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Volumn 32, Issue 5, 2010, Pages 3039-3070

Simulating biochemical signaling networks in complex moving geometries

Author keywords

Advection reaction diffusion equation; Level set methods; Numerical methods; Systems biology

Indexed keywords

ADVECTION; CELL CULTURE; CELL SIGNALING; DIFFUSION IN LIQUIDS; DROP BREAKUP; GEOMETRY; HYDROGELS; LEVEL MEASUREMENT; LINEAR EQUATIONS; PARTIAL DIFFERENTIAL EQUATIONS; SIGNALING;

EID: 78149334276     PISSN: 10648275     EISSN: None     Source Type: Journal    
DOI: 10.1137/090779693     Document Type: Article
Times cited : (18)

References (46)
  • 1
    • 0002108952 scopus 로고    scopus 로고
    • The fast construction of extension velocities in level set methods
    • D. Adalsteinsson and J. A. Sethian, The fast construction of extension velocities in level set methods, J. Comput. Phys., 148 (1999), pp. 2-22.
    • (1999) J. Comput. Phys. , vol.148 , pp. 2-22
    • Adalsteinsson, D.1    Sethian, J.A.2
  • 2
    • 0037429531 scopus 로고    scopus 로고
    • Transport and diffusion of material quantities on propagating interfaces via level set methods
    • D. Adalsteinsson and J. A. Sethian, Transport and diffusion of material quantities on propagating interfaces via level set methods, J. Comput. Phys., 185 (2003), pp. 271-288.
    • (2003) J. Comput. Phys. , vol.185 , pp. 271-288
    • Adalsteinsson, D.1    Sethian, J.A.2
  • 6
    • 0000286812 scopus 로고
    • Using Krylov methods in the solution of large-scale differential- algebraic systems
    • P. N. Brown, A. C. Hindmarsh, and L. R. Petzold, Using Krylov methods in the solution of large-scale differential-algebraic systems, SIAM J. Sci. Comput., 15 (1994), pp. 1467-1488.
    • (1994) SIAM J. Sci. Comput. , vol.15 , pp. 1467-1488
    • Brown, P.N.1    Hindmarsh, A.C.2    Petzold, L.R.3
  • 7
    • 0019169551 scopus 로고
    • Pattern formation by reaction-diffusion instabilities: Application to morphogenesis in Drosophila
    • B. Bunow, J. P. Kernevez, G. Joly, and D. Thomas, Pattern formation by reaction-diffusion instabilities: Application to morphogenesis in Drosophila, J. Theoret. Biol., 84 (1980), pp. 629-649.
    • (1980) J. Theoret. Biol. , vol.84 , pp. 629-649
    • Bunow, B.1    Kernevez, J.P.2    Joly, G.3    Thomas, D.4
  • 8
    • 0842281652 scopus 로고    scopus 로고
    • Rac and Rho take center stage
    • K. Burridge and K. Wennerberg, Rac and Rho take center stage, Cell, 116 (2004), pp. 167- 179.
    • (2004) Cell , vol.116 , pp. 167-179
    • Burridge, K.1    Wennerberg, K.2
  • 9
    • 25444445567 scopus 로고    scopus 로고
    • A Cartesian grid embedded boundary method for hyperbolic conservation laws
    • P. Colella, D. T. Graves, B. J. Keen, and D. Modiano, A Cartesian grid embedded boundary method for hyperbolic conservation laws, J. Comput. Phys., 211 (2006), pp. 347-366.
    • (2006) J. Comput. Phys. , vol.211 , pp. 347-366
    • Colella, P.1    Graves, D.T.2    Keen, B.J.3    Modiano, D.4
  • 10
    • 33846781374 scopus 로고    scopus 로고
    • Phosphoinositides and Rho proteins spatially regulate actin polymerization to initiate and maintain directed movement in a one-dimensional model of a motile cell
    • A. T. Dawes and L. Edelstein-Keshet, Phosphoinositides and Rho proteins spatially regulate actin polymerization to initiate and maintain directed movement in a one-dimensional model of a motile cell, Biophys. J., 92 (2007), pp. 744-768.
    • (2007) Biophys. J. , vol.92 , pp. 744-768
    • Dawes, A.T.1    Edelstein-Keshet, L.2
  • 11
    • 0015454185 scopus 로고
    • Theory of biological pattern formation
    • A. Gierer and H. Meinhardt, Theory of biological pattern formation, Kybernetik, 12 (1972), pp. 30-39.
    • (1972) Kybernetik , vol.12 , pp. 30-39
    • Gierer, A.1    Meinhardt, H.2
  • 12
    • 0000825469 scopus 로고
    • Simulation of the differential adhesion driven rearrangement of biological cells
    • J. A. Glazier and F. Graner, Simulation of the differential adhesion driven rearrangement of biological cells, Phys. Rev. E (3), 47 (1993), pp. 2128-2154.
    • (1993) Phys. Rev. E (3) , vol.47 , pp. 2128-2154
    • Glazier, J.A.1    Graner, F.2
  • 13
