol.121 , pp. 457-464
    • Gorba, C.1    Geyer, T.2    Helms, V.3
  • 12
    • 0031714012 scopus 로고    scopus 로고
    • Brownian dynamics simulation of protein-protein encounter
    • Gabdoulline RR, Wade RC. Brownian dynamics simulation of protein-protein encounter. Methods 1998, 3:329-341.
    • (1998) Methods , vol.3 , pp. 329-341
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 13
    • 0030891436 scopus 로고    scopus 로고
    • Simulation of the diffusional association of barnase and barstar
    • 10.1016/S0006-3495(97)78838-6, 1184389, 9129797
    • Gabdoulline RR, Wade RC. Simulation of the diffusional association of barnase and barstar. Biophys J 1997, 72:1917-1929. 10.1016/S0006-3495(97)78838-6, 1184389, 9129797.
    • (1997) Biophys J , vol.72 , pp. 1917-1929
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 14
    • 77956262968 scopus 로고    scopus 로고
    • BrownDye: A software package for Brownian dynamics
    • Huber GA, McCammon JA. BrownDye: A software package for Brownian dynamics. Comput Phys Comm 2010, 181:1896-1905.
    • (2010) Comput Phys Comm , vol.181 , pp. 1896-1905
    • Huber, G.A.1    McCammon, J.A.2
  • 15
    • 0001229341 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of globular proteins from their atomic-level structures
    • 1300675, 10653785
    • García de la Torre J, Huertas M, Carrasco B. Calculation of hydrodynamic properties of globular proteins from their atomic-level structures. Biophys J 2000, 78:719-730. 1300675, 10653785.
    • (2000) Biophys J , vol.78 , pp. 719-730
    • García de la Torre, J.1    Huertas, M.2    Carrasco, B.3
  • 16
    • 1842478913 scopus 로고    scopus 로고
    • Interfacing Brownian dynamics simulations
    • 10.1063/1.1647522, 15267316
    • Geyer T, Gorba C, Helms V. Interfacing Brownian dynamics simulations. J Chem Phys 2004, 120:4573-4580. 10.1063/1.1647522, 15267316.
    • (2004) J Chem Phys , vol.120 , pp. 4573-4580
    • Geyer, T.1    Gorba, C.2    Helms, V.3
  • 17
    • 70349289359 scopus 로고    scopus 로고
    • Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions
    • Winter U, Geyer T. Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions. J Chem Phys 2009, 131:104102.
    • (2009) J Chem Phys , vol.131 , pp. 104102
    • Winter, U.1    Geyer, T.2
  • 18
    • 63149129721 scopus 로고    scopus 로고
    • An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations
    • 10.1063/1.3089668, 19317564
    • Geyer T, Winter U. An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations. J Chem Phys 2009, 130:114905. 10.1063/1.3089668, 19317564.
    • (2009) J Chem Phys , vol.130 , pp. 114905
    • Geyer, T.1    Winter, U.2
  • 19
    • 0004272337 scopus 로고    scopus 로고
    • An introduction to dynamics of colloids
    • Amsterdam, Elsevier
    • Dhont JKG. An introduction to dynamics of colloids. 1996, Amsterdam, Elsevier.
    • (1996)
    • Dhont, J.K.G.1
  • 20
    • 7444247799 scopus 로고
    • The intrinsic viscosities and diffusion constants of flexible macromolecules in solution
    • Kirkwood JG, Riseman J. The intrinsic viscosities and diffusion constants of flexible macromolecules in solution. J Chem Phys 1948, 16:565-573.
    • (1948) J Chem Phys , vol.16 , pp. 565-573
    • Kirkwood, J.G.1    Riseman, J.2
  • 21
    • 84933517499 scopus 로고
    • Variational treatment of hydrodynamic interaction in polymers
    • Rotne J, Prager S. Variational treatment of hydrodynamic interaction in polymers. J Chem Phys 1969, 50:4831-4837.
    • (1969) J Chem Phys , vol.50 , pp. 4831-4837
    • Rotne, J.1    Prager, S.2
  • 22
    • 36849101815 scopus 로고
    • Transport properties of polymer chains in dilute solutions: hydrodynamic interactions
    • Yamakawa H. Transport properties of polymer chains in dilute solutions: hydrodynamic interactions. J Chem Phys 1970, 53:436-443.
