-
1
-
-
0141987862
-
Local calcium signaling in neurons
-
10.1016/S0896-6273(03)00639-1, 14556712
-
Augustine GJ, Santamaria F, Tanaka K. Local calcium signaling in neurons. Neuron 2003, 40:331-346. 10.1016/S0896-6273(03)00639-1, 14556712.
-
(2003)
Neuron
, vol.40
, pp. 331-346
-
-
Augustine, G.J.1
Santamaria, F.2
Tanaka, K.3
-
3
-
-
37149029370
-
Calcium signaling
-
10.1016/j.cell.2007.11.028, 18083096
-
Clapham DE. Calcium signaling. Cell 2007, 131:1047-1058. 10.1016/j.cell.2007.11.028, 18083096.
-
(2007)
Cell
, vol.131
, pp. 1047-1058
-
-
Clapham, D.E.1
-
4
-
-
0031011930
-
Single-channel kinetics, inactivation, and spatial distribution of inositol trisphosphate (IP3) receptors in Xenopus oocyte nucleus
-
10.1085/jgp.109.5.571, 2217068, 9154905
-
Mak DOD, Foskett JK. Single-channel kinetics, inactivation, and spatial distribution of inositol trisphosphate (IP3) receptors in Xenopus oocyte nucleus. J Gen Physiol 1997, 109:571-587. 10.1085/jgp.109.5.571, 2217068, 9154905.
-
(1997)
J Gen Physiol
, vol.109
, pp. 571-587
-
-
Mak, D.O.D.1
Foskett, J.K.2
-
5
-
-
0033598765
-
From calcium blips to calcium puffs: Theoretical analysis of the requirements for interchannnel communication
-
10.1073/pnas.96.24.13750, 24136, 10570144
-
Swillens S, Dupont G, Combettes L, Champeil P. From calcium blips to calcium puffs: Theoretical analysis of the requirements for interchannnel communication. Proc Natl Acad Sci U S A 1999, 96:13750-13755. 10.1073/pnas.96.24.13750, 24136, 10570144.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 13750-13755
-
-
Swillens, S.1
Dupont, G.2
Combettes, L.3
Champeil, P.4
-
6
-
-
33644847375
-
Microdomains of intracellular Ca2+: Molecular determinants and functional consequences
-
10.1152/physrev.00004.2005, 16371601
-
Rizzuto R, Pozzan T. Microdomains of intracellular Ca2+: Molecular determinants and functional consequences. Physiol Rev 2006, 86:369-408. 10.1152/physrev.00004.2005, 16371601.
-
(2006)
Physiol Rev
, vol.86
, pp. 369-408
-
-
Rizzuto, R.1
Pozzan, T.2
-
7
-
-
0037204094
-
The life cycle of Ca(2+) ions in dendritic spines
-
10.1016/S0896-6273(02)00573-1, 11832230
-
Sabatini BL, Oertner TG, Svoboda K. The life cycle of Ca(2+) ions in dendritic spines. Neuron 2002, 33:439-452. 10.1016/S0896-6273(02)00573-1, 11832230.
-
(2002)
Neuron
, vol.33
, pp. 439-452
-
-
Sabatini, B.L.1
Oertner, T.G.2
Svoboda, K.3
-
8
-
-
77951210976
-
The effect of noise on CaMKII activation in a dendritic spine during LTP induction
-
10.1152/jn.91235.2008, 2853279, 20107130
-
Zeng SY, Holmes WR. The effect of noise on CaMKII activation in a dendritic spine during LTP induction. J Neurophysiol 2010, 103:1798-1808. 10.1152/jn.91235.2008, 2853279, 20107130.
-
(2010)
J Neurophysiol
, vol.103
, pp. 1798-1808
-
-
Zeng, S.Y.1
Holmes, W.R.2
-
9
-
-
33751019968
-
Anomalous diffusion in Purkinje cell dendrites caused by spines
-
10.1016/j.neuron.2006.10.025, 1994115, 17114048
-
Santamaria F, Wils S, De Schutter E, Augustine GJ. Anomalous diffusion in Purkinje cell dendrites caused by spines. Neuron 2006, 52:635-648. 10.1016/j.neuron.2006.10.025, 1994115, 17114048.
-
(2006)
Neuron
, vol.52
, pp. 635-648
-
-
Santamaria, F.1
Wils, S.2
De Schutter, E.3
Augustine, G.J.4
-
10
-
-
55149086309
-
Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces
-
10.1137/070692017, 2819163, 20151023
-
Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang J-CJ SBB, Sejnowski TJ, Stiles JR. Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces. SIAM J Sci Comput 2008, 30:3126-3149. 10.1137/070692017, 2819163, 20151023.