    • 42049115235 scopus 로고    scopus 로고
    • Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity
    • A. B. Goryachev and A. V. Pokhilko, Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity, FEBS Lett., 582 (2008), pp. 1437-1443.
    • (2008) FEBS Lett. , vol.582 , pp. 1437-1443
    • Goryachev, A.B.1    Pokhilko, A.V.2
  • 14
    • 33749725182 scopus 로고
    • Uniformly high order accurate essentially non-oscillatory schemes, III
    • A. Harten, B. Engquist, S. Osher, and S. R. Chakravarthy, Uniformly high order accurate essentially non-oscillatory schemes, III, J. Comput. Phys., 71 (1987), pp. 231-303.
    • (1987) J. Comput. Phys. , vol.71 , pp. 231-303
    • Harten, A.1    Engquist, B.2    Osher, S.3    Chakravarthy, S.R.4
  • 17
    • 0001827481 scopus 로고    scopus 로고
    • A Cartesian grid embedded boundary method for Poisson's equation on irregular domains
    • H. Johansen and P. Colella, A Cartesian grid embedded boundary method for Poisson's equation on irregular domains, J. Comput. Phys., 147 (1998), pp. 60-85.
    • (1998) J. Comput. Phys. , vol.147 , pp. 60-85
    • Johansen, H.1    Colella, P.2
  • 18
    • 0034665002 scopus 로고    scopus 로고
    • Diffusion control of protein phosphorylation in signal transduction pathways
    • B. N. Kholodenko, G. C. Brown, and J. B. Hoek, Diffusion control of protein phosphorylation in signal transduction pathways, Biochem. J., 350 (2000), pp. 901-907.
    • (2000) Biochem. J. , vol.350 , pp. 901-907
    • Kholodenko, B.N.1    Brown, G.C.2    Hoek, J.B.3
  • 19
    • 33644524741 scopus 로고    scopus 로고
    • Cell-signalling dynamics in time and space
    • B. N. Kholodenko, Cell-signalling dynamics in time and space, Nat. Rev. Mol. Cell Biol., 7 (2006), pp. 165-176.
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 165-176
    • Kholodenko, B.N.1
  • 21
    • 66949136652 scopus 로고    scopus 로고
    • ICAM-1 signaling in endothelial cells
    • C. Lawson and S. Wolf, ICAM-1 signaling in endothelial cells, Pharmacol. Rep., 61 (2009), pp. 22-32.
    • (2009) Pharmacol. Rep. , vol.61 , pp. 22-32
    • Lawson, C.1    Wolf, S.2
  • 23
    • 33745594814 scopus 로고    scopus 로고
    • Directional sensing in eukaryotic chemotaxis: A balanced inactivation model
    • H. Levine, D. A. Kessler, and W. J. Rappel, Directional sensing in eukaryotic chemotaxis: A balanced inactivation model, Proc. Natl. Acad. Sci. USA, 103 (2006), pp. 9761-9766.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 9761-9766
    • Levine, H.1    Kessler, D.A.2    Rappel, W.J.3
  • 24
    • 65649108429 scopus 로고    scopus 로고
    • The critical role of toll-like receptor signaling pathways in the induction and progression of autoimmune diseases
    • M. Li, Y. Zhou, G. Feng, and S. B. Su, The critical role of toll-like receptor signaling pathways in the induction and progression of autoimmune diseases, Curr. Mol. Med., 9 (2009), pp. 365-374.
    • (2009) Curr. Mol. Med. , vol.9 , pp. 365-374
    • Li, M.1    Zhou, Y.2    Feng, G.3    Su, S.B.4
  • 25
    • 65749110884 scopus 로고    scopus 로고
    • Embedded boundary grid generation using the divergence theorem, implicit functions, and constructive solid geometry
    • T. J. Ligocki, P. O. Schwartz, J. Percelay, and P. Colella, Embedded boundary grid generation using the divergence theorem, implicit functions, and constructive solid geometry, J. Phys. Conf. Ser., 125 (2008), 012080.
    • (2008) J. Phys. Conf. Ser. , vol.125 , pp. 012080
    • Ligocki, T.J.1    Schwartz, P.O.2    Percelay, J.3    Colella, P.4
  • 26
    • 0030173610 scopus 로고    scopus 로고
    • A fast level set based algorithm for topology independent shape modeling
    • R. Malladi, J. A. Sethian, and B. C. Vemuri, A fast level set based algorithm for topology independent shape modeling, J. Math. Imaging Vision, 6 (1996), pp. 269-290.
    • (1996) J. Math. Imaging Vision , vol.6 , pp. 269-290
    • Malladi, R.1    Sethian, J.A.2    Vemuri, B.C.3
  • 29
    • 33750619877 scopus 로고    scopus 로고
    • Potential for control of signaling pathways via cell size and shape
    • J. Meyers, J. Craig, and D. J. Odde, Potential for control of signaling pathways via cell size and shape, Curr. Biol., 16 (2006), pp. 1685-1693.