    • (1970) J Chem Phys , vol.53 , pp. 436-443
    • Yamakawa, H.1
  • 24
    • 0003061782 scopus 로고
    • Many-sphere hydrodynamic interactions and mobilities in a suspension
    • Mazur P, van Saarloos W. Many-sphere hydrodynamic interactions and mobilities in a suspension. Physica 1982, 115A:21-57.
    • (1982) Physica , vol.115 A , pp. 21-57
    • Mazur, P.1    van Saarloos, W.2
  • 25
    • 0017403408 scopus 로고
    • Hydrodynamic properties of macromolecular complexes. I. Translation
    • García de la Torre J, Bloomfeld VA. Hydrodynamic properties of macromolecular complexes. I. Translation. Biopolymers 1977, 16:1747-1763.
    • (1977) Biopolymers , vol.16 , pp. 1747-1763
    • García de la Torre, J.1    Bloomfeld, V.A.2
  • 26
    • 0017391665 scopus 로고
    • Hydrodynamic properties of macromolecular complexes. II. Rotation
    • García de la Torre J, Bloomfeld VA. Hydrodynamic properties of macromolecular complexes. II. Rotation. Biopolymers 1977, 16:1765-1778.
    • (1977) Biopolymers , vol.16 , pp. 1765-1778
    • García de la Torre, J.1    Bloomfeld, V.A.2
  • 27
    • 26444587212 scopus 로고    scopus 로고
    • Lubrication corrections for three-particle contributions to short-time self-diffusion coefficients in colloidal dispersions
    • Cichocki B, Ekiel-Jezewska ML, Wajnryb E. Lubrication corrections for three-particle contributions to short-time self-diffusion coefficients in colloidal dispersions. J Chem Phys 1999, 111:3265-3273.
    • (1999) J Chem Phys , vol.111 , pp. 3265-3273
    • Cichocki, B.1    Ekiel-Jezewska, M.L.2    Wajnryb, E.3
  • 28
    • 0017750547 scopus 로고
    • Hydrodynamics of macromolecular complexes. III. Bacterial viruses
    • García de la Torre J, Bloomfield VA. Hydrodynamics of macromolecular complexes. III. Bacterial viruses. Biopolymers 1977, 16:1779-1793.
    • (1977) Biopolymers , vol.16 , pp. 1779-1793
    • García de la Torre, J.1    Bloomfield, V.A.2
  • 29
    • 77950559055 scopus 로고    scopus 로고
    • Hydrodynamic multibead modelling: problems, pitfalls, and solutions. 1. Ellipsoid models
    • 10.1007/s00249-009-0424-2, 19280183
    • Zipper P, Durchschlag H. Hydrodynamic multibead modelling: problems, pitfalls, and solutions. 1. Ellipsoid models. Eur Biophys J 2010, 39:437-447. 10.1007/s00249-009-0424-2, 19280183.
    • (2010) Eur Biophys J , vol.39 , pp. 437-447
    • Zipper, P.1    Durchschlag, H.2
  • 30
    • 5844278702 scopus 로고
    • Construction of Langevin forces in the simulation of hydrodynamic interaction
    • Fixman M. Construction of Langevin forces in the simulation of hydrodynamic interaction. Macromolecules 1986, 19:1204-1207.
    • (1986) Macromolecules , vol.19 , pp. 1204-1207
    • Fixman, M.1
  • 31
    • 0038608221 scopus 로고    scopus 로고
    • Accelerated Stokesian dynamics: Brownian motion
    • Banchio AJ, Brady JF. Accelerated Stokesian dynamics: Brownian motion. J Chem Phys 2003, 118:10323-10332.
    • (2003) J Chem Phys , vol.118 , pp. 10323-10332
    • Banchio, A.J.1    Brady, J.F.2
  • 32
    • 0034246730 scopus 로고    scopus 로고
    • Simulation method of colloidal suspensions with hydrodynamic interactions: Fluid particle dynamics
    • 10.1103/PhysRevLett.85.1338, 10991546
    • Tanaka H, Araki T. Simulation method of colloidal suspensions with hydrodynamic interactions: Fluid particle dynamics. Phys Rev Lett 2000, 85:1338-1341. 10.1103/PhysRevLett.85.1338, 10991546.
