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journal-article
Elsevier BV
Biophysical Chemistry (78)
References
121
Referenced
38
10.1016/j.gde.2004.05.002
/ Current Opinion in Genetics and Development / Models of cell signaling pathways by Bhalla (2004)10.1146/annurev.bioeng.2.1.31
/ Annual Review of Biomedical Engineering / Bioengineering models of cell signaling by Asthagiri (2000){'key': '10.1016/j.bpc.2006.01.008_bib3', 'first-page': '191', 'volume': 'vol. 23', 'author': 'Rao', 'year': '2005'}
by Rao (2005)10.1126/science.1069981
/ Science / Reverse engineering of biological complexity by Csete (2002)10.1126/science.1069492
/ Science / Systems biology: a brief overview by Kitano (2002)10.1146/annurev.biophys.34.040204.144415
/ Annual Review of Biophysics and Biomolecular Structure / Toward predictive models of mammalian cells by Ma'ayan (2005)10.1016/j.febslet.2005.10.034
/ FEBS Letters / Current challenges in quantitative modeling of epidermal growth factor signaling by Breitling (2005)10.1042/BJ20050908
/ Biochemical Journal / Computational modelling of the receptor-tyrosine-kinase-activated MAR pathway by Orton (2005)10.1016/S0962-8924(02)00009-0
/ Trends in Cell Biology / Computational modeling of the EGF-receptor system: a paradigm for systems biology by Wiley (2003)10.1038/nature01258
/ Nature / Control, exploitation and tolerance of intracellular noise by Rao (2002)10.1146/annurev.biophys.27.1.59
/ Annual Review of Biophysics and Biomolecular Structure / Signaling complexes: biophysical constraints on intracellular communication by Bray (1998)10.1101/gr.1763203
/ Genome Research / Systems biology is taking off by Ehrenberg (2003)10.1016/j.febslet.2005.01.072
/ FEBS Letters / Space in systems biology of signaling pathways — towards intracellular molecular crowding in silico by Takahashi (2005){'year': '1993', 'series-title': 'Receptors Models for Binding, Trafficking, and Signaling', 'author': 'Lauffenburger', 'key': '10.1016/j.bpc.2006.01.008_bib14'}
/ Receptors Models for Binding, Trafficking, and Signaling by Lauffenburger (1993)10.1016/S0006-3495(01)75837-7
/ Biophysical Journal / Spatial range of autocrine signaling: modeling and computational analysis by Shvartsman (2001)10.1016/S0014-5793(99)01058-3
/ FEBS Letters / Spatial gradients of cellular phospho-proteins by Brown (1999)10.1016/S0006-3495(97)78146-3
/ Biophysical Journal / A general computational framework for modeling cellular structure and function by Schaff (1997)10.1016/S0006-3495(97)78846-5
/ Biophysical Journal / Physical modulation of intracellular signaling processes by locational regulation by Haugh (1997)10.1016/S0006-3495(98)77610-6
/ Biophysical Journal / Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model by Smart (1998)10.1529/biophysj.104.041517
/ Biophysical Journal / Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis by Song (2004)10.1016/S0006-3495(04)74263-0
/ Biophysical Journal / Finite element solution of the steady-state Smoluchowski equation for rate constant calculations by Song (2004)10.1006/jtbi.1993.1029
/ Journal of Theoretical Biology / Reaction diffusion coupling in a structured system — application to the quantitative simulation of end-plate currents by Friboulet (1993)10.1016/S0006-3495(03)75029-2
/ Biophysical Journal / Finite element simulations of acetylcholine diffusion in neuromuscular junctions by Tai (2003)10.1529/biophysj.104.053850
/ Biophysical Journal / Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods by Zhang (2005)10.1016/S0006-3495(02)75424-6
/ Biophysical Journal / A unified model for signal transduction reactions in cellular membranes by Haugh (2002)10.1016/S0006-3495(85)83879-0
/ Biophysical Journal / The effect of diffusion on the binding of membrane-bound receptors to coated pits by Keizer (1985)10.1016/S0006-3495(88)83117-5