    • (2006) Curr. Biol. , vol.16 , pp. 1685-1693
    • Meyers, J.1    Craig, J.2    Odde, D.J.3
  • 32
    • 4644266043 scopus 로고    scopus 로고
    • Activation of endogenous Cdc42 visualized in living cells
    • P. Nalbant, L. Hodgson, V. Kraynov, A. Toutchkine, and K. M. Hahn, Activation of endogenous Cdc42 visualized in living cells, Science, 305 (2004), pp. 1615-1619.
    • (2004) Science , vol.305 , pp. 1615-1619
    • Nalbant, P.1    Hodgson, L.2    Kraynov, V.3    Toutchkine, A.4    Hahn, K.M.5
  • 34
    • 3042841518 scopus 로고    scopus 로고
    • Level set methods and dynamic implicit surfaces
    • Springer, New York
    • S. Osher and R. P. Fedkiw, Level Set Methods and Dynamic Implicit Surfaces, Appl. Math. Sci. 153, Springer, New York, 2003.
    • (2003) Appl. Math. Sci. , vol.153
    • Osher, S.1    Fedkiw, R.P.2
  • 35
    • 44749084234 scopus 로고
    • Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulation
    • S. Osher and J. A. Sethian, Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulation, J. Comput. Phys., 79 (1988), pp. 12-49.
    • (1988) J. Comput. Phys. , vol.79 , pp. 12-49
    • Osher, S.1    Sethian, J.A.2
  • 36
    • 33646197411 scopus 로고    scopus 로고
    • Spatiotemporal dynamics of RhoA activity in migrating cells
    • O. Pertz, L. Hodgson, R. Klemke, and K. Hahn, Spatiotemporal dynamics of RhoA activity in migrating cells, Nature, 440 (2006), pp. 1069-1072.
    • (2006) Nature , vol.440 , pp. 1069-1072
    • Pertz, O.1    Hodgson, L.2    Klemke, R.3    Hahn, K.4
  • 37
    • 21844458415 scopus 로고    scopus 로고
    • Multiscale two-dimensional modeling of a motile simple-shaped cell
    • B. Rubinstein, K. Jacobson, and A. Mogilner, Multiscale two-dimensional modeling of a motile simple-shaped cell, Multiscale Model Simul., 3 (2005), pp. 413-439.
    • (2005) Multiscale Model Simul. , vol.3 , pp. 413-439
    • Rubinstein, B.1    Jacobson, K.2    Mogilner, A.3
  • 39
    • 0000048673 scopus 로고
    • GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems
    • Y. Saad and M. H. Schultz, GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems, SIAM J. Sci. Statist. Comput., 7 (1986), pp. 856-869.
    • (1986) SIAM J. Sci. Statist. Comput. , vol.7 , pp. 856-869
    • Saad, Y.1    Schultz, M.H.2
  • 40
    • 0347057016 scopus 로고    scopus 로고
    • Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell
    • J. C. Schaff, B. M. Slepchenko, Y. Choi, J. Wagner, D. Resasco, and L. Loew, Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell, Chaos, 11 (2001), pp. 115-131.
    • (2001) Chaos , vol.11 , pp. 115-131
    • Schaff, J.C.1    Slepchenko, B.M.2    Choi, Y.3    Wagner, J.4    Resasco, D.5    Loew, L.6
  • 41
    • 23244462276 scopus 로고    scopus 로고
    • Spatial analysis of 3' phosphoinositide signaling in living fibroblasts, III: Influence of cell morphology and morphological polarity
    • I. C. Schneider, E. M. Parrish, and J. M. Haugh, Spatial analysis of 3' phosphoinositide signaling in living fibroblasts, III: Influence of cell morphology and morphological polarity, Biophys. J., 89 (2005), pp. 1420-1430.
    • (2005) Biophys. J. , vol.89 , pp. 1420-1430
    • Schneider, I.C.1    Parrish, E.M.2    Haugh, J.M.3
  • 43
    • 84979999914 scopus 로고    scopus 로고
    • A cut cell method for simulating spatial models of biochemical reaction networks in arbitrary geometries
    • W. Strychalski, D. Adalsteinsson, and T. C. Elston, A cut cell method for simulating spatial models of biochemical reaction networks in arbitrary geometries, Commun. Appl. Math. Comput. Sci., 1 (2010), pp. 31-53.
    • (2010) Commun. Appl. Math. Comput. Sci. , vol.1 , pp. 31-53
    • Strychalski, W.1    Adalsteinsson, D.2    Elston, T.C.3
  • 45
    • 0141727533 scopus 로고    scopus 로고
    • Slow diffusion of proteins in the yeast plasma membrane allows polarity to be maintained by endocytic cycling
    • J. Valdez-Taubas and H. R. B. Pelham, Slow diffusion of proteins in the yeast plasma membrane allows polarity to be maintained by endocytic cycling, Curr. Biol., 13 (2003), pp. 1636-1640.
    • (2003) Curr. Biol. , vol.13 , pp. 1636-1640
    • Valdez-Taubas, J.1    Pelham, H.R.B.2


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