    • (2000) Phys Rev Lett , vol.85 , pp. 1338-1341
    • Tanaka, H.1    Araki, T.2
  • 33
    • 37649027979 scopus 로고    scopus 로고
    • Simulation method to resolve hydrodynamic interactions in colloidal dispersions
    • Nakayama Y, Yamamoto R. Simulation method to resolve hydrodynamic interactions in colloidal dispersions. Phys Rev E 2005, 71:036707.
    • (2005) Phys Rev E , vol.71 , pp. 036707
    • Nakayama, Y.1    Yamamoto, R.2
  • 34
    • 84950109965 scopus 로고
    • Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics
    • Hoogerbrugge PJ, Koelman JMVA. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys Lett 1992, 19:155-160.
    • (1992) Europhys Lett , vol.19 , pp. 155-160
    • Hoogerbrugge, P.J.1    Koelman, J.M.V.A.2
  • 35
    • 84956259119 scopus 로고
    • Statistical mechanics of dissipative particle dynamics
    • Español P, Warren P. Statistical mechanics of dissipative particle dynamics. Europhys Lett 1995, 30:191-196.
    • (1995) Europhys Lett , vol.30 , pp. 191-196
    • Español, P.1    Warren, P.2
  • 36
    • 0001468477 scopus 로고    scopus 로고
    • Mesoscopic model for solvent dynamics
    • Malevanets A, Kapral R. Mesoscopic model for solvent dynamics. J Chem Phys 1999, 110:8605-8613.
    • (1999) J Chem Phys , vol.110 , pp. 8605-8613
    • Malevanets, A.1    Kapral, R.2
  • 37
    • 60749102237 scopus 로고    scopus 로고
    • Multi-particle collision dynamics: A particle-based mesoscale simulation approach to the hydrodynamics of complex fluids
    • Gompper G, Ihle T, Kroll DM, Winkler RG. Multi-particle collision dynamics: A particle-based mesoscale simulation approach to the hydrodynamics of complex fluids. Adv Polymer Science 2009, 221:1-87.
    • (2009) Adv Polymer Science , vol.221 , pp. 1-87
    • Gompper, G.1    Ihle, T.2    Kroll, D.M.3    Winkler, R.G.4
  • 38
    • 0033546455 scopus 로고    scopus 로고
    • An alternative approach to dissipative particle dynamics
    • Lowe CP. An alternative approach to dissipative particle dynamics. Europhys Lett 1999, 47:145-151.
    • (1999) Europhys Lett , vol.47 , pp. 145-151
    • Lowe, C.P.1
  • 39
    • 1542471855 scopus 로고    scopus 로고
    • Lattice Boltzmann method for fluid flows
    • Chen S, Doolen GD. Lattice Boltzmann method for fluid flows. Annu Rev Fluid Mech 1998, 30:329-364.
    • (1998) Annu Rev Fluid Mech , vol.30 , pp. 329-364
    • Chen, S.1    Doolen, G.D.2
  • 40
    • 0035475865 scopus 로고    scopus 로고
    • Screening of hydrodynamic interactions in semidilute polymer solutions: A computer simulation study
    • Ahlrichs P, Everaers R, Dünweg B. Screening of hydrodynamic interactions in semidilute polymer solutions: A computer simulation study. Phys Rev E 2001, 64:040501(R).
    • (2001) Phys Rev E , vol.64
    • Ahlrichs, P.1    Everaers, R.2    Dünweg, B.3
  • 41
    • 0002782364 scopus 로고
    • Diffusion-controlled association rate of cytochrome c and cytochrome c peroxidase in a simple electrostatic model
    • Northrup SH, Reynolds JCL, Miller CM, Forrest KJ, Boles JO. Diffusion-controlled association rate of cytochrome c and cytochrome c peroxidase in a simple electrostatic model. J Am Chem Soc 1986, 108:8162-8170.
    • (1986) J Am Chem Soc , vol.108 , pp. 8162-8170
    • Northrup, S.H.1    Reynolds, J.C.L.2    Miller, C.M.3    Forrest, K.J.4    Boles, J.O.5
  • 42
    • 21844483292 scopus 로고
    • Critical exponents, hyperscaling, and universal amplitude ratios for two- and three-dimensional self-avoiding walks
    • Li B, Madras N, Sokol AD. Critical exponents, hyperscaling, and universal amplitude ratios for two- and three-dimensional self-avoiding walks. J Stat Phys 1995, 80:661-754.