/ Biophysical Journal / Effect of membrane flow on the capture of receptors by coated pits — theoretical results by Goldstein (1988)10.1016/S0006-3495(98)77836-1
/ Biophysical Journal / Theory for ligand rebinding at cell membrane surfaces by Lagerholm (1998)10.1016/S0006-3495(03)74783-3
/ Biophysical Journal / Stochastic model of autocrine and paracrine signals in cell culture assays by Batsilas (2003)10.1529/biophysj.104.051425
/ Biophysical Journal / Ligand accumulation in autocrine cell cultures by Monine (2005)10.1016/S0006-3495(03)75093-0
/ Biophysical Journal / Discrete models of autocrine cell communication in epithelial layers by Pribyl (2003)10.1016/S0006-3495(03)74906-6
/ Biophysical Journal / Long-range signal transmission in autocrine relays by Pribyl (2003)10.1016/S0006-3495(82)84455-X
/ Biophysical Journal / Role of diffusion in ligand binding to macromolecules and cell-bound receptors by Shoup (1982)10.1016/S0006-3495(95)80298-5
/ Biophysical Journal / Approximating the effects of diffusion on reversible reactions at the cell surface: ligand–receptor kinetics by Goldstein (1995)10.1073/pnas.87.15.5856
/ PNAS / Diffusion-controlled ligand binding to spheres partially covered by receptors: an effective medium treatment by Zwanzig (1990)10.1016/S0006-3495(77)85544-6
/ Biophysical Journal / Physics of chemoreception by Berg (1977)10.1016/S0006-3495(89)82741-9
/ Biophysical Journal / Competition between solution and cell surface receptors for ligand. Dissociation of hapten bound to surface antibody in the presence of solution antibody by Goldstein (1989)10.1007/BF01007611
/ European Biophysics Journal (Historical Archive) / Kinetics of ligand binding to a cluster of membrane-associated receptors by Potanin (1994)10.1016/S0006-3495(87)83258-7
/ Biophysical Journal / The effect of receptor density on the forward rate constant for binding of ligands to cell surface receptors by Erickson (1987)10.1016/0301-4622(92)80027-3
/ Biophysical Chemistry / Reaction rate enhancement by surface diffusion of adsorbates by Wang (1992)10.1016/S0006-3495(91)82096-3
/ Biophysical Journal / Time dependent rate of diffusion-influenced ligand binding to receptors on cell surfaces by Zwanzig (1991)10.1103/PhysRevA.44.2388
/ Physical Review A / Diffusion-controlled reaction A+B→0 in one dimension — the role of particle mobilities and the diffusion-equation approach by Sokolov (1991)10.1021/j100234a023
/ Journal of Physical Chemistry / Diffusion-limited reactions in one dimension by Torney (1983)10.1021/j100019a041
/ Journal of Physical Chemistry / Reaction–diffusion model for A+A reaction by Lindenberg (1995)10.1016/S0001-8686(00)00053-1
/ Advances in Colloid and Interface Science / Kinetics of diffusion-assisted reactions in microheterogeneous systems by Barzykin (2001)10.1021/cr00077a009
/ Chemical Reviews / Diffusion effects on rapid bimolecular chemical-reactions by Keizer (1987){'key': '10.1016/j.bpc.2006.01.008_bib47', 'first-page': '129', 'article-title': 'Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen', 'volume': '92', 'author': 'Smoluchowski', 'year': '1917', 'journal-title': 'Zeitschrift fūr Physikalische Chemie'}
/ Zeitschrift fūr Physikalische Chemie / Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen by Smoluchowski (1917)10.1103/PhysRevLett.61.2496
/ Physical Review Letters / Diffusion-controlled reactions with mobile traps by Szabo (1988)10.1016/0095-8522(49)90023-9
/ Journal of Colloid Science / Diffusion-controlled reaction rates by Collins (1949)10.1063/1.1744102
/ Journal of Chemical Physics / Free energy of a nonuniform system: I. Interfacial free energy by Cahn (1958)10.1016/j.ces.2004.07.116
/ Chemical Engineering Science / Mesoscopic modeling of chemical reactivity by Chatterjee (2004)10.1098/rspa.1983.0055
/ Proceedings of the Royal Society of London. A / Diffusion-limited reaction theory for two-dimensional systems by Torney (1983)10.1063/1.441789
/ Journal of Chemical Physics / Extended Brownian dynamics approach to diffusion-controlled processes by Lamm (1981)10.1063/1.445002
/ Journal of Chemical Physics / Extended Brownian dynamics: 2. Reactive, non-linear diffusion by Lamm (1983)10.1063/1.446900
/ Journal of Chemical Physics / Brownian dynamics simulation of diffusion-influenced bimolecular reactions by Northrup (1984)10.1063/1.450381
/ Journal of Chemical Physics / Optimization of Brownian dynamics methods for diffusion-influenced rate-constant calculations by Northrup (1986)10.1016/S0006-3495(97)78805-2
/ Biophysical Journal / Collective binding properties of receptor arrays by Agmon (1997)10.1042/bst0240254
/ Biochemical Society Transactions / Brownian dynamics simulations of enzyme–substrate encounter by Wade (1996)10.1021/j100408a015
/ Journal of Physical Chemistry / Diffusional dynamics of ligand receptor association by McCammon (1986)10.1021/j100388a010
/ Journal of Physical Chemistry / Kinetics of diffusion-influenced reactions studied by Brownian dynamics by Zhou (1990)10.1063/1.466302
/ Journal of Chemical Physics / The long-time behavior of reversible binary reactions — theory, Brownian simulations and experiment by Agmon (1994)10.1063/1.458533
/ Journal of Chemical Physics / Theory of reversible diffusion-influenced reactions by Agmon (1990)10.1006/meth.1998.0588
/ Methods / Brownian dynamics simulation of protein–protein diffusional encounter by Gabdoulline (1998)10.1016/S0006-3495(03)74641-4
/ Biophysical Journal / Robust biased Brownian dynamics for rate constant calculation by Zou (2003)10.1063/1.2000236
/ The Journal of Chemical Physics / Reactions on cell membranes: comparison of continuum theory and Brownian dynamics simulations by Monine (2005)10.1146/annurev.biophys.31.101101.140930
/ Annual Review of Biophysics and Biomolecular Structure / Computational cell biology: spatiotemporal simulation of cellular events by Slepchenko (2002)10.1016/j.febslet.2005.02.009
/ FEBS Letters / Space as the final frontier in stochastic simulations of biological systems by Lemerle (2005)10.1088/1478-3967/1/3/001
/ Physical Biology / Stochastic simulation of chemical reactions with spatial resolution and single molecule detail by Andrews (2004)10.1016/S0006-3495(97)78323-1
/ Biophysical Journal / Calculation of diffusion-limited kinetics for the reactions in collision coupling and receptor cross-linking by Shea (1997){'key': '10.1016/j.bpc.2006.01.008_bib70', 'series-title': 'Computational Neuroscience', 'first-page': '279', 'author': 'Stiles', 'year': '1998'}
/ Computational Neuroscience by Stiles (1998)10.1006/jcph.2001.6877
/ Journal of Computational Physics / Monte Carlo algorithms for complex surface reaction mechanisms: efficiency and accuracy by Reese (2001)10.1016/S0022-2836(03)00437-6
/ Journal of Molecular Biology / A spatially extended stochastic model of the bacterial chemotaxis signalling pathway by Shimizu (2003){'key': '10.1016/j.bpc.2006.01.008_bib73', 'series-title': 'Computational Neuroscience: Realistic Modeling for Experimentalists', 'article-title': 'Monte Carlo methods for simulating realistic synaptic micro-physiology using MCell', 'author': 'Stiles', 'year': '2000'}
/ Computational Neuroscience: Realistic Modeling for Experimentalists / Monte Carlo methods for simulating realistic synaptic micro-physiology using MCell by Stiles (2000)10.1016/S0006-3495(00)76769-5
/ Biophysical Journal / The probability of quantal secretion near a single calcium channel of an active zone by Bennett (2000)10.1093/bioinformatics/bti308
/ Bioinformatics / Time accelerated Monte Carlo simulations of biological networks using the binomial {tau}-leap method by Chatterjee (2005)10.1016/S0006-3495(03)74516-0
/ Biophysical Journal / An integrated model of epidermal growth factor receptor trafficking and signal transduction by Resat (2003)10.1038/nbt991
/ Nature Biotechnology / In silico simulation of biological network dynamics by Salwinski (2004)10.1038/ng869
/ Nature Genetics / Regulation of noise in the expression of a single gene by Ozbudak (2002)10.1063/1.1835951
/ Journal of Chemical Physics / Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions by Salis (2005)10.1126/science.1070919
/ Science / Stochastic gene expression in a single cell by Elowitz (2002)10.1038/nature01546
/ Nature / Noise in eukaryotic gene expression by Blake (2003)10.1073/pnas.1332550100
/ PNAS / Dynamic, yet structured: the cell membrane three decades after the Singer–Nicolson model by Vereb (2003)10.1529/biophysj.103.035717
/ Biophysical Journal / Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques by Murase (2004)10.1073/pnas.0401354101
/ PNAS / Single-molecule imaging analysis of Ras activation in living cells by Murakoshi (2004)10.1091/mbc.E03-08-0574
/ Molecular Biology of the Cell / Markers for detergent-resistant lipid rafts occupy distinct and dynamic domains in native membranes by Wilson (2004)10.1016/S0955-0674(02)00351-4
/ Current Opinion in Cell Biology / Plasma membrane microdomains by Maxfield (2002)10.1016/j.bbamem.2004.05.005
/ Biochimica et Biophysica Acta (BBA) — Biomembranes / In vivo plasma membrane organization: results of biophysical approaches by Lommerse (2004)10.1080/09687680410001700517
/ Molecular Membrane Biology / Plasma membrane microdomains: organization, function and trafficking (Review) by Laude (2004)10.1146/annurev.biophys.34.040204.144637
/ Annual Review of Biophysics and Biomolecular Structure / 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 by Kusumi (2005)10.1038/35036052
/ Nature Reviews Molecular Cell Biology / Lipid rafts and signal transduction by Simons (2000)10.1194/jlr.R200021-JLR200
/ Journal of Lipid Research / Lipid rafts: bringing order to chaos by Pike (2003)10.1038/nbt929
/ Nature Biotechnology / Quantum dot ligands provide new insights into erbB/HER receptor-mediated signal transduction by Lidke (2004)10.1073/pnas.151588598
/ PNAS / Intrinsic noise in gene regulatory networks by Thattai (2001)10.1146/annurev.bioeng.5.040202.121553
/ Annual Review of Biomedical Engineering / The engineering of gene regulatory networks by Kærn (2003)10.1073/pnas.0504321102
/ PNAS / Physical limits to biochemical signaling by Bialek (2005)10.1529/biophysj.104.040469
/ Biophysical Journal / Signaling in small subcellular volumes: I. Stochastic and diffusion effects on individual pathways by Bhalla (2004)10.1529/biophysj.104.040501
/ Biophysical Journal / Signaling in small subcellular volumes: II. Stochastic and diffusion effects on synaptic network properties by Bhalla (2004)10.1103/PhysRevLett.87.068103
/ Physical Review Letters / The future is noisy: the role of spatial fluctuations in genetic switching by Metzler (2001)10.1186/1471-2121-6-41
/ BMC Cell Biology / Computational modeling reveals molecular details of epidermal growth factor binding by Mayawala (2005)10.1038/nbt0402-370
/ Nature Biotechnology / Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors by Schoeberl (2002)10.1016/S0968-0004(97)01096-7
/ Trends in Biochemical Sciences / Computer simulation studies of biological membranes: progress, promise and pitfalls by Jakobsson (1997){'year': '1999', 'series-title': 'Kirk-Othmer Encyclopedia of Chemical Technology', 'author': 'Kirk-Othmer', 'key': '10.1016/j.bpc.2006.01.008_bib102'}
