메뉴 건너뛰기




Volumn 400, Issue , 2007, Pages 295-321

Modeling 2D and 3D diffusion

(1)  Saxton, Michael J a  

a NONE

Author keywords

Brownian dynamics; Diffusion; Event driven algorithm; Monte Carlo; n fold way; Random number generation; Random walk

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CELL FUNCTION; CELL MEMBRANE; COMPUTER SIMULATION; DIFFUSION; METABOLISM; MONTE CARLO METHOD;

EID: 36549074600     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-519-9:295     Document Type: Article
Times cited : (41)

References (167)
  • 1
    • 77956697875 scopus 로고    scopus 로고
    • Lateral diffusion of lipids and proteins
    • Saxton, M. J. (1999) Lateral diffusion of lipids and proteins. Curr. Topics Membr. 48, 229-282.
    • (1999) Curr. Topics Membr , vol.48 , pp. 229-282
    • Saxton, M.J.1
  • 2
    • 0041931122 scopus 로고    scopus 로고
    • Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges
    • Hall, D. and Minton, A. P. (2003) Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges. Biochim. Biophys. Acta 1649, 127-139.
    • (2003) Biochim. Biophys. Acta , vol.1649 , pp. 127-139
    • Hall, D.1    Minton, A.P.2
  • 3
    • 0030956033 scopus 로고    scopus 로고
    • Single-particle tracking: Applications to membrane dynamics
    • Saxton, M. J. and Jacobson, K. (1997) Single-particle tracking: Applications to membrane dynamics. Annu. Rev. Biophys. Biomol. Struct. 26, 373-399.
    • (1997) Annu. Rev. Biophys. Biomol. Struct , vol.26 , pp. 373-399
    • Saxton, M.J.1    Jacobson, K.2
  • 4
    • 85052507481 scopus 로고    scopus 로고
    • Allen, M. P. and Tildesley, D. J. (1989) Computer Simulation of Liquids. Oxford University Press, Oxford. Fortran programs from the appendix are available at www.ccp5.ac.uk/librar.shtml.
    • Allen, M. P. and Tildesley, D. J. (1989) Computer Simulation of Liquids. Oxford University Press, Oxford. Fortran programs from the appendix are available at www.ccp5.ac.uk/librar.shtml.
  • 7
    • 0029946890 scopus 로고    scopus 로고
    • Constrained diffusion or immobile fraction on cell surfaces: A new interpretation
    • Feder, T. J., Brust-Mascher, I., Slattery, J. P., Baird, B., and Webb, W. W. (1996) Constrained diffusion or immobile fraction on cell surfaces: A new interpretation. Biophys. J. 70, 2767-2773.
    • (1996) Biophys. J , vol.70 , pp. 2767-2773
    • Feder, T.J.1    Brust-Mascher, I.2    Slattery, J.P.3    Baird, B.4    Webb, W.W.5
  • 8
    • 0040307478 scopus 로고
    • Anomalous diffusion in disordered media: Statistical mechanisms, models and physical applications
    • Bouchaud, J.-P. and Georges, A. (1990) Anomalous diffusion in disordered media: Statistical mechanisms, models and physical applications. Phys. Reports 195, 127-293.
    • (1990) Phys. Reports , vol.195 , pp. 127-293
    • Bouchaud, J.-P.1    Georges, A.2
  • 9
    • 0028140412 scopus 로고
    • Anomalous diffusion due to obstacles: A Monte Carlo study
    • Saxton, M. J. (1994) Anomalous diffusion due to obstacles: A Monte Carlo study. Biophys. J. 66, 394-401.
    • (1994) Biophys. J , vol.66 , pp. 394-401
    • Saxton, M.J.1
  • 10
    • 0030050141 scopus 로고    scopus 로고
    • Anomalous diffusion due to binding: A Monte Carlo study
    • Saxton, M. J. (1996) Anomalous diffusion due to binding: A Monte Carlo study. Biophys. J. 70, 1250-1262.
    • (1996) Biophys. J , vol.70 , pp. 1250-1262
    • Saxton, M.J.1
  • 11
    • 0027504198 scopus 로고
    • Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells
    • Kusumi, A., Sako, Y., and Yamamoto, M. (1993) Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells. Biophys. J. 65, 2021-2040.
    • (1993) Biophys. J , vol.65 , pp. 2021-2040
    • Kusumi, A.1    Sako, Y.2    Yamamoto, M.3
  • 12
    • 0027197103 scopus 로고
    • Lateral diffusion in an archipelago: Single-particle diffusion
    • Saxton, M. J. (1993) Lateral diffusion in an archipelago: Single-particle diffusion. Biophys. J. 64, 1766-1780.
    • (1993) Biophys. J , vol.64 , pp. 1766-1780
    • Saxton, M.J.1
  • 13
    • 36549074349 scopus 로고    scopus 로고
    • Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1992) Numerical Recipes in FORTRAN: The Art of Scientific Computing, 2nd ed., Cambridge University Press, Cambridge. Also available in C and C++ editions.
    • Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1992) Numerical Recipes in FORTRAN: The Art of Scientific Computing, 2nd ed., Cambridge University Press, Cambridge. Also available in C and C++ editions.
  • 14
    • 0034805503 scopus 로고    scopus 로고
    • Anomalous subdiffusion in fluorescence photobleaching recovery: A Monte Carlo study
    • Saxton, M. J. (2001) Anomalous subdiffusion in fluorescence photobleaching recovery: A Monte Carlo study. Biophys. J. 81, 2226-2240.
    • (2001) Biophys. J , vol.81 , pp. 2226-2240
    • Saxton, M.J.1
  • 15
    • 20444492647 scopus 로고    scopus 로고
    • Membrane lateral mobility obstructed by polymer-tethered lipids studied at the single molecule level
    • Deverall, M. A., Gindl, E., Sinner, E.-K., et al. (2005) Membrane lateral mobility obstructed by polymer-tethered lipids studied at the single molecule level. Biophys. J. 88, 1875-1886.
    • (2005) Biophys. J , vol.88 , pp. 1875-1886
    • Deverall, M.A.1    Gindl, E.2    Sinner, E.-K.3
  • 16
    • 4043151477 scopus 로고    scopus 로고
    • The restaurant at the end of the random walk: Recent developments in the description of anomalous transport by fractional dynamics
    • Metzler, R. and Klafter, J. (2004) The restaurant at the end of the random walk: Recent developments in the description of anomalous transport by fractional dynamics. J. Phys. A 37, R161-R208.
    • (2004) J. Phys. A , vol.37
    • Metzler, R.1    Klafter, J.2
  • 18
    • 0000895333 scopus 로고
    • Exact analytic solutions for diffusion impeded by an infinite array of partially permeable barriers
    • Powles, J. G., Mallett, M. J. D., Rickayzen, G., and Evans, W. A. B. (1992) Exact analytic solutions for diffusion impeded by an infinite array of partially permeable barriers. Proc. R. Soc. Lond. A 436, 391-403.