-
(2008)
SIAM J Sci Comput
, vol.30
, pp. 3126-3149
-
-
Kerr, R.A.1
Bartol, T.M.2
Kaminsky, B.3
Dittrich, M.4
Chang J-CJ, S.B.B.5
Sejnowski, T.J.6
Stiles, J.R.7
-
11
-
-
85057660342
-
Monte Carlo methods for simulating realistic synaptic microphysiology using MCell
-
CRC Press, Bota Racon, FL, Schutter E
-
Stiles JR, Bartol TM. Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. Computational neuroscience: realistic modeling for experimentalists 2000, 127. CRC Press, Bota Racon, FL, Schutter E.
-
(2000)
Computational neuroscience: realistic modeling for experimentalists
, pp. 127
-
-
Stiles, J.R.1
Bartol, T.M.2
-
12
-
-
77950833499
-
Detailed Simulations of Cell Biology with Smoldyn 2.1
-
10.1371/journal.pcbi.1000705, 2837389, 20300644
-
Andrews SS, Addy NJ, Brent R, Arkin AP. Detailed Simulations of Cell Biology with Smoldyn 2.1. PLoS Comput Biol 2010, 6:e1000705. 10.1371/journal.pcbi.1000705, 2837389, 20300644.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Andrews, S.S.1
Addy, N.J.2
Brent, R.3
Arkin, A.P.4
-
13
-
-
50149096614
-
GridCell: a stochastic particle-based biological system simulator
-
10.1186/1752-0509-2-66, 2517591, 18651956
-
Boulianne L, Al Assaad S, Dumontier M, Gross WJ. GridCell: a stochastic particle-based biological system simulator. BMC Syst Biol 2008, 2:66. 10.1186/1752-0509-2-66, 2517591, 18651956.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 66
-
-
Boulianne, L.1
Al Assaad, S.2
Dumontier, M.3
Gross, W.J.4
-
14
-
-
33947418109
-
Particle simulation approach for subcellular dynamics and interactions of biological molecules
-
Azuma R, Kitagawa T, Kobayashi H, Konagaya A. Particle simulation approach for subcellular dynamics and interactions of biological molecules. BMC Bioinforma 2006, 7(Suppl 4):S20.
-
(2006)
BMC Bioinforma
, vol.7
, Issue.SUPPL. 4
-
-
Azuma, R.1
Kitagawa, T.2
Kobayashi, H.3
Konagaya, A.4
-
15
-
-
2142781569
-
Diffusion
-
MIT Press, Cambridge, MA, Bower JM, Bolouri H
-
Bormann G, Brosens F, De Schutter E. Diffusion. Computational modeling of genetic and biochemical networks 2001, 224. MIT Press, Cambridge, MA, Bower JM, Bolouri H.
-
(2001)
Computational modeling of genetic and biochemical networks
, pp. 224
-
-
Bormann, G.1
Brosens, F.2
De Schutter, E.3
-
16
-
-
84861328087
-
Reaction-diffusion Modeling
-
MIT Press, Cambridge, MA, Schutter E
-
Bhalla US, Wils S. Reaction-diffusion Modeling. Computational Modeling Methods for Neuroscientists 2010, 61-92. MIT Press, Cambridge, MA, Schutter E.
-
(2010)
Computational Modeling Methods for Neuroscientists
, pp. 61-92
-
-
Bhalla, U.S.1
Wils, S.2
-
17
-
-
33645429016
-
Exact Stochastic Simulation of Coupled Chemical-Reactions
-
Gillespie DT. Exact Stochastic Simulation of Coupled Chemical-Reactions. J Phys Chem Us 1977, 81:2340-2361.
-
(1977)
J Phys Chem Us
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
18
-
-
62249111459
-
The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems
-
10.1063/1.3074302, 2671688, 19275393
-
Lampoudi S, Gillespie DT, Petzold LR. The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems. J Chem Phys 2009, 130:094104. 10.1063/1.3074302, 2671688, 19275393.
-
(2009)
J Chem Phys
, vol.130
, pp. 094104
-
-
Lampoudi, S.1
Gillespie, D.T.2
Petzold, L.R.3
-
19
-
-
20844432892
-
Stochastic reaction-diffusion simulation with MesoRD
-
10.1093/bioinformatics/bti431, 15817692
-
Hattne J, Fange D, Elf J. Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics 2005, 21:2923-2924. 10.1093/bioinformatics/bti431, 15817692.
