메뉴 건너뛰기




Volumn 110, Issue , 2012, Pages 195-221

Spatial Modeling of Cell Signaling Networks

Author keywords

Diffusion; Downstream; Memory; Neuronal; Segregation; Supramolecular

Indexed keywords


EID: 84859339035     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-388403-9.00008-4     Document Type: Chapter
Times cited : (108)

References (51)
  • 1
    • 33745075591 scopus 로고    scopus 로고
    • Tools for kinetic modeling of biochemical networks
    • Alves R., Antunes F., Salvador A. Tools for kinetic modeling of biochemical networks. Nat. Biotechnol. 2006, 24:667-672.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 667-672
    • Alves, R.1    Antunes, F.2    Salvador, A.3
  • 3
    • 33748520215 scopus 로고    scopus 로고
    • Stochastic simulation of chemical reactions with spatial resolution and single molecule detail
    • Andrews S.S., Bray D. Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Phys. Biol. 2004, 1:137-151.
    • (2004) Phys. Biol. , vol.1 , pp. 137-151
    • Andrews, S.S.1    Bray, D.2
  • 4
    • 50349096740 scopus 로고    scopus 로고
    • Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines
    • Brown S.A., Morgan F., Watras J., Loew L.M. Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines. Biophys J. 2008, 95:1795-1812.
    • (2008) Biophys J. , vol.95 , pp. 1795-1812
    • Brown, S.A.1    Morgan, F.2    Watras, J.3    Loew, L.M.4
  • 5
    • 0041324718 scopus 로고    scopus 로고
    • Mesoscopic reaction-diffusion in intracellular signalling
    • Elf J., Doncic A., Ehrenberg M. Mesoscopic reaction-diffusion in intracellular signalling. SPIE 2003, 5110:114-124.
    • (2003) SPIE , vol.5110 , pp. 114-124
    • Elf, J.1    Doncic, A.2    Ehrenberg, M.3
  • 6
    • 33745591124 scopus 로고    scopus 로고
    • Noise-induced min phenotypes in E. coli
    • Fange D., Elf J. Noise-induced min phenotypes in E. coli. PLoS Comput. Biol. 2006, 2.
    • (2006) PLoS Comput. Biol. , pp. 2
    • Fange, D.1    Elf, J.2
  • 10
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical system with many species and many channels
    • Gibson M.A., Bruck J. Efficient exact stochastic simulation of chemical system with many species and many channels. J. Phys. Chem. A 2000, 104:1876-1889.
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 11
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and many channels
    • Gibson M.A., Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A. 2000, 104:1876-1889.
    • (2000) J. Phys. Chem. A. , vol.104 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 12
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie D.T. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 1976, 22:403-434.
    • (1976) J. Comput. Phys. , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 13
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977, 81:2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 14
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting systems
    • Gillespie D.T. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 2001, 115:1715-1733.
    • (2001) J. Chem. Phys. , vol.115 , pp. 1715-1733
    • Gillespie, D.T.1
  • 15
    • 42049115235 scopus 로고    scopus 로고
    • Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity
    • Goryachev A.B., Pokhilko A.V. Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity. FEBS Lett. 2008, 582:1437-1443.
    • (2008) FEBS Lett. , vol.582 , pp. 1437-1443
    • Goryachev, A.B.1    Pokhilko, A.V.2
  • 16
    • 28444444583 scopus 로고    scopus 로고
    • Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells
    • Hernjak N., Slepchenko B.M., Fernald K., Fink C.C., Fortin D., Moraru I.I., Watras J., Loew L.M. Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells. Biophys J. 2005, 89:3790-3806.
    • (2005) Biophys J. , vol.89 , pp. 3790-3806
    • Hernjak, N.1    Slepchenko, B.M.2    Fernald, K.3    Fink, C.C.4    Fortin, D.5    Moraru, I.I.6    Watras, J.7    Loew, L.M.8
  • 17
    • 1242310783 scopus 로고    scopus 로고
    • High mobility of vesicles supports continuous exocytosis at a ribbon synapse