    • (1992) Proc. R. Soc. Lond. A , vol.436 , pp. 391-403
    • Powles, J.G.1    Mallett, M.J.D.2    Rickayzen, G.3    Evans, W.A.B.4
  • 19
    • 17844364513 scopus 로고    scopus 로고
    • Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: High-speed single-molecule tracking of membrane molecules
    • Kusumi, A., Nakada, C., Ritchie, K., et al. (2005) Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: High-speed single-molecule tracking of membrane molecules. Annu. Rev. Biophys. Biomol. Struct. 34, 351-378.
    • (2005) Annu. Rev. Biophys. Biomol. Struct , vol.34 , pp. 351-378
    • Kusumi, A.1    Nakada, C.2    Ritchie, K.3
  • 20
    • 0026528045 scopus 로고
    • Tracking of cell surface receptors by fluorescence digital imaging microscopy using a charge-coupled device camera. Low-density lipoprotein and influenza virus receptor mobility at 4 C
    • Anderson, C. M., Georgiou, G. N., Morrison, I. E. G., Stevenson, G. V. W., and Cherry, R. J. (1992) Tracking of cell surface receptors by fluorescence digital imaging microscopy using a charge-coupled device camera. Low-density lipoprotein and influenza virus receptor mobility at 4 C. J. Cell Sci. 101, 415-425.
    • (1992) J. Cell Sci , vol.101 , pp. 415-425
    • Anderson, C.M.1    Georgiou, G.N.2    Morrison, I.E.G.3    Stevenson, G.V.W.4    Cherry, R.J.5
  • 21
    • 0039587949 scopus 로고    scopus 로고
    • Single-molecule microscopy on model membranes reveals anomalous diffusion
    • Schütz, G. J., Schindler, H., and Schmidt, T. (1997) Single-molecule microscopy on model membranes reveals anomalous diffusion. Biophys. J. 73, 1073-1080.
    • (1997) Biophys. J , vol.73 , pp. 1073-1080
    • Schütz, G.J.1    Schindler, H.2    Schmidt, T.3
  • 23
    • 0000561844 scopus 로고
    • Dynamics of colloidal hard spheres in thin aqueous suspension layers-Particle tracking by digital image processing and Brownian dynamics computer simulations
    • Schaertl, W. and Sillescu, H. (1993) Dynamics of colloidal hard spheres in thin aqueous suspension layers-Particle tracking by digital image processing and Brownian dynamics computer simulations. J. Colloid Interface Sci. 155, 313-318.
    • (1993) J. Colloid Interface Sci , vol.155 , pp. 313-318
    • Schaertl, W.1    Sillescu, H.2
  • 24
    • 0029977418 scopus 로고    scopus 로고
    • Methods of digital video microscopy for colloidal studies
    • Crocker, J. C. and Grier, D. G. (1996) Methods of digital video microscopy for colloidal studies. J. Colloid Interface Sci. 179, 298-310.
    • (1996) J. Colloid Interface Sci , vol.179 , pp. 298-310
    • Crocker, J.C.1    Grier, D.G.2
  • 25
    • 0033963565 scopus 로고    scopus 로고
    • Direct observation of dynamical heterogeneities in colloidal hard-sphere suspensions
    • Kegel, W. K. and van Blaaderen, A. (2000) Direct observation of dynamical heterogeneities in colloidal hard-sphere suspensions. Science 287, 290-293.
    • (2000) Science , vol.287 , pp. 290-293
    • Kegel, W.K.1    van Blaaderen, A.2
  • 26
    • 0037179384 scopus 로고    scopus 로고
    • Properties of cage rearrangements observed near the colloidal glass transition
    • Weeks, E. R. and Weitz, D. A. (2002) Properties of cage rearrangements observed near the colloidal glass transition. Phys. Rev. Lett. 89, 095704.
    • (2002) Phys. Rev. Lett , vol.89 , pp. 095704
    • Weeks, E.R.1    Weitz, D.A.2
  • 27
    • 0002934557 scopus 로고
    • Analogies between the dynamics of concentrated charged colloidal suspensions and dense atomic liquids
    • Pusey, P. N., Lekkerkerker, H. N. W., Cohen, E. G. D., and de Schepper, I. M. (1990) Analogies between the dynamics of concentrated charged colloidal suspensions and dense atomic liquids. Physica A 164, 12-27.
    • (1990) Physica A , vol.164 , pp. 12-27
    • Pusey, P.N.1    Lekkerkerker, H.N.W.2    Cohen, E.G.D.3    de Schepper, I.M.4
  • 28
    • 0009368319 scopus 로고
    • Note on transport processes in dense colloidal suspensions
    • Cohen, E. G. D. and de Schepper, I. M. (1991) Note on transport processes in dense colloidal suspensions. J. Stat. Phys. 63, 241-248.
    • (1991) J. Stat. Phys , vol.63 , pp. 241-248
    • Cohen, E.G.D.1    de Schepper, I.M.2
  • 29
    • 0028482825 scopus 로고
    • Molecular simulations of colloidal liquids
    • Heyes, D. M. (1994) Molecular simulations of colloidal liquids. Adv. Colloid Interface Sci. 51, 247-268.
    • (1994) Adv. Colloid Interface Sci , vol.51 , pp. 247-268
    • Heyes, D.M.1
  • 30
    • 21344490410 scopus 로고
    • Brownian dynamics simulations of colloidal hard spheres. Effects of sample dimensionality on self-diffusion
    • Schaertl, W. and Sillescu, H. (1994) Brownian dynamics simulations of colloidal hard spheres. Effects of sample dimensionality on self-diffusion. J. Stat. Phys. 74, 687-703.
    • (1994) J. Stat. Phys , vol.74 , pp. 687-703
    • Schaertl, W.1    Sillescu, H.2
  • 31
    • 0012783159 scopus 로고    scopus 로고
    • Diffusion of hard disks and rod-like molecules on surfaces
    • Lahtinen, J. M., Hjelt, T., Ala-Nissila, T., and Chvoj, Z. (2001) Diffusion of hard disks and rod-like molecules on surfaces. Phys. Rev. E 64, 021204.
    • (2001) Phys. Rev. E , vol.64 , pp. 021204
    • Lahtinen, J.M.1    Hjelt, T.2    Ala-Nissila, T.3    Chvoj, Z.4
  • 32
    • 0000421436 scopus 로고
    • Long-time self-diffusion coefficient in colloidal suspensions: Theory versus simulation
    • Löwen, H. and Szamel, G. (1993) Long-time self-diffusion coefficient in colloidal suspensions: theory versus simulation. J. Phys. Cond. Matter 5, 2295-2306.
    • (1993) J. Phys. Cond. Matter , vol.5 , pp. 2295-2306
    • Löwen, H.1    Szamel, G.2
  • 33
    • 0033832403 scopus 로고    scopus 로고
    • Interactions and phase transitions in protein solutions
    • Piazza, R. (2000) Interactions and phase transitions in protein solutions. Curr. Opin. Colloid Interface Sci. 5, 38-43.
    • (2000) Curr. Opin. Colloid Interface Sci , vol.5 , pp. 38-43
    • Piazza, R.1
  • 35
    • 33847005283 scopus 로고
    • Correlations in the motion of atoms in liquid argon
    • Rahman, A. (1964) Correlations in the motion of atoms in liquid argon. Phys. Rev. 136, A405-A411.
    • (1964) Phys. Rev , vol.136
    • Rahman, A.1
  • 36
    • 0033615312 scopus 로고    scopus 로고
    • Interpretation of NOESY cross-relaxation rates from molecular dynamics simulation of a lipid bilayer
    • Feller, S. E., Huster, D., and Gawrisch, K. (1999) Interpretation of NOESY cross-relaxation rates from molecular dynamics simulation of a lipid bilayer. J. Am. Chem. Soc. 121, 8963-8964.
    • (1999) J. Am. Chem. Soc , vol.121 , pp. 8963-8964
    • Feller, S.E.1    Huster, D.2    Gawrisch, K.3
  • 37
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak, D. L. and McCammon, J. A. (1978) Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69, 1352-1360.
    • (1978) J. Chem. Phys , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 38
    • 0029633152 scopus 로고
    • Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program
    • Madura, J. D., Briggs, J. M., Wade, R. C., et al. (1995) Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program. Comput. Phys. Comm. 91, 57-95.
    • (1995) Comput. Phys. Comm , vol.91 , pp. 57-95
    • Madura, J.D.1    Briggs, J.M.2    Wade, R.C.3
  • 39
    • 1642423672 scopus 로고    scopus 로고
    • Molecular simulations of diffusion and association in multimacromolecular systems
    • Elcock, A. H. (2004) Molecular simulations of diffusion and association in multimacromolecular systems. Methods Enzymol. 383, 166-198.
    • (2004) Methods Enzymol , vol.383 , pp. 166-198
    • Elcock, A.H.1
  • 40
    • 0347948979 scopus 로고    scopus 로고
    • Computational challenges in simulating large DNA over long times
    • Schlick, T., Beard, D. A., Huang, J., Strahs, D. A., and Qian, X. (2000) Computational challenges in simulating large DNA over long times. Comput. Sci. Eng. 2, 38-51.
    • (2000) Comput. Sci. Eng , vol.2 , pp. 38-51
    • Schlick, T.1    Beard, D.A.2    Huang, J.3    Strahs, D.A.4    Qian, X.5
  • 41
    • 36549098189 scopus 로고
    • A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models
    • Iniesta, A. and Garcia de la Torre, J. (1990) A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models. J. Chem. Phys. 92, 2015-2018.
    • (1990) J. Chem. Phys , vol.92 , pp. 2015-2018
    • Iniesta, A.1    Garcia de la Torre, J.2
  • 44
    • 22944447427 scopus 로고    scopus 로고
    • Composition dependence of bilayer elasticity
    • Brannigan, G. and Brown, F. L. H. (2005) Composition dependence of bilayer elasticity. J. Chem. Phys. 122, 074905.
    • (2005) J. Chem. Phys , vol.122 , pp. 074905
    • Brannigan, G.1    Brown, F.L.H.2
  • 45
    • 36448998595 scopus 로고
    • Theoretical foundations of dynamic Monte Carlo simulations
    • Fichthorn, K. A. and Weinberg, W. H. (1991) Theoretical foundations of dynamic Monte Carlo simulations. J. Chem. Phys. 95, 1090-1096.
    • (1991) J. Chem. Phys , vol.95 , pp. 1090-1096
    • Fichthorn, K.A.1    Weinberg, W.H.2
  • 46
    • 5244272475 scopus 로고
    • Dynamic Monte Carlo simulations of surface-rate processes
    • Kang, H. C. and Weinberg, W. H. (1992) Dynamic Monte Carlo simulations of surface-rate processes. Acc. Chem. Res. 25, 253-259.
    • (1992) Acc. Chem. Res , vol.25 , pp. 253-259
    • Kang, H.C.1    Weinberg, W.H.2
  • 47
    • 1642423671 scopus 로고    scopus 로고
    • Modeling lipid-sterol bilayers: Applications to structural evolution, lateral diffusion and rafts
    • Zuckermann, M. J., Ipsen, J. H., Miao, L., et al. (2004) Modeling lipid-sterol bilayers: Applications to structural evolution, lateral diffusion and rafts. Methods Enzymol. 383, 198-229.
    • (2004) Methods Enzymol , vol.383 , pp. 198-229
    • Zuckermann, M.J.1    Ipsen, J.H.2    Miao, L.3
  • 48
    • 5544242655 scopus 로고    scopus 로고
    • Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation
    • Groot, R. D. and Warren, P. B. (1997) Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys. 107, 4423-4435.
    • (1997) J. Chem. Phys , vol.107 , pp. 4423-4435
    • Groot, R.D.1    Warren, P.B.2
  • 49
    • 0037044173 scopus 로고    scopus 로고
    • Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations
    • Shillcock, J. C. and Lipowsky, R. (2002) Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations. J. Chem. Phys. 117, 5048-5061.
    • (2002) J. Chem. Phys , vol.117 , pp. 5048-5061
    • Shillcock, J.C.1    Lipowsky, R.2
  • 50
    • 19944423783 scopus 로고    scopus 로고
    • A seamless approach to multiscale complex fluid simulation
    • Symeonidis, V., Karniadakis, G. E., and Caswell, B. (2005) A seamless approach to multiscale complex fluid simulation. Comput. Sci. Eng. 1, 39-46.
    • (2005) Comput. Sci. Eng , vol.1 , pp. 39-46
    • Symeonidis, V.1    Karniadakis, G.E.2    Caswell, B.3
  • 51
    • 0027163092 scopus 로고
    • Lateral diffusion in an archipelago: Dependence on tracer size
    • Saxton, M. J. (1993) Lateral diffusion in an archipelago: Dependence on tracer size. Biophys. J. 64, 1053-1062.
    • (1993) Biophys. J , vol.64 , pp. 1053-1062
    • Saxton, M.J.1
  • 52
    • 36549011042 scopus 로고
    • Molecular crowding and protein organization in biological membranes
    • Jackson, M. B, ed, CRC Press, Boca Raton, FL, pp
    • Abney, J. R. and Scalettar, B. A. (1992) Molecular crowding and protein organization in biological membranes, in Thermodynamics of Membrane Receptors and Channels. (Jackson, M. B., ed.), CRC Press, Boca Raton, FL, pp. 183-226.
    • (1992) Thermodynamics of Membrane Receptors and Channels , pp. 183-226
    • Abney, J.R.1    Scalettar, B.A.2
  • 53
    • 77957083058 scopus 로고
    • Lateral diffusion in membranes
    • Lipowsky, R. and Sackmann, E, eds, Elsevier, Amsterdam, pp
    • Almeida, P. F. F. and Vaz, W. L. C. (1995) Lateral diffusion in membranes, in Structure and Dynamics of Membranes, vol. 1, (Lipowsky, R. and Sackmann, E., eds.) Elsevier, Amsterdam, pp. 305-357.
    • (1995) Structure and Dynamics of Membranes , vol.1 , pp. 305-357
    • Almeida, P.F.F.1    Vaz, W.L.C.2
  • 55
    • 8744294882 scopus 로고    scopus 로고
    • How to simulate anisotropic diffusion processes on curved surfaces
    • Christensen, M. (2004) How to simulate anisotropic diffusion processes on curved surfaces. J. Comput. Phys. 201, 421-438.
    • (2004) J. Comput. Phys , vol.201 , pp. 421-438
    • Christensen, M.1
  • 56
    • 24144448719 scopus 로고    scopus 로고
    • Effects of organelle shape on fluorescence recovery after photobleaching
    • Sbalzarini, I. F., Mezzacasa, A., Helenius, A., and Koumoutsakos, P. (2005) Effects of organelle shape on fluorescence recovery after photobleaching. Biophys. J. 89, 1482-1492.
    • (2005) Biophys. J , vol.89 , pp. 1482-1492
    • Sbalzarini, I.F.1    Mezzacasa, A.2    Helenius, A.3    Koumoutsakos, P.4
  • 57
    • 0029163176 scopus 로고
    • Single-particle tracking: Effect of corrals
    • Saxton, M. J. (1995) Single-particle tracking: Effect of corrals. Biophys. J. 69, 389-398.
    • (1995) Biophys. J , vol.69 , pp. 389-398
    • Saxton, M.J.1
  • 58
    • 0026783791 scopus 로고
    • Long tail kinetics in biophysics?
    • Nagle, J. F. (1992) Long tail kinetics in biophysics? Biophys. J. 63, 366-370.
    • (1992) Biophys. J , vol.63 , pp. 366-370
    • Nagle, J.F.1
  • 59
    • 0012307377 scopus 로고    scopus 로고
    • Simulation and identification of the fractional Brownian motion: A bibliographical and comparative study
    • Coeurjolly, J. -F. (2000) Simulation and identification of the fractional Brownian motion: a bibliographical and comparative study. J. Stat. Software 5, Issue 7 (www.jstatsoft.org).
    • (2000) J. Stat. Software , vol.5 , Issue.7
    • Coeurjolly, J.-F.1
  • 60
    • 12044256185 scopus 로고
    • Random and cooperative sequential adsorption
    • Evans, J. W. (1993) Random and cooperative sequential adsorption. Revs. Mod. Phys. 65, 1281-1329.
    • (1993) Revs. Mod. Phys , vol.65 , pp. 1281-1329
    • Evans, J.W.1
  • 61
    • 0033969782 scopus 로고    scopus 로고
    • From car parking to protein adsorption: An overview of sequential adsorption processes
    • Talbot, J., Tarjus, G., Van Tassel, P. R., and Viot, P. (2000) From car parking to protein adsorption: an overview of sequential adsorption processes. Colloids Surf. A 165, 287-324.
    • (2000) Colloids Surf. A , vol.165 , pp. 287-324
    • Talbot, J.1    Tarjus, G.2    Van Tassel, P.R.3    Viot, P.4
  • 62
    • 21844490046 scopus 로고
    • A fast algorithm for random sequential adsorption of disks
    • Wang, J. S. (1994) A fast algorithm for random sequential adsorption of disks. Int. J. Mod. Phys. C5, 707-715.
    • (1994) Int. J. Mod. Phys , vol.C5 , pp. 707-715
    • Wang, J.S.1
  • 63
    • 42749099977 scopus 로고    scopus 로고
    • Systematic errors due to linear congruential random-number generators with the Swendsen-Wang algorithm: A warning
    • Ossola, G. and Sokal, A. D. (2004) Systematic errors due to linear congruential random-number generators with the Swendsen-Wang algorithm: A warning. Phys. Rev. E 70, 027701.
    • (2004) Phys. Rev. E , vol.70 , pp. 027701
    • Ossola, G.1    Sokal, A.D.2
  • 64
    • 0023452103 scopus 로고
    • Diffusion in disordered media
    • Havlin, S. and Ben-Avraham, D. (1987) Diffusion in disordered media. Adv. Phys. 36, 695-798.
    • (1987) Adv. Phys , vol.36 , pp. 695-798
    • Havlin, S.1    Ben-Avraham, D.2
  • 67
    • 0000296406 scopus 로고
    • Random-walk calculation of conductivity in continuum percolation
    • Tobochnik, J., Laing, D., and Wilson, G. (1990) Random-walk calculation of conductivity in continuum percolation. Phys. Rev. A 41, 3052-3058.
    • (1990) Phys. Rev. A , vol.41 , pp. 3052-3058
    • Tobochnik, J.1    Laing, D.2    Wilson, G.3
  • 68
    • 44949269794 scopus 로고
    • Dynamic computer simulation of concentrated hard sphere suspensions. I. Simulation technique and mean square displacement data
    • Cichocki, B. and Hinsen, K. (1990) Dynamic computer simulation of concentrated hard sphere suspensions. I. Simulation technique and mean square displacement data. Physica A166, 473-491.
    • (1990) Physica A , vol.166 , pp. 473-491
    • Cichocki, B.1    Hinsen, K.2
  • 69
    • 0028557777 scopus 로고
    • Molecular and Brownian dynamics simulations of selfdiffusion in inverse power fluids
    • Heyes, D. M. and Branka, A. C. (1994) Molecular and Brownian dynamics simulations of selfdiffusion in inverse power fluids. Phys. Chem. Liq. 28, 95-115.
    • (1994) Phys. Chem. Liq , vol.28 , pp. 95-115
    • Heyes, D.M.1    Branka, A.C.2
  • 70
    • 0031714012 scopus 로고    scopus 로고
    • Brownian dynamics simulation of protein-protein diffusional encounter
    • Gabdoulline, R. R. and Wade, R. C. (1998) Brownian dynamics simulation of protein-protein diffusional encounter. Methods 14, 329-341.
    • (1998) Methods , vol.14 , pp. 329-341
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 71
    • 0036536969 scopus 로고    scopus 로고
    • Modeling supramolecular assemblages
    • Elcock, A. H. (2002) Modeling supramolecular assemblages. Curr. Opin. Struct. Biol. 12, 154-160.
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 154-160
    • Elcock, A.H.1
  • 73
    • 1642464809 scopus 로고    scopus 로고
    • Poisson-Boltzmann methods for biomolecular electrostatics
    • Baker, N. A. (2004) Poisson-Boltzmann methods for biomolecular electrostatics. Methods Enzymol. 383, 94-118.
    • (2004) Methods Enzymol , vol.383 , pp. 94-118
    • Baker, N.A.1
  • 74
    • 0029310846 scopus 로고
    • Numerical simulations of the effect of hydrodynamic interactions on diffusivities of integral membrane proteins
    • Dodd, T. L., Hammer, D. A., Sangani, A. S., and Koch, D. L. (1995) Numerical simulations of the effect of hydrodynamic interactions on diffusivities of integral membrane proteins. J. Fluid Mech. 293, 147-180.
    • (1995) J. Fluid Mech , vol.293 , pp. 147-180
    • Dodd, T.L.1    Hammer, D.A.2    Sangani, A.S.3    Koch, D.L.4
  • 76
    • 0033030953 scopus 로고    scopus 로고
    • Toward a realistic theory of the interaction of membrane inclusions
    • Marcelja, S. (1999) Toward a realistic theory of the interaction of membrane inclusions. Biophys. J. 76, 593-594.
    • (1999) Biophys. J , vol.76 , pp. 593-594
    • Marcelja, S.1
  • 77
    • 0034172777 scopus 로고    scopus 로고
    • Effect of protein shape on multibody interactions between membrane inclusions
    • Kim, K. S., Neu, J., and Oster, G. (2000) Effect of protein shape on multibody interactions between membrane inclusions. Phys. Rev. E 61, 4281-4285.
    • (2000) Phys. Rev. E , vol.61 , pp. 4281-4285
    • Kim, K.S.1    Neu, J.2    Oster, G.3
  • 78
    • 0034950310 scopus 로고    scopus 로고
    • Lipid-mediated interactions between intrinsic membrane proteins: Dependence on protein size and lipid composition
    • Lagüe, P., Zuckermann, M. J., and Roux, B. (2001) Lipid-mediated interactions between intrinsic membrane proteins: Dependence on protein size and lipid composition. Biophys. J. 81, 276-284.
    • (2001) Biophys. J , vol.81 , pp. 276-284
    • Lagüe, P.1    Zuckermann, M.J.2    Roux, B.3
  • 79
    • 0142211230 scopus 로고    scopus 로고
    • Interaction between two cylindrical inclusions in a symmetric lipid bilayer
    • Bohinc, K., Kralj-Iglic, V., and May, S. (2003) Interaction between two cylindrical inclusions in a symmetric lipid bilayer. J. Chem. Phys. 119, 7435-7444.
    • (2003) J. Chem. Phys , vol.119 , pp. 7435-7444
    • Bohinc, K.1    Kralj-Iglic, V.2    May, S.3
  • 80
    • 0042344866 scopus 로고    scopus 로고
    • Lateral heterogeneity of photosystems in thylakoid membranes studied by Brownian dynamics simulations
    • Borodich, A., Rojdestvenski, L., and Cottam, M. (2003) Lateral heterogeneity of photosystems in thylakoid membranes studied by Brownian dynamics simulations. Biophys. J. 85, 774-789.
    • (2003) Biophys. J , vol.85 , pp. 774-789
    • Borodich, A.1    Rojdestvenski, L.2    Cottam, M.3
  • 81
    • 0030953956 scopus 로고    scopus 로고
    • Single-particle tracking: The distribution of diffusion coefficients
    • Saxton, M. J. (1997) Single-particle tracking: The distribution of diffusion coefficients. Biophys. J. 72, 1744-1753.
    • (1997) Biophys. J , vol.72 , pp. 1744-1753
    • Saxton, M.J.1
  • 82
    • 0035691159 scopus 로고    scopus 로고
    • Software for uniform random number generation: Distinguishing the good and the bad
    • Peters, B. A, Smith, J. S, Medeiros, D. J, and Rohrer, M. W, eds, Association for Computing Machinery, New York
    • L'Ecuyer, P. (2001) Software for uniform random number generation: distinguishing the good and the bad. Proceedings of the 2001 Winter Simulation Conference (Peters, B. A., Smith, J. S., Medeiros, D. J., and Rohrer, M. W., eds.) Association for Computing Machinery, New York, Vol. 1, pp. 95-105.
    • (2001) Proceedings of the 2001 Winter Simulation Conference , vol.1 , pp. 95-105
    • L'Ecuyer, P.1
  • 84
    • 0002773602 scopus 로고
    • Random numbers fall mainly in the planes
    • Marsaglia, G. (1968) Random numbers fall mainly in the planes. Proc. Natl. Acad. Sci USA 61, 25-28.
    • (1968) Proc. Natl. Acad. Sci USA , vol.61 , pp. 25-28
    • Marsaglia, G.1
  • 85
    • 0001352740 scopus 로고    scopus 로고
    • Effective boundary extrapolation length to account for finite-size effects in the percolation crossing function
    • Ziff, R. M. (1996) Effective boundary extrapolation length to account for finite-size effects in the percolation crossing function. Phys. Rev. E. 54, 2547-2554.
    • (1996) Phys. Rev. E , vol.54 , pp. 2547-2554
    • Ziff, R.M.1
  • 86
    • 10044277008 scopus 로고    scopus 로고
    • On the accuracy of statistical distributions in Microsoft Excel 2003
    • Knüsel, L. (2005) On the accuracy of statistical distributions in Microsoft Excel 2003. Comput. Statist. Data Anal. 48, 445-449.
    • (2005) Comput. Statist. Data Anal , vol.48 , pp. 445-449
    • Knüsel, L.1
  • 87
    • 19044363551 scopus 로고    scopus 로고
    • On the accuracy of statistical procedures in Microsoft Excel
    • McCullough, B. D. and Wilson, B. (2005) On the accuracy of statistical procedures in Microsoft Excel. Comput. Statist. Data Anal. 49, 1244-1252.
    • (2005) Comput. Statist. Data Anal , vol.49 , pp. 1244-1252
    • McCullough, B.D.1    Wilson, B.2
  • 89
    • 0030502105 scopus 로고    scopus 로고
    • Tests of random number generators using Ising model simulations
    • Coddington, P. D. (1996) Tests of random number generators using Ising model simulations. Int. J. Mod. Phys. C 7, 295-303.
    • (1996) Int. J. Mod. Phys. C , vol.7 , pp. 295-303
    • Coddington, P.D.1
  • 90
    • 0001224853 scopus 로고
    • Portable random number generators
    • Press, W. H. and Teukolsky, S. A. (1992) Portable random number generators. Comput. Phys. 6, 522-524.
    • (1992) Comput. Phys , vol.6 , pp. 522-524
    • Press, W.H.1    Teukolsky, S.A.2
  • 93
    • 0000948269 scopus 로고    scopus 로고
    • Four-tap shift-register-sequence random-number generators
    • Ziff, R. M. (1998) Four-tap shift-register-sequence random-number generators. Comput. Phys. 12, 385-392.
    • (1998) Comput. Phys , vol.12 , pp. 385-392
    • Ziff, R.M.1
  • 94
    • 0031599142 scopus 로고    scopus 로고
    • Mersenne twister: A 623-dimensionally equidistributed uniform pseudo-random number generator
    • Available in various languages at
    • Matsumoto, M. and Nishimura, T. (1998) Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Trans. Modeling Comput. Simul. 8, 3-30. Available in various languages at www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/eindex.html.
    • (1998) ACM Trans. Modeling Comput. Simul , vol.8 , pp. 3-30
    • Matsumoto, M.1    Nishimura, T.2
  • 95
    • 0000407060 scopus 로고
    • Some portable very-long-period random number generators
    • Marsaglia, G. and Zaman, A. (1994) Some portable very-long-period random number generators. Comput. Phys. 8, 117-121.
    • (1994) Comput. Phys , vol.8 , pp. 117-121
    • Marsaglia, G.1    Zaman, A.2
  • 96
    • 0031144701 scopus 로고    scopus 로고
    • Acceleration of RANLUX
    • Has a Fortran version
    • Hamilton, K. G. and James, F. (1997) Acceleration of RANLUX. Comput. Phys. Comm. 101, 241-248. Has a Fortran version.
    • (1997) Comput. Phys. Comm , vol.101 , pp. 241-248
    • Hamilton, K.G.1    James, F.2
  • 97
    • 0024090481 scopus 로고
    • Random number generators-good ones are hard to find
    • Park, S. K. and Miller, K. W. (1988) Random number generators-good ones are hard to find. Commun. ACM 31, 1192-1201.
    • (1988) Commun. ACM , vol.31 , pp. 1192-1201
    • Park, S.K.1    Miller, K.W.2
  • 100
    • 0038763414 scopus 로고
    • Mission impossible: Find a random pseudorandom number generator
    • Vattulainen, I. and Ala-Nissila, T. (1995) Mission impossible: find a random pseudorandom number generator. Comput. Phys. 9, 500-504.
    • (1995) Comput. Phys , vol.9 , pp. 500-504
    • Vattulainen, I.1    Ala-Nissila, T.2
  • 101
    • 0000270728 scopus 로고    scopus 로고
    • Good random number generators are (not so) easy to find
    • Hellekalek, P. (1998) Good random number generators are (not so) easy to find. Math. Comput. Simulation 46, 485-505.
    • (1998) Math. Comput. Simulation , vol.46 , pp. 485-505
    • Hellekalek, P.1
  • 103
    • 36549020354 scopus 로고    scopus 로고
    • Random number generation
    • Henderson, S. G. and Nelson, B. L, eds, Elsevier, Amsterdam, pp
    • L'Ecuyer, P. (2006) Random number generation, in Simulation (Henderson, S. G. and Nelson, B. L., eds.), Elsevier, Amsterdam, pp. 55-81.
    • (2006) Simulation , pp. 55-81
    • L'Ecuyer, P.1
  • 104
    • 36549040252 scopus 로고    scopus 로고
    • Rukhin, A., Soto, J., Nechvatal, J., et al. (2001) A statistical test suite for random and pseudorandom number generators for cryptographic applications. National Institute of Standards and Technology (NIST) Special Publication 800-22 (with revisions May 15, 2001). Available at csrc.nist.gov/publications/nistpubs/ along with Unix and PC forms of the NIST Statistical Test Suite.
    • Rukhin, A., Soto, J., Nechvatal, J., et al. (2001) A statistical test suite for random and pseudorandom number generators for cryptographic applications. National Institute of Standards and Technology (NIST) Special Publication 800-22 (with revisions May 15, 2001). Available at csrc.nist.gov/publications/nistpubs/ along with Unix and PC forms of the NIST Statistical Test Suite.
  • 105
    • 0001290917 scopus 로고    scopus 로고
    • SPRNG: A scalable library for pseudorandom number generation
    • Mascagni, M. and Srinivasan, A. (2000) SPRNG: a scalable library for pseudorandom number generation. ACM Trans. Math. Software 26, 436-461.
    • (2000) ACM Trans. Math. Software , vol.26 , pp. 436-461
    • Mascagni, M.1    Srinivasan, A.2
  • 106
    • 0001359130 scopus 로고    scopus 로고
    • Framework for testing random numbers in parallel calculations
    • Vattulainen, I. (1999) Framework for testing random numbers in parallel calculations. Phys. Rev. E 59, 7200-7204.
    • (1999) Phys. Rev. E , vol.59 , pp. 7200-7204
    • Vattulainen, I.1
  • 107
    • 11944269419 scopus 로고
    • Monte Carlo simulations: Hidden errors from good random number generators
    • Ferrenberg, A. M., Landau, D. P., and Wong, Y. J. (1992) Monte Carlo simulations: Hidden errors from good random number generators. Phys. Rev. Lett. 69, 3382-3384.
    • (1992) Phys. Rev. Lett , vol.69 , pp. 3382-3384
    • Ferrenberg, A.M.1    Landau, D.P.2    Wong, Y.J.3
  • 108
    • 0347476179 scopus 로고
    • Errors in Monte Carlo simulations using shift register random number generators
    • Schmid, F. and Wilding, N. B. (1995) Errors in Monte Carlo simulations using shift register random number generators. Int. J. Mod. Phys. C6, 781-787.
    • (1995) Int. J. Mod. Phys , vol.C6 , pp. 781-787
    • Schmid, F.1    Wilding, N.B.2
  • 109
    • 0001668857 scopus 로고
    • Pseudorandom number generator for massively parallel molecular-dynamics simulations
    • Holian, B. L., Perc;us, O. E., Warnock, T. T., and Whitlock, P. A. (1994) Pseudorandom number generator for massively parallel molecular-dynamics simulations. Phys. Rev. E 50, 1607-1615.
    • (1994) Phys. Rev. E , vol.50 , pp. 1607-1615
    • Holian, B.L.1    Perc2    us, O.E.3    Warnock, T.T.4    Whitlock, P.A.5
  • 110
    • 0001153533 scopus 로고    scopus 로고
    • Efficient Monte Carlo simulations using a shuffled nested Weyl sequence random number generator
    • Tretiakov, K. V. and Wojciechowski, K. W. (1999) Efficient Monte Carlo simulations using a shuffled nested Weyl sequence random number generator. Phys. Rev. E60, 7626-7628.
    • (1999) Phys. Rev. E , vol.60 , pp. 7626-7628
    • Tretiakov, K.V.1    Wojciechowski, K.W.2
  • 111
    • 0002280823 scopus 로고
    • On correlations in good random number generators
    • Grassberger, P. (1993) On correlations in good random number generators. Phys. Lett. A 181, 43-46.
    • (1993) Phys. Lett. A , vol.181 , pp. 43-46
    • Grassberger, P.1
  • 112
    • 0000259451 scopus 로고    scopus 로고
    • Hurst's rescaled range statistical analysis for pseudorandom number generators used in physical simulations
    • Gammel, B. M. (1998) Hurst's rescaled range statistical analysis for pseudorandom number generators used in physical simulations. Phys. Rev. E58, 2586-2597.
    • (1998) Phys. Rev. E , vol.58 , pp. 2586-2597
    • Gammel, B.M.1
  • 113
    • 0031177234 scopus 로고    scopus 로고
    • Simulation of a directed random-walk model. The effect of pseudo-random-number correlations
    • Shchur, L. N., Heringa, J. R., and Blöte, H. W. J. (1997) Simulation of a directed random-walk model. The effect of pseudo-random-number correlations. Physica A 241, 579-592.
    • (1997) Physica A , vol.241 , pp. 579-592
    • Shchur, L.N.1    Heringa, J.R.2    Blöte, H.W.J.3
  • 114
    • 0000210190 scopus 로고
    • Operational conditions for random-number generation
    • Compagner, A. (1995) Operational conditions for random-number generation. Phys. Rev. E52, 5634-5645.
    • (1995) Phys. Rev. E , vol.52 , pp. 5634-5645
    • Compagner, A.1
  • 115
    • 0033184874 scopus 로고    scopus 로고
    • On the quality of random number generators with taps
    • Shchur, L. N. (1999) On the quality of random number generators with taps. Comput. Phys. Comm. 121-122, 83-85.