/ Kirk-Othmer Encyclopedia of Chemical Technology by Kirk-Othmer (1999)10.1038/nrm1571
/ Nature Reviews Molecular Cell Biology / Clathrin- and non-clathrin-mediated endocytic regulation of cell signalling by Roy (2005)10.1016/S0065-2377(05)30001-9
/ Advances in Chemical Engineering / A review of multiscale analysis: examples from systems biology, materials engineering, and other fluid–surface interacting systems by Vlachos (2005)10.1016/S0006-3495(94)80606-X
/ Biophysical Journal / A Monte Carlo study of the dynamics of G-protein activation by Mahama (1994)10.1083/jcb.107.2.801
/ Journal of Cell Biology / Anomalous binding of epidermal growth factor to A431 cells is due to the effect of high receptor densities and a saturable endocytic system by Wiley (1988)10.1083/jcb.106.6.1903
/ Journal of Cell Biology / Overexpression of epidermal growth factor receptor in NIH-3T3-transfected cells slows its lateral diffusion and rate of endocytosis by Benveniste (1988)10.1126/science.7770769
/ Science / Revisiting the fluid mosaic model of membranes by Jacobson (1995)10.1016/S0955-0674(96)80036-6
/ Current Opinion in Cell Biology / Cell surface organization by the membrane skeleton by Kusumi (1996)10.1046/j.0014-2956.2001.02715.x
/ European Journal of Biochemistry / Lipid rafts and little caves. Compartmentalized signalling in membrane microdomains by Zajchowski (2002)10.1016/j.tcb.2004.02.001
/ Trends in Cell Biology / Lipid rafts and plasma membrane microorganization: insights from Ras by Parton (2004)10.1016/j.febslet.2005.04.059
/ FEBS Letters / Heterogeneities in EGF receptor density at the cell surface can lead to concave up Scatchard plot of EGF binding by Mayawala (2005)10.1016/S0006-3495(93)81253-0
/ Biophysical Journal / Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells by Kusumi (1993)10.1083/jcb.103.1.87
/ Journal of Cell Biology / Epidermal growth factor receptors associated to cytoskeletal elements of epidermoid carcinoma (A431) cells by Wiegant (1986)10.1083/jcb.148.5.997
/ Journal of Cell Biology / Sphingolipid-cholesterol rafts diffuse as small entities in the plasma membrane of mammalian cells by Pralle (2000)10.1242/jeb.00298
/ The Journal of Experimental Biology / Four-dimensional organization of protein kinase signaling cascades: the role of diffusion, endocytosis, molecular motors by Kholodenko (2003)10.1101/gr.1196503
/ Genome Research / Fast evaluation of fluctuations in biochemical networks with the linear noise approximation by Elf (2003)10.1093/bioinformatics/bth479
/ Bioinformatics / A method for estimating stochastic noise in large genetic regulatory networks by Orrell (2005)10.1073/pnas.231499798
/ PNAS / Degeneracy and complexity in biological systems by Edelman (2001)10.1016/S0168-9525(98)01659-X
/ Trends in Genetics / It's a noisy business! Genetic regulation at the nanomolar scale by McAdams (1999)10.1073/pnas.95.26.15641
/ PNAS / Modeling stochastic gene expression: implications for haploinsufficiency by Cook (1998)
Dates
Type | When |
---|---|
Created | 19 years, 6 months ago (March 1, 2006, 2:37 p.m.) |
Deposited | 6 years, 7 months ago (Jan. 18, 2019, 12:53 a.m.) |
Indexed | 1 month ago (July 30, 2025, 9:58 a.m.) |
Issued | 19 years, 3 months ago (June 1, 2006) |
Published | 19 years, 3 months ago (June 1, 2006) |
Published Print | 19 years, 3 months ago (June 1, 2006) |
@article{Mayawala_2006, title={Spatial modeling of dimerization reaction dynamics in the plasma membrane: Monte Carlo vs. continuum differential equations}, volume={121}, ISSN={0301-4622}, url={http://dx.doi.org/10.1016/j.bpc.2006.01.008}, DOI={10.1016/j.bpc.2006.01.008}, number={3}, journal={Biophysical Chemistry}, publisher={Elsevier BV}, author={Mayawala, Kapil and Vlachos, Dionisios G. and Edwards, Jeremy S.}, year={2006}, month=jun, pages={194–208} }