    • (1995) J Stat Phys , vol.80 , pp. 661-754
    • Li, B.1    Madras, N.2    Sokol, A.D.3
  • 43
    • 77950580593 scopus 로고    scopus 로고
    • Intrinsic viscosity of bead models for macromolecules and nanoparticles
    • García de la Torre J, Amorós D, Ortega A. Intrinsic viscosity of bead models for macromolecules and nanoparticles. Eur Biophys J 2010, 39:381-388.
    • (2010) Eur Biophys J , vol.39 , pp. 381-388
    • García de la Torre, J.1    Amorós, D.2    Ortega, A.3
  • 44
    • 78349288528 scopus 로고    scopus 로고
    • Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: The role of intermolecular hydrodynamic interactions in barnase-barstar association
    • 10.1016/j.bpj.2010.09.006, 21044566
    • Frembgen-Kesner T, Elcock AH. Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: The role of intermolecular hydrodynamic interactions in barnase-barstar association. Biophys J 2010, 99:L75-L77. 10.1016/j.bpj.2010.09.006, 21044566.
    • (2010) Biophys J , vol.99
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 45
    • 65249094240 scopus 로고    scopus 로고
    • Striking effects of hydrodynamic interactions on the simulated diffusion and folding of proteins
    • Frembgen-Kesner T, Elcock AH. Striking effects of hydrodynamic interactions on the simulated diffusion and folding of proteins. J Chem Theory Comput 2009, 5:242-256.
    • (2009) J Chem Theory Comput , vol.5 , pp. 242-256
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 46
    • 0034318343 scopus 로고    scopus 로고
    • Brownian dynamics simulation of the motion of a rigid sphere in a viscous fluid very near a wall
    • Sholl DS, Fenwick MK, Atman E, Prieve DC. Brownian dynamics simulation of the motion of a rigid sphere in a viscous fluid very near a wall. J Chem Phys 2000, 113:9268-9278.
    • (2000) J Chem Phys , vol.113 , pp. 9268-9278
    • Sholl, D.S.1    Fenwick, M.K.2    Atman, E.3    Prieve, D.C.4
  • 47
    • 65249177183 scopus 로고    scopus 로고
    • Graph measures reveal fine structure of complexes forming in multiparticle simulations
    • Lauck F, Helms V, Geyer T. Graph measures reveal fine structure of complexes forming in multiparticle simulations. J Chem Theory Comput 2009, 5:641-648.
    • (2009) J Chem Theory Comput , vol.5 , pp. 641-648
    • Lauck, F.1    Helms, V.2    Geyer, T.3
  • 49
    • 36749107291 scopus 로고
    • On the interaction of spherical double layers
    • Medina-Noyola M, McQuarrie DA. On the interaction of spherical double layers. J Chem Phys 1980, 73:6279-6283.
    • (1980) J Chem Phys , vol.73 , pp. 6279-6283
    • Medina-Noyola, M.1    McQuarrie, D.A.2
  • 50
    • 0032827044 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres
    • 10.1007/s002490050233, 10460344
    • Carrasco B, García de la Torre J, Zipper P. Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres. Eur Biophys J 1999, 28:510-515. 10.1007/s002490050233, 10460344.
    • (1999) Eur Biophys J , vol.28 , pp. 510-515
    • Carrasco, B.1    García de la Torre, J.2    Zipper, P.3
  • 51
    • 0000274247 scopus 로고
    • Molecular theory of Brownian motion for several particles
    • Deutch JM, Oppenheim I. Molecular theory of Brownian motion for several particles. J Chem Phys 1971, 54:3547-3555.
    • (1971) J Chem Phys , vol.54 , pp. 3547-3555
    • Deutch, J.M.1    Oppenheim, I.2
  • 52
    • 0034247779 scopus 로고    scopus 로고
    • Hydrodynamic interactions in long chain polymers: Application of the Chebyshev polynomial approximation in stochastic simulations
    • Jendrejack RM, Graham MD, de Pablo JJ. Hydrodynamic interactions in long chain polymers: Application of the Chebyshev polynomial approximation in stochastic simulations. J Chem Phys 2000, 113:2894-2900.
    • (2000) J Chem Phys , vol.113 , pp. 2894-2900
    • Jendrejack, R.M.1    Graham, M.D.2    de Pablo, J.J.3


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