-
(2005)
Bioinformatics
, vol.21
, pp. 2923-2924
-
-
Hattne, J.1
Fange, D.2
Elf, J.3
-
20
-
-
77955374442
-
The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations
-
10.1371/journal.pone.0011725, 2908681, 20661441
-
Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W, Kim M, Zaccolo M, Blackwell KT. The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PLoS One 2010, 5:e11725. 10.1371/journal.pone.0011725, 2908681, 20661441.
-
(2010)
PLoS One
, vol.5
-
-
Oliveira, R.F.1
Terrin, A.2
Di Benedetto, G.3
Cannon, R.C.4
Koh, W.5
Kim, M.6
Zaccolo, M.7
Blackwell, K.T.8
-
21
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
10.1093/bioinformatics/btg015, 12611808
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novere, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.42
Wang, J.43
more..
-
22
-
-
77950545445
-
STEPS: Modeling and Simulating Complex Reaction-diffusion Systems with Python
-
Wils S, De Schutter E. STEPS: Modeling and Simulating Complex Reaction-diffusion Systems with Python. Front Neuroinformatics 2009, 3:15.
-
(2009)
Front Neuroinformatics
, vol.3
, pp. 15
-
-
Wils, S.1
De Schutter, E.2
-
23
-
-
0031599142
-
Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator
-
Matsumoto M, Nishimura T. Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator. ACM Trans Model Comput Simulat 1998, 8:3-30.
-
(1998)
ACM Trans Model Comput Simulat
, vol.8
, pp. 3-30
-
-
Matsumoto, M.1
Nishimura, T.2
-
24
-
-
0004161838
-
-
Cambridge University Press, New York, NY, 2
-
Press WH, Teukolsky SA, Vetterling WT, Flannery BP. Numerical recipes in C: the art of scientific computing 1992, Cambridge University Press, New York, NY, 2.
-
(1992)
Numerical recipes in C: the art of scientific computing
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
25
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
10.1146/annurev.physchem.58.032806.104637, 17037977
-
Gillespie DT. Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 2007, 58:35-55. 10.1146/annurev.physchem.58.032806.104637, 17037977.
-
(2007)
Annu Rev Phys Chem
, vol.58
, pp. 35-55
-
-
Gillespie, D.T.1
-
26
-
-
0002296942
-
A New Algorithm for Monte Carlo Simulation of Ising Spin Systems
-
Bortz AB, Kalos MH, Lebowitz JL. A New Algorithm for Monte Carlo Simulation of Ising Spin Systems. J Comput Phys 1975, 17:10-18.
-
(1975)
J Comput Phys
, vol.17
, pp. 10-18
-
-
Bortz, A.B.1
Kalos, M.H.2
Lebowitz, J.L.3
-
27
-
-
0001455869
-
The relationship between Stochastic and Deterministic Models for Chemical Reactions
-
Kurtz TG. The relationship between Stochastic and Deterministic Models for Chemical Reactions. J Chem Phys 1972, 57:2976-2978.
-
(1972)
J Chem Phys
, vol.57
, pp. 2976-2978
-
-
Kurtz, T.G.1
-
28
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
Gibson MA, 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
-
29
-
-
84861328087
-
Reaction-diffusion Modeling
-
MIT Press, Cambridge, MA, Schutter E
-
Bhalla U, Wils S. Reaction-diffusion Modeling. Computational Modeling Methods for Neuroscientists 2010, 61-92. MIT Press, Cambridge, MA, Schutter E.
-
(2010)
Computational Modeling Methods for Neuroscientists
, pp. 61-92
-
-
Bhalla, U.1
Wils, S.2
-
31
-
-
44649178886
-
A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks
-
10.1063/1.2919546, 18513044
-
Slepoy A, Thompson AP, Plimpton SJ. A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks. Journal of Chemical Physics 2008, 128:205101. 10.1063/1.2919546, 18513044.
-
(2008)
Journal of Chemical Physics
, vol.128
, pp. 205101
-
-
Slepoy, A.1
Thompson, A.P.2
Plimpton, S.J.3
-
32
-
-
30744467210
-
CUBIT Geometry and Mesh Generation Toolkit
-
CUBIT Geometry and Mesh Generation Toolkit. http://cubit.sandia.gov/.
-
-
-
-
33
-
-
84860701988
-
TetGen: A Quality Tetrahedral Mesh Generator
-
TetGen: A Quality Tetrahedral Mesh Generator. http://tetgen.berlios.de/.