    • Holt M., Cooke A., Neef A., Lagnado L. High mobility of vesicles supports continuous exocytosis at a ribbon synapse. Curr. Biol. 2004, 14:173-183.
    • (2004) Curr. Biol. , vol.14 , pp. 173-183
    • Holt, M.1    Cooke, A.2    Neef, A.3    Lagnado, L.4
  • 18
    • 33751568004 scopus 로고    scopus 로고
    • Incorporating diffusion in complex geometries into stochastic chemical kinetics simulations
    • Isaacson S.A., Peskin C.S. Incorporating diffusion in complex geometries into stochastic chemical kinetics simulations. SIAM J. Sci. Comput. 2006, 28:47-74.
    • (2006) SIAM J. Sci. Comput. , vol.28 , pp. 47-74
    • Isaacson, S.A.1    Peskin, C.S.2
  • 19
    • 77955900382 scopus 로고    scopus 로고
    • Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics
    • Kapustina M., Vitriol E., Elston T.C., Loew L.M., Jacobson K. Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics. Cytoskeleton (Hoboken) 2010, 67:519-534.
    • (2010) Cytoskeleton (Hoboken) , vol.67 , pp. 519-534
    • Kapustina, M.1    Vitriol, E.2    Elston, T.C.3    Loew, L.M.4    Jacobson, K.5
  • 22
    • 0000435781 scopus 로고    scopus 로고
    • Exact solution of the reversible diffusion-influenced reaction for an isolated pair in three dimensions
    • Kim H., Shin K.J. Exact solution of the reversible diffusion-influenced reaction for an isolated pair in three dimensions. Phys. Rev. Lett. 1999, 82:1578-1581.
    • (1999) Phys. Rev. Lett. , vol.82 , pp. 1578-1581
    • Kim, H.1    Shin, K.J.2
  • 23
    • 0348198275 scopus 로고    scopus 로고
    • Jacobian-free Newton-Krylov methods: a survey of approaches and applications
    • Knoll D.A., Keyes D.E. Jacobian-free Newton-Krylov methods: a survey of approaches and applications. J. Comput. Phys. 2004, 193:357-397.
    • (2004) J. Comput. Phys. , vol.193 , pp. 357-397
    • Knoll, D.A.1    Keyes, D.E.2
  • 25
    • 10044250005 scopus 로고    scopus 로고
    • Two complementary, local excitation, global inhibition mechanisms acting in parallel can explain the chemoattractant-induced regulation of PI(3,4,5)P3 response in dictyostelium cells
    • Ma L., Janetopoulos C., Yang L., Devreotes P.N., Iglesias P.A. Two complementary, local excitation, global inhibition mechanisms acting in parallel can explain the chemoattractant-induced regulation of PI(3,4,5)P3 response in dictyostelium cells. Biophys J. 2004, 87:3764-3774.
    • (2004) Biophys J. , vol.87 , pp. 3764-3774
    • Ma, L.1    Janetopoulos, C.2    Yang, L.3    Devreotes, P.N.4    Iglesias, P.A.5
  • 27
    • 49349114529 scopus 로고    scopus 로고
    • Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network
    • Morelli M.J., ten Wolde P.R. Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network. J. Chem. Phys. 2008, 129:054112.
    • (2008) J. Chem. Phys. , vol.129 , pp. 054112
    • Morelli, M.J.1    ten Wolde, P.R.2
  • 28
    • 0032492834 scopus 로고    scopus 로고
    • Predicting temporal fluctuations in an intracellular signalling pathway
    • Morton-Firth C.J., Bray D. Predicting temporal fluctuations in an intracellular signalling pathway. J. Theor. Biol. 1998, 192:117-128.
    • (1998) J. Theor. Biol. , vol.192 , pp. 117-128
    • Morton-Firth, C.J.1    Bray, D.2
  • 30
    • 34548697081 scopus 로고    scopus 로고
    • Diffusion on a curved surface coupled to diffusion in the volume: application to cell biology
    • Novak I.L., Gao F., Choi Y.-S., Resasco D., Schaff J.C., Slepchenko B.M. Diffusion on a curved surface coupled to diffusion in the volume: application to cell biology. J. Comput. Phys. 2007, 226:1271-1290.
    • (2007) J. Comput. Phys. , vol.226 , pp. 1271-1290
    • Novak, I.L.1    Gao, F.2    Choi, Y.-S.3    Resasco, D.4    Schaff, J.C.5    Slepchenko, B.M.6
  • 31
    • 34548681253 scopus 로고    scopus 로고
    • ChemCell: A Particle-Based Model of Protein Chemistry and Diffusion in Microbial Cells
    • Sandia Technical Report SAND2003-4509
    • Plimpton, S., Slepoy, A., ChemCell: A Particle-Based Model of Protein Chemistry and Diffusion in Microbial Cells. Sandia Technical Report SAND2003-4509, 2003.
    • (2003)
    • Plimpton, S.1    Slepoy, A.2
  • 32
    • 24344437156 scopus 로고    scopus 로고
    • Microbial cell modeling via reacting diffusive particles
    • Plimpton S.J., Slepoy A. Microbial cell modeling via reacting diffusive particles. J. Phys. Conf. Ser. 2005, 16:305-309.
    • (2005) J. Phys. Conf. Ser. , vol.16 , pp. 305-309
    • Plimpton, S.J.1    Slepoy, A.2
  • 34
    • 0035947763 scopus 로고    scopus 로고
    • Local photorelease of caged thymosin beta4 in locomoting keratocytes causes cell turning
    • Roy P., Rajfur Z., Jones D., Marriott G., Loew L., Jacobson K. Local photorelease of caged thymosin beta4 in locomoting keratocytes causes cell turning. J. Cell. Biol. 2001, 153:1035-1048.
    • (2001) J. Cell. Biol. , vol.153 , pp. 1035-1048
    • Roy, P.1    Rajfur, Z.2    Jones, D.3    Marriott, G.4    Loew, L.5    Jacobson, K.6
  • 37
    • 36549074600 scopus 로고    scopus 로고
    • Modeling 2D and 3D diffusion
    • Saxton M.J. Modeling 2D and 3D diffusion. Methods Mol. Biol. 2007, 400:295-321.
    • (2007) Methods Mol. Biol. , vol.400 , pp. 295-321
    • Saxton, M.J.1
  • 38
    • 0030739712 scopus 로고    scopus 로고
    • A general computational framework for modeling cellular structure and function
    • Schaff J., Fink C.C., Slepchenko B., Carson J.H., Loew L.M. A general computational framework for modeling cellular structure and function. Biophys J. 1997, 73:1135-1146.
    • (1997) Biophys J. , vol.73 , pp. 1135-1146
    • Schaff, J.1    Fink, C.C.2    Slepchenko, B.3    Carson, J.H.4    Loew, L.M.5
  • 39
    • 0347057016 scopus 로고    scopus 로고
    • Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell
    • Schaff J.C., Slepchenko B.M., Choi Y.S., Wagner J., Resasco D., Loew L.M. Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell. Chaos 2001, 11:115-131.
    • (2001) Chaos , vol.11 , pp. 115-131
    • Schaff, J.C.1    Slepchenko, B.M.2    Choi, Y.S.3    Wagner, J.4    Resasco, D.5    Loew, L.M.6
  • 40
  • 42
    • 44149105668 scopus 로고    scopus 로고
    • The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state
    • Shen L., Weber C.R., Turner J.R. The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state. J. Cell. Biol. 2008, 181:683-695.
    • (2008) J. Cell. Biol. , vol.181 , pp. 683-695
    • Shen, L.1    Weber, C.R.2    Turner, J.R.3
  • 43
    • 77956138710 scopus 로고    scopus 로고
    • Use of Virtual Cell in studies of cellular dynamics
    • Slepchenko B.M., Loew L.M. Use of Virtual Cell in studies of cellular dynamics. Int. Rev. Cell. Mol. Biol. 2010, 283:1-56.
    • (2010) Int. Rev. Cell. Mol. Biol. , vol.283 , pp. 1-56
    • Slepchenko, B.M.1    Loew, L.M.2
  • 44
    • 0000896334 scopus 로고    scopus 로고
    • Numerical approach to fast reactions in reaction-diffusion systems: application to buffered calcium waves in bistable models
    • Slepchenko B.M., Schaff J.C., Choi Y.S. Numerical approach to fast reactions in reaction-diffusion systems: application to buffered calcium waves in bistable models. J. Comput. Phys. 2000, 162:186-218.
    • (2000) J. Comput. Phys. , vol.162 , pp. 186-218
    • Slepchenko, B.M.1    Schaff, J.C.2    Choi, Y.S.3
  • 46
    • 0001446261 scopus 로고    scopus 로고
    • An analysis of operating splitting techniques in the stiff case
    • Sportisse B. An analysis of operating splitting techniques in the stiff case. J. Comput. Phys. 2000, 161:140-168.
    • (2000) J. Comput. Phys. , vol.161 , pp. 140-168
    • Sportisse, B.1
  • 47
    • 0030211187 scopus 로고    scopus 로고
    • Stochastic simulation of coupled reaction-diffusion processes
    • Stundzia A.B., Lumsden C.J. Stochastic simulation of coupled reaction-diffusion processes. J. Comput. Phys. 1996, 127:196-207.
    • (1996) J. Comput. Phys. , vol.127 , pp. 196-207
    • Stundzia, A.B.1    Lumsden, C.J.2
  • 49
    • 18244404300 scopus 로고    scopus 로고
    • Simulating biochemical networks at the particle level and in time and space
    • van Zon J.S., ten Wolde P.R. Simulating biochemical networks at the particle level and in time and space. Phys. Rev. Lett. 2005, 94:128103.
    • (2005) Phys. Rev. Lett. , vol.94 , pp. 128103
    • van Zon, J.S.1    ten Wolde, P.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.