    • (1999) Comput. Phys. Comm , vol.121-122 , pp. 83-85
    • Shchur, L.N.1
  • 116
    • 0346536032 scopus 로고
    • Long range correlations in random number generators and their influence on Monte Carlo simulations
    • Filk, T., Marcu, M., and Fredenhagen, K. (1985) Long range correlations in random number generators and their influence on Monte Carlo simulations. Phys. Lett. B 165, 125-130.
    • (1985) Phys. Lett. B , vol.165 , pp. 125-130
    • Filk, T.1    Marcu, M.2    Fredenhagen, K.3
  • 118
    • 0004007880 scopus 로고
    • Wiley, New York. Has Fortran listings
    • Ripley, B. D. (1987) Stochastic Simulation. Wiley, New York. Has Fortran listings.
    • (1987) Stochastic Simulation
    • Ripley, B.D.1
  • 122
    • 0040833010 scopus 로고    scopus 로고
    • The ziggurat method for generating random variables
    • Has a C listing
    • Marsaglia, G. and Tsang, W. W. (2000) The ziggurat method for generating random variables. J. Stat. Software 5, Issue 8 (www.jstatsoft.org). Has a C listing.
    • (2000) J. Stat. Software , vol.5 , Issue.8
    • Marsaglia, G.1    Tsang, W.W.2
  • 126
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 1, 306-317.
    • (2001) J. Mol. Model , vol.1 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 127
    • 0029230950 scopus 로고
    • A new approach to an old algorithm for the simulation of Ising-like systems
    • Novotny, M. A. (1995) A new approach to an old algorithm for the simulation of Ising-like systems. Comput. Phys. 9, 46-52.
    • (1995) Comput. Phys , vol.9 , pp. 46-52
    • Novotny, M.A.1
  • 128
    • 0002296942 scopus 로고
    • New algorithm for Monte Carlo simulation of Ising spin systems
    • Bortz, A. B., Kalos, M. H., and Lebowitz, J. L. (1975) New algorithm for Monte Carlo simulation of Ising spin systems. J. Comput. Phys. 17, 10-18.
    • (1975) J. Comput. Phys , vol.17 , pp. 10-18
    • Bortz, A.B.1    Kalos, M.H.2    Lebowitz, J.L.3
  • 129
    • 0001256492 scopus 로고    scopus 로고
    • A kinetic Monte Carlo method for the atomic-scale simulation of chemical vapor deposition: Application to diamond
    • Battaile, C. C., Srolovitz, D. J., and Butler, J. E. (1997) A kinetic Monte Carlo method for the atomic-scale simulation of chemical vapor deposition: Application to diamond. J. Appl. Phys. 82, 6293-6300.
    • (1997) J. Appl. Phys , vol.82 , pp. 6293-6300
    • Battaile, C.C.1    Srolovitz, D.J.2    Butler, J.E.3
  • 130
    • 0000239610 scopus 로고
    • Random sequential adsorption of parallel squares
    • Brosilow, B. J., Ziff, R. M., and Vigil, R. D. (1991) Random sequential adsorption of parallel squares. Phys. Rev. E 43, 631-638.
    • (1991) Phys. Rev. E , vol.43 , pp. 631-638
    • Brosilow, B.J.1    Ziff, R.M.2    Vigil, R.D.3
  • 131
    • 0141513340 scopus 로고
    • Computer simulation of diffusion-controlled reactions in dispersions of spherical sinks
    • Zheng, L. H. and Chiew, Y. C. (1989) Computer simulation of diffusion-controlled reactions in dispersions of spherical sinks. J. Chem. Phys. 90, 322-327.
    • (1989) J. Chem. Phys , vol.90 , pp. 322-327
    • Zheng, L.H.1    Chiew, Y.C.2
  • 132
    • 0343417007 scopus 로고
    • Efficient random walk algorithm for computing conductivity in continuum percolation systems
    • Tobochnik, J. (1990) Efficient random walk algorithm for computing conductivity in continuum percolation systems. Comput. Phys. 4, 181-184.
    • (1990) Comput. Phys , vol.4 , pp. 181-184
    • Tobochnik, J.1
  • 133
    • 0001554978 scopus 로고
    • Efficient simulation technique to compute effective properties of heterogeneous media
    • Torquato, S. and Kim, I. C. (1989) Efficient simulation technique to compute effective properties of heterogeneous media. Appl. Phys. Lett. 55, 1847-1849.
    • (1989) Appl. Phys. Lett , vol.55 , pp. 1847-1849
    • Torquato, S.1    Kim, I.C.2
  • 134
    • 0001292416 scopus 로고    scopus 로고
    • Effective conductivity, dielectric constant, and diffusion coefficient of digitized composite media via first-passage-time equations
    • Torquato, S., Kim, I. C., and Cule, D. (1999) Effective conductivity, dielectric constant, and diffusion coefficient of digitized composite media via first-passage-time equations. J. Appl. Phys. 85, 1560-1571.
    • (1999) J. Appl. Phys , vol.85 , pp. 1560-1571
    • Torquato, S.1    Kim, I.C.2    Cule, D.3
  • 135
    • 0035842841 scopus 로고    scopus 로고
    • The simulation-tabulation method for classical diffusion Monte Carlo
    • Hwang, C. O., Given, J. A., and Mascagni, M. (2001) The simulation-tabulation method for classical diffusion Monte Carlo. J. Comput. Phys. 114, 925-946.
    • (2001) J. Comput. Phys , vol.114 , pp. 925-946
    • Hwang, C.O.1    Given, J.A.2    Mascagni, M.3
  • 136
    • 18244404300 scopus 로고    scopus 로고
    • Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics
    • van Zon, J. S. and ten Wolde, P. R. (2005) Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics. Phys. Rev. Lett. 94, 128103.
    • (2005) Phys. Rev. Lett , vol.94 , pp. 128103
    • van Zon, J.S.1    ten Wolde, P.R.2
  • 137
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D. T. (1977) Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361.
    • (1977) J. Phys. Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 139
    • 30444444426 scopus 로고    scopus 로고
    • Special issue: Modern tools for macromolecular simulation and modeling
    • Brooks, C. L. (2005) Special issue: Modern tools for macromolecular simulation and modeling. J. Comput. Chem. 26, 1667.
    • (2005) J. Comput. Chem , vol.26 , pp. 1667
    • Brooks, C.L.1
  • 140
    • 14844321288 scopus 로고    scopus 로고
    • Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico
    • Takahashi, K., Arjunan, S. N. V., and Tomita, M. (2005) Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico. FEBS Lett. 579, 1783-1788.
    • (2005) FEBS Lett , vol.579 , pp. 1783-1788
    • Takahashi, K.1    Arjunan, S.N.V.2    Tomita, M.3
  • 141
    • 32544450348 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy simulation of photophysical phenomena and molecular interactions: A molecular dynamics/Monte Carlo approach
    • Dix, J. A., Horn, E. F. Y., and Verkman, A. S. (2006) Fluorescence correlation spectroscopy simulation of photophysical phenomena and molecular interactions: A molecular dynamics/Monte Carlo approach. J. Phys. Chem. B 110, 1896-1906.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 1896-1906
    • Dix, J.A.1    Horn, E.F.Y.2    Verkman, A.S.3
  • 142
    • 22244450050 scopus 로고    scopus 로고
    • Evidence for ectopic neurotransmission at a neuronal synapse
    • Coggan, J. S., Bartol, T. M., Esquenazi, E., et al. (2005) Evidence for ectopic neurotransmission at a neuronal synapse. Science 309, 446-451.