-
-
-
-
34
-
-
67650149648
-
Gmsh: A 3-D finite element mesh generator with built-in pre- and post-processing facilities
-
Remacle JF, Geuzaine C. Gmsh: A 3-D finite element mesh generator with built-in pre- and post-processing facilities. Int J Numer Meth Eng 2009, 79:1309-1331.
-
(2009)
Int J Numer Meth Eng
, vol.79
, pp. 1309-1331
-
-
Remacle, J.F.1
Geuzaine, C.2
-
35
-
-
17144363197
-
Reconstruct: a free editor for serial section microscopy
-
Fiala JC. Reconstruct: a free editor for serial section microscopy. J Microsc Oxf 2005, 218:52-61.
-
(2005)
J Microsc Oxf
, vol.218
, pp. 52-61
-
-
Fiala, J.C.1
-
36
-
-
84867641294
-
MeshLab
-
MeshLab. http://meshlab.sourceforge.net/.
-
-
-
-
37
-
-
33751568004
-
Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations
-
Isaacson SA, Peskin CS. Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations. SIAM J Sci Comput 2006, 28:47.
-
(2006)
SIAM J Sci Comput
, vol.28
, pp. 47
-
-
Isaacson, S.A.1
Peskin, C.S.2
-
38
-
-
70350729439
-
Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions
-
10.1088/1478-3975/6/4/046001, 19700812
-
Erban R, Chapman SJ. Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions. Phys Biol 2009, 6:046001. 10.1088/1478-3975/6/4/046001, 19700812.
-
(2009)
Phys Biol
, vol.6
, pp. 046001
-
-
Erban, R.1
Chapman, S.J.2
-
39
-
-
16644369510
-
Correct diffusion coefficients of proteins in fluorescence correlation spectroscopy. Application to tubulin oligomers induced by Mg2+ and paclitaxel
-
10.1529/biophysj.104.040717, 1304682, 15454458
-
Krouglova T, Vercammen J, Engelborghs Y. Correct diffusion coefficients of proteins in fluorescence correlation spectroscopy. Application to tubulin oligomers induced by Mg2+ and paclitaxel. Biophys J 2004, 87:2635-2646. 10.1529/biophysj.104.040717, 1304682, 15454458.
-
(2004)
Biophys J
, vol.87
, pp. 2635-2646
-
-
Krouglova, T.1
Vercammen, J.2
Engelborghs, Y.3
-
40
-
-
0027146418
-
Fluorescence Photobleaching with Spatial Fourier-Analysis - Measurement of Diffusion in Light-Scattering Media
-
10.1016/S0006-3495(93)81326-2, 1225983, 8312481
-
Berk DA, Yuan F, Leunig M, Jain RK. Fluorescence Photobleaching with Spatial Fourier-Analysis - Measurement of Diffusion in Light-Scattering Media. Biophys J 1993, 65:2428-2436. 10.1016/S0006-3495(93)81326-2, 1225983, 8312481.
-
(1993)
Biophys J
, vol.65
, pp. 2428-2436
-
-
Berk, D.A.1
Yuan, F.2
Leunig, M.3
Jain, R.K.4
-
41
-
-
0034077947
-
Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells
-
10.1016/S0006-3495(00)76647-1, 1300692, 10653802
-
Arrio-Dupont M, Foucault G, Vacher M, Devaux PF, Cribier S. Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells. Biophys J 2000, 78:901-907. 10.1016/S0006-3495(00)76647-1, 1300692, 10653802.
-
(2000)
Biophys J
, vol.78
, pp. 901-907
-
-
Arrio-Dupont, M.1
Foucault, G.2
Vacher, M.3
Devaux, P.F.4
Cribier, S.5
-
42
-
-
0035253217
-
Macromolecular crowding: an important but neglected aspect of the intracellular environment
-
10.1016/S0959-440X(00)00172-X, 11179900
-
Ellis RJ. 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.J.1
-
43
-
-
0035815743
-
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
-
10.1074/jbc.R100005200, 11279227
-
Minton AP. The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 2001, 276:10577-10580. 10.1074/jbc.R100005200, 11279227.
-
(2001)
J Biol Chem
, vol.276
, pp. 10577-10580
-
-
Minton, A.P.1
-
44
-
-
41049090929
-
Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
-
10.1146/annurev.biophys.37.032807.125817, 2826134, 18573087
-
Zhou HX, Rivas GN, Minton AP. Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 2008, 37:375-397. 10.1146/annurev.biophys.37.032807.125817, 2826134, 18573087.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 375-397
-
-
Zhou, H.X.1
Rivas, G.N.2
Minton, A.P.3
-
46
-
-
0024203547
-
Dendritic Spines of Rat Cerebellar Purkinje-Cells - Serial Electron-Microscopy with Reference to Their Biophysical Characteristics
-
Harris KM, Stevens JK. Dendritic Spines of Rat Cerebellar Purkinje-Cells - Serial Electron-Microscopy with Reference to Their Biophysical Characteristics. J Neurosci 1988, 8:4455-4469.
-
(1988)
J Neurosci
, vol.8
, pp. 4455-4469
-
-
Harris, K.M.1
Stevens, J.K.2
-
48
-
-
41649121478
-
Exponential temporal asymptotics of the A + B- > 0 reaction-diffusion process with initially separated reactants
-
Kisilevich S, Sinder M, Pelleg J, Sokolovsky V. Exponential temporal asymptotics of the A + B- > 0 reaction-diffusion process with initially separated reactants. Phys Rev E Stat Nonlin Soft Matter Phys 2008, 77:046103.
-
(2008)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.77
, pp. 046103
-
-
Kisilevich, S.1
Sinder, M.2
Pelleg, J.3
Sokolovsky, V.4
-
49
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
10.1186/1752-0509-4-92, 2909940, 20587024
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He EU, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, Laibe C. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4:92. 10.1186/1752-0509-4-92, 2909940, 20587024.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.U.8
Henry, A.9
Stefan, M.I.10
Snoep, J.L.11
Hucka, M.12
Le Novere, N.13
Laibe, C.14
-
50
-
-
41049095967
-
A mathematical model of spontaneous calcium(II) oscillations in astrocytes
-
10.1016/j.jtbi.2007.12.011, 18275973
-
Lavrentovich M, Hemkin S. A mathematical model of spontaneous calcium(II) oscillations in astrocytes. J Theor Biol 2008, 251:553-560. 10.1016/j.jtbi.2007.12.011, 18275973.
-
(2008)
J Theor Biol
, vol.251
, pp. 553-560
-
-
Lavrentovich, M.1
Hemkin, S.2
-
51
-
-
33845991193
-
DARPP-32 is a robust integrator of dopamine and glutamate signals
-
Fernandez E, Schiappa R, Girault JA, Le Novere N. DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Comput Biol 2006, 2:1619-1633.
-
(2006)
PLoS Comput Biol
, vol.2
, pp. 1619-1633
-
-
Fernandez, E.1
Schiappa, R.2
Girault, J.A.3
Le Novere, N.4
-
52
-
-
77953106373
-
Run-time interoperability between neuronal network simulators based on the MUSIC framework
-
10.1007/s12021-010-9064-z, 2846392, 20195795
-
Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Kotaleski JH, Ekeberg O. Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics 2010, 8:43-60. 10.1007/s12021-010-9064-z, 2846392, 20195795.
-
(2010)
Neuroinformatics
, vol.8
, pp. 43-60
-
-
Djurfeldt, M.1
Hjorth, J.2
Eppler, J.M.3
Dudani, N.4
Helias, M.5
Potjans, T.C.6
Bhalla, U.S.7
Diesmann, M.8
Kotaleski, J.H.9
Ekeberg, O.10
-
53
-
-
33646475011
-
Macromolecular crowding
-
10.1016/j.cub.2006.03.047, 16631567
-
Minton AP. Macromolecular crowding. Curr Biol 2006, 16:R269-R271. 10.1016/j.cub.2006.03.047, 16631567.
-
(2006)
Curr Biol
, vol.16
-
-
Minton, A.P.1
-
54
-
-
0000267310
-
Versuch einer mathematischen Theorie der koagulationskinetik Kolloider Lösungen
-
von 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
-
-
von Smoluchowski, M.1
-
55
-
-
0000770829
-
Non-Equilibrium Statistical Thermodynamics and the Effect of Diffusion on Chemical-Reaction Rates
-
Keizer J. Non-Equilibrium Statistical Thermodynamics and the Effect of Diffusion on Chemical-Reaction Rates. J Phys Chem Us 1982, 86:5052-5067.
-
(1982)
J Phys Chem Us
, vol.86
, pp. 5052-5067
-
-
Keizer, J.1
-
56
-
-
0001387613
-
Diffusion Effects on Rapid Bimolecular Chemical-Reactions
-
Keizer J. Diffusion Effects on Rapid Bimolecular Chemical-Reactions. Chem Rev 1987, 87:167-180.
-
(1987)
Chem Rev
, vol.87
, pp. 167-180
-
-
Keizer, J.1
-
57
-
-
33846417230
-
Effect of reactant size on discrete stochastic chemical kinetics
-
10.1063/1.2424461, 17249866
-
Gillespie DT, Lampoudi S, