메뉴 건너뛰기




Volumn 5, Issue , 2011, Pages

Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; CYTOPLASM; CYTOSKELETON; DIFFUSION; ENVIRONMENT; KINETICS; METABOLISM; METHODOLOGY; MOVEMENT (PHYSIOLOGY); SIGNAL TRANSDUCTION; STATISTICS; SYSTEMS BIOLOGY;

EID: 79955815642     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-71     Document Type: Article
Times cited : (55)

References (60)
  • 1
    • 0033991590 scopus 로고    scopus 로고
    • Cytoarchitecture and Physical Properties of Cytoplasm: Volume, Viscosity, Diffusion, Intracellular Surface Area
    • Luby-Phelps K. Cytoarchitecture and Physical Properties of Cytoplasm: Volume, Viscosity, Diffusion, Intracellular Surface Area. Int Rev Cytol 2000, 192:189-221.
    • (2000) Int Rev Cytol , vol.192 , pp. 189-221
    • Luby-Phelps, K.1
  • 2
    • 0018594103 scopus 로고
    • The 6-Phosphogluconate Dehydrogenase Reaction in Escherichia coli
    • De Silva A, Fraenkel D. The 6-Phosphogluconate Dehydrogenase Reaction in Escherichia coli. Journal of Biological Chemistry 1979, 254(20):10237-10242.
    • (1979) Journal of Biological Chemistry , vol.254 , Issue.20 , pp. 10237-10242
    • De Silva, A.1    Fraenkel, D.2
  • 3
    • 0035253217 scopus 로고    scopus 로고
    • Macromolecular crowding: an important but neglected aspect of the intracellular environment
    • 10.1016/S0959-440X(00)00172-X, 11179900
    • Ellis R. Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr Opin Struct Biol 2001, 11:114-119. 10.1016/S0959-440X(00)00172-X, 11179900.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 114-119
    • Ellis, R.1
  • 4
    • 0035815743 scopus 로고    scopus 로고
    • The Inuence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media
    • Minton AP. The Inuence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media. J Bio Chem 2001, 276(14):10577-10580.
    • (2001) J Bio Chem , vol.276 , Issue.14 , pp. 10577-10580
    • Minton, A.P.1
  • 5
    • 33746813983 scopus 로고    scopus 로고
    • How can biochemical reactions within cells differ from those in test tubes?
    • 10.1242/jcs.03063, 16825427
    • Minton A. How can biochemical reactions within cells differ from those in test tubes?. Journal of Cell Science 2006, 119(14):2863. 10.1242/jcs.03063, 16825427.
    • (2006) Journal of Cell Science , vol.119 , Issue.14 , pp. 2863
    • Minton, A.1
  • 6
    • 68949103682 scopus 로고    scopus 로고
    • Stochastic Simulation of Signal Transduction: Impact of the Cellular Architecture on Diffusion
    • 10.1016/j.bpj.2009.03.049, 2712048, 19527672
    • Klann M, Lapin A, Reuss M. Stochastic Simulation of Signal Transduction: Impact of the Cellular Architecture on Diffusion. Biophys J 2009, 96(12):5122-5129. 10.1016/j.bpj.2009.03.049, 2712048, 19527672.
    • (2009) Biophys J , vol.96 , Issue.12 , pp. 5122-5129
    • Klann, M.1    Lapin, A.2    Reuss, M.3
  • 7
    • 0021098487 scopus 로고
    • Diffusion-Limited Reaction Rate Theory for Two-Dimensional Systems
    • Torney D, McConnel H. Diffusion-Limited Reaction Rate Theory for Two-Dimensional Systems. Proc R Soc Lond A 1983, 387(1792):147-170.
    • (1983) Proc R Soc Lond A , vol.387 , Issue.1792 , pp. 147-170
    • Torney, D.1    McConnel, H.2
  • 9
    • 14844331313 scopus 로고    scopus 로고
    • Anomalous Subdiffusion Is a Measure for Cytoplasmic Crowding in Living Cells
    • 10.1529/biophysj.104.044263, 1304817, 15339818
    • Weiss M, Elsner M, Kartberg F, Nilsson T. Anomalous Subdiffusion Is a Measure for Cytoplasmic Crowding in Living Cells. Biophys J 2004, 87:3518-3524. 10.1529/biophysj.104.044263, 1304817, 15339818.
    • (2004) Biophys J , vol.87 , pp. 3518-3524
    • Weiss, M.1    Elsner, M.2    Kartberg, F.3    Nilsson, T.4
  • 10
    • 2442543316 scopus 로고    scopus 로고
    • Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws
    • 10.1016/j.pbiomolbio.2004.01.012, 15142746
    • Schnell S, Turner T. Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws. Progress in biophysics and molecular biology 2004, 85(2-3):235-260. 10.1016/j.pbiomolbio.2004.01.012, 15142746.
    • (2004) Progress in biophysics and molecular biology , vol.85 , Issue.2-3 , pp. 235-260
    • Schnell, S.1    Turner, T.2
  • 11
    • 33748977501 scopus 로고    scopus 로고
    • A systematic investigation of the rate laws valid in intracellular environments
    • 10.1016/j.bpc.2006.04.019, 16781049
    • Grima R, Schnell S. A systematic investigation of the rate laws valid in intracellular environments. Biophys chem 2006, 124:1-10. 10.1016/j.bpc.2006.04.019, 16781049.
    • (2006) Biophys chem , vol.124 , pp. 1-10
    • Grima, R.1    Schnell, S.2
  • 12
    • 68949136901 scopus 로고    scopus 로고
    • Analysis of Reaction-Diffusion Systems with Anomalous Subdiffusion
    • 10.1016/j.bpj.2009.05.014, 2711345, 19619457
    • Haugh J. Analysis of Reaction-Diffusion Systems with Anomalous Subdiffusion. Biophys J 2009, 97(2):435-442. 10.1016/j.bpj.2009.05.014, 2711345, 19619457.
    • (2009) Biophys J , vol.97 , Issue.2 , pp. 435-442
    • Haugh, J.1
  • 14
    • 0037044862 scopus 로고    scopus 로고
    • Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography
    • 10.1126/science.1076184, 12424373
    • Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W. Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography. Science 2002, 298:1209-1213. 10.1126/science.1076184, 12424373.
    • (2002) Science , vol.298 , pp. 1209-1213
    • Medalia, O.1    Weber, I.2    Frangakis, A.S.3    Nicastro, D.4    Gerisch, G.5    Baumeister, W.6
  • 15
    • 68949119721 scopus 로고    scopus 로고
    • Diffusion in Cytoplasm: Effects of Excluded Volume Due to Internal Membranes and Cytoskeletal Structures
    • 10.1016/j.bpj.2009.05.036, 2718152, 19651034
    • Novak I, P K, Slepchenko B. Diffusion in Cytoplasm: Effects of Excluded Volume Due to Internal Membranes and Cytoskeletal Structures. Biophys J 2009, 97(3):758-767. 10.1016/j.bpj.2009.05.036, 2718152, 19651034.
    • (2009) Biophys J , vol.97 , Issue.3 , pp. 758-767
    • Novak, I.1    P, K.2    Slepchenko, B.3
  • 16
    • 0034114310 scopus 로고    scopus 로고
    • Effective Diffusivities of Point-Like Molecules in Isotropic Porous Media by Monte Carlo Simulation
    • Trinh S, Arce P, Locke BR. Effective Diffusivities of Point-Like Molecules in Isotropic Porous Media by Monte Carlo Simulation. Transport in Porous Media 2000, 38:241-259.
    • (2000) Transport in Porous Media , vol.38 , pp. 241-259
    • Trinh, S.1    Arce, P.2    Locke, B.R.3
  • 17
    • 0001516161 scopus 로고
    • Computer simulation studies of anomalous diffusion in gels: Structural properties and probe-size dependence
    • Netz P, Dorfmüller T. Computer simulation studies of anomalous diffusion in gels: Structural properties and probe-size dependence. J Chem Phys 1995, 103(20):9074-9082.
    • (1995) J Chem Phys , vol.103 , Issue.20 , pp. 9074-9082
    • Netz, P.1    Dorfmüller, T.2
  • 18
    • 42749103490 scopus 로고    scopus 로고
    • Diffusion of hard sphere fluids in disordered media: A molecular dynamics simulation study
    • Chang R, Jagannathan K, Yethiraj A. Diffusion of hard sphere fluids in disordered media: A molecular dynamics simulation study. PhysRev E 2004, 69:051101.
    • (2004) PhysRev E , vol.69 , pp. 051101
    • Chang, R.1    Jagannathan, K.2    Yethiraj, A.3
  • 19
    • 58149199635 scopus 로고    scopus 로고
    • The 'fuzzy' interactome
    • 10.1016/j.tibs.2008.10.007, 19028099
    • Welch G. The 'fuzzy' interactome. Trends in Biochemical Sciences 2009, 34:1-2. 10.1016/j.tibs.2008.10.007, 19028099.
    • (2009) Trends in Biochemical Sciences , vol.34 , pp. 1-2
    • Welch, G.1
  • 20
    • 33846844797 scopus 로고    scopus 로고
    • A Biological Interpretation of Transient Anomalous Subdiffusion. I. Qualitative Model
    • 10.1529/biophysj.106.092619, 1783867, 17142285
    • Saxton M. A Biological Interpretation of Transient Anomalous Subdiffusion. I. Qualitative Model. Biophys J 2007, 92:1178-1191. 10.1529/biophysj.106.092619, 1783867, 17142285.
    • (2007) Biophys J , vol.92 , pp. 1178-1191
    • Saxton, M.1
  • 21
    • 0028304634 scopus 로고
    • Metabolic channeling versus free diffusion: transition-time analysis
    • 10.1016/0968-0004(94)90019-1, 8048159
    • Welch G, Easterby J. Metabolic channeling versus free diffusion: transition-time analysis. Trends in biochemical sciences 1994, 19(5):193-197. 10.1016/0968-0004(94)90019-1, 8048159.
    • (1994) Trends in biochemical sciences , vol.19 , Issue.5 , pp. 193-197
    • Welch, G.1    Easterby, J.2
  • 23
    • 0033991699 scopus 로고    scopus 로고
    • Macromolecular compartmentation and channeling
    • Ovadi J, Sreret P. Macromolecular compartmentation and channeling. International Review of Cytology 1999, 192:255-280.
    • (1999) International Review of Cytology , vol.192 , pp. 255-280
    • Ovadi, J.1    Sreret, P.2
  • 24
    • 0028913916 scopus 로고
    • Microcompartmentation, metabolic channelling and carbohydrate metabolism
    • 10.1016/1357-2725(94)00079-Q, 7767780
    • Al-Habori M. Microcompartmentation, metabolic channelling and carbohydrate metabolism. International Journal of Biochemistry and Cell Biology 1995, 27(2):123-132. 10.1016/1357-2725(94)00079-Q, 7767780.
    • (1995) International Journal of Biochemistry and Cell Biology , vol.27 , Issue.2 , pp. 123-132
    • Al-Habori, M.1
  • 25
    • 0021129923 scopus 로고
    • Interactions between glycolytic enzymes and components of the cytomatrix
    • Masters C. Interactions between glycolytic enzymes and components of the cytomatrix. Journal of Cell Biology 1984, 99:222-225.
    • (1984) Journal of Cell Biology , vol.99 , pp. 222-225
    • Masters, C.1
  • 26
    • 0023768225 scopus 로고
    • Old pathway-new concept: control of glycolysis by metabolite-modulated dynamic enzyme associations
    • 10.1016/0968-0004(88)90237-X, 3075372
    • Ovadi J. Old pathway-new concept: control of glycolysis by metabolite-modulated dynamic enzyme associations. Trends in biochemical sciences 1988, 13:486-450. 10.1016/0968-0004(88)90237-X, 3075372.
    • (1988) Trends in biochemical sciences , vol.13 , pp. 486-1450
    • Ovadi, J.1
  • 27
    • 34548049053 scopus 로고    scopus 로고
    • Mathematical modeling of intracellular signaling pathways
    • 10.1186/1471-2202-7-S1-S10, 1775040, 17118154
    • Klipp E, Liebermeister W. Mathematical modeling of intracellular signaling pathways. BMC neuroscience 2006, 7(Suppl 1):S10. 10.1186/1471-2202-7-S1-S10, 1775040, 17118154.
    • (2006) BMC neuroscience , vol.7 , Issue.SUPPL. 1
    • Klipp, E.1    Liebermeister, W.2
  • 28
    • 67650488974 scopus 로고    scopus 로고
    • Signaling dynamics of the KSR1 scaffold complex
    • 10.1073/pnas.0901590106, 2708738, 19541618
    • McKay M, Ritt D, Morrison D. Signaling dynamics of the KSR1 scaffold complex. PNAS 2009, 106(27):11022-11027. 10.1073/pnas.0901590106, 2708738, 19541618.
    • (2009) PNAS , vol.106 , Issue.27 , pp. 11022-11027
    • McKay, M.1    Ritt, D.2    Morrison, D.3
  • 29
    • 34548422439 scopus 로고    scopus 로고
    • Molecular Scaffolds Regulate Bidirectional Crosstalk Between Wnt and Classical Seven-Transmembrane Domain Receptor Signaling Pathways
    • Force T, Woulfe K, Koch W, Kerkela R. Molecular Scaffolds Regulate Bidirectional Crosstalk Between Wnt and Classical Seven-Transmembrane Domain Receptor Signaling Pathways. Science Signaling 2007, 2007(397).
    • (2007) Science Signaling , vol.2007 , Issue.397
    • Force, T.1    Woulfe, K.2    Koch, W.3    Kerkela, R.4
  • 30
    • 18844364205 scopus 로고    scopus 로고
    • Subcellular localization determines MAP kinase signal output
    • 10.1016/j.cub.2005.04.020, 15886107
    • Harding A, Tian T, Westbury E, Frische E, Hancock J. Subcellular localization determines MAP kinase signal output. Current Biology 2005, 15(9):869-873. 10.1016/j.cub.2005.04.020, 15886107.
    • (2005) Current Biology , vol.15 , Issue.9 , pp. 869-873
    • Harding, A.1    Tian, T.2    Westbury, E.3    Frische, E.4    Hancock, J.5
  • 31
    • 0034193240 scopus 로고    scopus 로고
    • The p65/RelA Subunit of NF-κB Interacts with Actin-Containing Structures
    • 10.1006/excr.2000.4830, 10772825
    • Are A, Galkin V, Pospelova T, Pinaev G. The p65/RelA Subunit of NF-κB Interacts with Actin-Containing Structures. Experimental Cell Research 2000, 256:533-544. 10.1006/excr.2000.4830, 10772825.
    • (2000) Experimental Cell Research , vol.256 , pp. 533-544
    • Are, A.1    Galkin, V.2    Pospelova, T.3    Pinaev, G.4
  • 32
    • 48649097820 scopus 로고    scopus 로고
    • Introducing Spatial Information into Predictive NF-κB Modelling - An Agent-Based Approach
    • 10.1371/journal.pone.0002367, 2391290, 18523553
    • Pogson M, Holcombe M, Smallwood R, Qwarnstrom E. Introducing Spatial Information into Predictive NF-κB Modelling - An Agent-Based Approach. PLoS ONE 2008, 3(6):e2367. 10.1371/journal.pone.0002367, 2391290, 18523553.
    • (2008) PLoS ONE , vol.3 , Issue.6
    • Pogson, M.1    Holcombe, M.2    Smallwood, R.3    Qwarnstrom, E.4
  • 33
    • 46449097700 scopus 로고    scopus 로고
    • Prediction of the pharmacokinetics of atorvastatin, cerivastatin, and indomethacin using kinetic models applied to isolated rat hepatocytes
    • 10.1124/dmd.107.019455, 18426955
    • Paine S, Parker A, Gardiner P, Webborn P, Riley R. Prediction of the pharmacokinetics of atorvastatin, cerivastatin, and indomethacin using kinetic models applied to isolated rat hepatocytes. Drug Metabolism and Disposition 2008, 36(7):1365-1374. 10.1124/dmd.107.019455, 18426955.
    • (2008) Drug Metabolism and Disposition , vol.36 , Issue.7 , pp. 1365-1374
    • Paine, S.1    Parker, A.2    Gardiner, P.3    Webborn, P.4    Riley, R.5
  • 34
    • 77951261774 scopus 로고    scopus 로고
    • Assessment of in silico models for fraction of unbound drug in human liver microsomes
    • Gao H, Steyn S, Chang G, Lin J. Assessment of in silico models for fraction of unbound drug in human liver microsomes. Expert Opinion on Drug Metabolism & Toxicology 2010, 2010(5):533-542.
    • (2010) Expert Opinion on Drug Metabolism & Toxicology , vol.2010 , Issue.5 , pp. 533-542
    • Gao, H.1    Steyn, S.2    Chang, G.3    Lin, J.4
  • 36
    • 0038608273 scopus 로고    scopus 로고
    • Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors
    • 10.1242/jeb.00298, 12756289
    • Kholodenko B. Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors. J Exp Biol 2003, 206(12):2073-2082. 10.1242/jeb.00298, 12756289.
    • (2003) J Exp Biol , vol.206 , Issue.12 , pp. 2073-2082
    • Kholodenko, B.1
  • 37
    • 33846042014 scopus 로고    scopus 로고
    • Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades
    • Markevich N, Tsyganov M, Hoek J, Kholodenko B. Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades. Mol Syst Biol 2006, 2(61).
    • (2006) Mol Syst Biol , vol.2 , Issue.61
    • Markevich, N.1    Tsyganov, M.2    Hoek, J.3    Kholodenko, B.4
  • 38
    • 0033991590 scopus 로고    scopus 로고
    • Cytoarchitecture and Physical Properties of Cytoplasm: Volume, Viscosity, Diffusion, Intracellular Surface Area
    • Luby-Phelps K. Cytoarchitecture and Physical Properties of Cytoplasm: Volume, Viscosity, Diffusion, Intracellular Surface Area. Int Rev Cytol 2000, 192:189-221.
    • (2000) Int Rev Cytol , vol.192 , pp. 189-221
    • Luby-Phelps, K.1
  • 39
    • 79959721346 scopus 로고    scopus 로고
    • Effects of macromolecular crowding on intracellular diffusion from a single particle perspective
    • 10.1007/s12551-010-0029-0, 2957576, 21088688
    • Hall D, Hoshino M. Effects of macromolecular crowding on intracellular diffusion from a single particle perspective. Biophys Rev 2010, 2:39-53. 10.1007/s12551-010-0029-0, 2957576, 21088688.
    • (2010) Biophys Rev , vol.2 , pp. 39-53
    • Hall, D.1    Hoshino, M.2
  • 40
    • 0021905844 scopus 로고
    • Diffusion-controlled macromolecular interactions
    • 10.1146/annurev.bb.14.060185.001023, 3890878
    • Berg O, von Hippel P. Diffusion-controlled macromolecular interactions. Annual Review of Biophysics and Biophysical Chemistry 1985, 14:131-158. 10.1146/annurev.bb.14.060185.001023, 3890878.
    • (1985) Annual Review of Biophysics and Biophysical Chemistry , vol.14 , pp. 131-158
    • Berg, O.1    von Hippel, P.2
  • 41
    • 0000267310 scopus 로고
    • Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen
    • Smoluchowski M. Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen. Z phys Chem 1917, 92:129-168.
    • (1917) Z phys Chem , vol.92 , pp. 129-168
    • Smoluchowski, M.1
  • 43
    • 0017030517 scopus 로고
    • A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
    • Gillespie D. A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. J Comp Phys 1976, 22:403-434.
    • (1976) J Comp Phys , vol.22 , pp. 403-434
    • Gillespie, D.1
  • 44
    • 77952050895 scopus 로고    scopus 로고
    • Channeling by proximity: the catalytic advantages of active site colocalization using Brownian dynamics
    • 10.1021/jz1002007, 2865391, 20454551
    • Bauler P, Huber G, Leyh T, McCammon J. Channeling by proximity: the catalytic advantages of active site colocalization using Brownian dynamics. The Journal of Physical Chemistry Letters 2010, 1(9):1332-1335. 10.1021/jz1002007, 2865391, 20454551.
    • (2010) The Journal of Physical Chemistry Letters , vol.1 , Issue.9 , pp. 1332-1335
    • Bauler, P.1    Huber, G.2    Leyh, T.3    McCammon, J.4
  • 45
    • 0032167971 scopus 로고    scopus 로고
    • Implications of macromolecular crowding for signal transduction and metabolite channeling
    • 10.1073/pnas.95.18.10547, 27931, 9724740
    • Rohwer J, Postma P, Kholodenko B, Westerhoff H. Implications of macromolecular crowding for signal transduction and metabolite channeling. PNAS 1998, 95(18):10547-10552. 10.1073/pnas.95.18.10547, 27931, 9724740.
    • (1998) PNAS , vol.95 , Issue.18 , pp. 10547-10552
    • Rohwer, J.1    Postma, P.2    Kholodenko, B.3    Westerhoff, H.4
  • 46
    • 14844321288 scopus 로고    scopus 로고
    • Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico
    • 10.1016/j.febslet.2005.01.072, 15763552
    • Takahashi K, Arjunan S, Tomita M. Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico. FEBS Lett 2005, 579:1783-1788. 10.1016/j.febslet.2005.01.072, 15763552.
    • (2005) FEBS Lett , vol.579 , pp. 1783-1788
    • Takahashi, K.1    Arjunan, S.2    Tomita, M.3
  • 48
    • 77952955542 scopus 로고    scopus 로고
    • Insight or illusion? Seeing inside the cell with mesoscopic simulations
    • 10.2976/1.2833599, 2640998, 19404447
    • Shillcock J. Insight or illusion? Seeing inside the cell with mesoscopic simulations. HFSP Journal 2008, 2:1-6. 10.2976/1.2833599, 2640998, 19404447.
    • (2008) HFSP Journal , vol.2 , pp. 1-6
    • Shillcock, J.1
  • 49
    • 33846027696 scopus 로고    scopus 로고
    • Particle-Based Stochastic Simulation in Systems Biology
    • Tolle D, Le Novere N. Particle-Based Stochastic Simulation in Systems Biology. Curr Bioinf 2006, 1(3):315-320.
    • (2006) Curr Bioinf , vol.1 , Issue.3 , pp. 315-320
    • Tolle, D.1    Le Novere, N.2
  • 51
  • 52
  • 53
    • 33744899088 scopus 로고    scopus 로고
    • Formal agent-based modelling of intracellular chemical interactions
    • 10.1016/j.biosystems.2006.02.004, 16581178
    • Pogson M, Smallwood R, Qwarnstrom E, Holcombe M. Formal agent-based modelling of intracellular chemical interactions. Biosystems 2006, 85:37-45. 10.1016/j.biosystems.2006.02.004, 16581178.
    • (2006) Biosystems , vol.85 , pp. 37-45
    • Pogson, M.1    Smallwood, R.2    Qwarnstrom, E.3    Holcombe, M.4
  • 54
    • 33748520215 scopus 로고    scopus 로고
    • Stochastic simulation of chemical reactions with spatial resolution and single molecule detail
    • 10.1088/1478-3967/1/3/001, 16204833
    • Andrews S, Bray D. Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Phys Biol 2004, 1:137-151. 10.1088/1478-3967/1/3/001, 16204833.
    • (2004) Phys Biol , vol.1 , pp. 137-151
    • Andrews, S.1    Bray, D.2
  • 55
    • 49349114529 scopus 로고    scopus 로고
    • Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network
    • 10.1063/1.2958287, 18698893
    • Morelli M, Ten Wolde P. Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network. J chem phys 2008, 129:054112. 10.1063/1.2958287, 18698893.
    • (2008) J chem phys , vol.129 , pp. 054112
    • Morelli, M.1    Ten Wolde, P.2
  • 56
    • 43849103490 scopus 로고    scopus 로고
    • Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm
    • 10.1529/biophysj.107.116053, 2367169, 18234819
    • Ridgway D, Broderick G, Lopez-Campistrous A, Ru'aini M, Winter P, Hamilton M, Boulanger P, Kovalenko A, Ellison M. Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys J 2008, 94(10):3748-3759. 10.1529/biophysj.107.116053, 2367169, 18234819.
    • (2008) Biophys J , vol.94 , Issue.10 , pp. 3748-3759
    • Ridgway, D.1    Broderick, G.2    Lopez-Campistrous, A.3    Ru'aini, M.4    Winter, P.5    Hamilton, M.6    Boulanger, P.7    Kovalenko, A.8    Ellison, M.9
  • 57
    • 76149129015 scopus 로고    scopus 로고
    • A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation
    • Arjunan S, Tomita M. A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. M Syst Synth Biol 2010, 4:35-53.
    • (2010) M Syst Synth Biol , vol.4 , pp. 35-53
    • Arjunan, S.1    Tomita, M.2
  • 58
    • 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, Ten Wolde P. Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics. Phys rev let 2005, 94(12):128103.
    • (2005) Phys rev let , vol.94 , Issue.12 , pp. 128103
    • van Zon, J.1    Ten Wolde, P.2
  • 59
    • 77956394404 scopus 로고    scopus 로고
    • Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology
    • 10.1007/s12021-010-9066-x, 2933752, 20361275
    • Byrne M, Waxham M, Kubota Y. Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology. Neuroinformatics 2010, 8(2):63-82. 10.1007/s12021-010-9066-x, 2933752, 20361275.
    • (2010) Neuroinformatics , vol.8 , Issue.2 , pp. 63-82
    • Byrne, M.1    Waxham, M.2    Kubota, Y.3
  • 60
    • 0141902430 scopus 로고
    • Diffusion-controlled reaction rates
    • Collins F, Kimball G. Diffusion-controlled reaction rates. J Colloid Sci 1949, 4(4):425-437.
    • (1949) J Colloid Sci , vol.4 , Issue.4 , pp. 425-437
    • Collins, F.1    Kimball, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.