    • (2005) Science , vol.309 , pp. 446-451
    • Coggan, J.S.1    Bartol, T.M.2    Esquenazi, E.3
  • 143
    • 0004232671 scopus 로고
    • 2nd ed, Princeton University Press, Princeton, NJ
    • Berg, H. C. (1993) Random Walks in Biology, 2nd ed., Princeton University Press, Princeton, NJ.
    • (1993) Random Walks in Biology
    • Berg, H.C.1
  • 145
    • 36549083851 scopus 로고    scopus 로고
    • Hughes, B. D. (1995, 1996) Random Walks and Random Environments, 2 vols. Oxford University Press, Oxford.
    • Hughes, B. D. (1995, 1996) Random Walks and Random Environments, 2 vols. Oxford University Press, Oxford.
  • 152
    • 0004112038 scopus 로고
    • Addison-Wesley, Reading, MA
    • Sedgewick, R. (1988) Algorithms. Addison-Wesley, Reading, MA.
    • (1988) Algorithms
    • Sedgewick, R.1
  • 153
    • 0004236205 scopus 로고    scopus 로고
    • Springer TELOS-The Electronic Library of Science, Santa Clara, CA
    • Skiena, S. S. (1998) The Algorithm Design Manual. Springer TELOS-The Electronic Library of Science, Santa Clara, CA.
    • (1998) The Algorithm Design Manual
    • Skiena, S.S.1
  • 155
    • 36549035942 scopus 로고
    • Graphics Gems. Academic Press, Boston
    • in the series, with various editors
    • Glassner, A. S. (1990) Graphics Gems. Academic Press, Boston. There are now 5 volumes in the series, with various editors.
    • (1990) There are , vol.5
    • Glassner, A.S.1
  • 156
    • 4344589066 scopus 로고    scopus 로고
    • Analytical approximation of the percolation threshold for overlapping ellipsoids of revolution
    • Yi, Y. -B. and Sastry, A. M. (2004) Analytical approximation of the percolation threshold for overlapping ellipsoids of revolution. Proc. R. Soc. Lond. A 460, 2353-2380.
    • (2004) Proc. R. Soc. Lond. A , vol.460 , pp. 2353-2380
    • Yi, Y.-B.1    Sastry, A.M.2
  • 157
    • 0345170107 scopus 로고    scopus 로고
    • Dependence of plastoquinol diffusion on the shape, size, and density of integral thylakoid proteins
    • Tremmel, I. G., Kirchhoff, H., Weis, E., and Farquhar, G. D. (2003) Dependence of plastoquinol diffusion on the shape, size, and density of integral thylakoid proteins. Biochim. Biophys. Acta 1607, 97-109.
    • (2003) Biochim. Biophys. Acta , vol.1607 , pp. 97-109
    • Tremmel, I.G.1    Kirchhoff, H.2    Weis, E.3    Farquhar, G.D.4
  • 158
    • 22144439716 scopus 로고    scopus 로고
    • The influence of protein-protein interactions on the organization of proteins within thylakoid membranes
    • Tremmel, I. G., Weis, E., and Farquhar, G. D. (2005) The influence of protein-protein interactions on the organization of proteins within thylakoid membranes. Biophys. J. 88, 2650-2660.
    • (2005) Biophys. J , vol.88 , pp. 2650-2660
    • Tremmel, I.G.1    Weis, E.2    Farquhar, G.D.3
  • 159
    • 0037418340 scopus 로고    scopus 로고
    • Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage
    • Elcock, A. H. (2003) Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage. Proc. Natl. Acad. Sci USA 100, 2340-2344.
    • (2003) Proc. Natl. Acad. Sci USA , vol.100 , pp. 2340-2344
    • Elcock, A.H.1
  • 160
  • 161
    • 0001229341 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of globular proteins from their atomic-level structure
    • Garcia de la Torre, J., Huertas, M. L., and Carrasco, B. (2000) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys. J. 78, 719-730.
    • (2000) Biophys. J , vol.78 , pp. 719-730
    • Garcia de la Torre, J.1    Huertas, M.L.2    Carrasco, B.3
  • 162
    • 5244275439 scopus 로고    scopus 로고
    • Stochastic dynamics simulations of macromolecular diffusion in a model of the cytoplasm of Escherichia coli
    • Bicout, D. J. and Field, M. J. (1996) Stochastic dynamics simulations of macromolecular diffusion in a model of the cytoplasm of Escherichia coli. J. Phys. Chem. 100, 2489-2497.
    • (1996) J. Phys. Chem , vol.100 , pp. 2489-2497
    • Bicout, D.J.1    Field, M.J.2
  • 163
    • 0025292782 scopus 로고
    • Brownian motion of inert tracer macromolecules in polymerized and spontaneously bundled mixtures of actin and filamin
    • Hou, L., Luby-Phelps, K., and Lanni, F. (1990) Brownian motion of inert tracer macromolecules in polymerized and spontaneously bundled mixtures of actin and filamin. J. Cell Biol. 110, 1645-1654.
    • (1990) J. Cell Biol , vol.110 , pp. 1645-1654
    • Hou, L.1    Luby-Phelps, K.2    Lanni, F.3
  • 164
    • 0025277334 scopus 로고
    • Tracer diffusion in F actin and Ficoll mixtures. Toward a model for cytoplasm
    • Hou, L., Lanni, F., and Luby-Phelps, K. (1990) Tracer diffusion in F actin and Ficoll mixtures. Toward a model for cytoplasm. Biophys. J. 58, 31-44.
    • (1990) Biophys. J , vol.58 , pp. 31-44
    • Hou, L.1    Lanni, F.2    Luby-Phelps, K.3
  • 165
    • 0001504102 scopus 로고
    • Random walks: Theory and selected applications
    • Eq. 2.156
    • Weiss, G. H. and Rubin, R. J. (1983) Random walks: Theory and selected applications. Adv. Chem. Phys. 52, 363-505, Eq. 2.156.
    • (1983) Adv. Chem. Phys , vol.52 , pp. 363-505
    • Weiss, G.H.1    Rubin, R.J.2
  • 166
    • 36549082656 scopus 로고    scopus 로고
    • Gradshteyn, I. S. and Ryzhik, I. M. (2000) Table of Integrals, Series, and Products, 6th ed., Academic Press, San Diego, p. 609, Eq. 4.632.2.
    • Gradshteyn, I. S. and Ryzhik, I. M. (2000) Table of Integrals, Series, and Products, 6th ed., Academic Press, San Diego, p. 609, Eq. 4.632.2.
  • 167
    • 36549019273 scopus 로고    scopus 로고
    • Abramowitz, M. and Stegun, I. A. (1972) Handbook of Mathematical Functions. U. S. Government Printing Office, Washington, DC, p. 255, Eq. 6.1.1.
    • Abramowitz, M. and Stegun, I. A. (1972) Handbook of Mathematical Functions. U. S. Government Printing Office, Washington, DC, p. 255, Eq. 6.1.1.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.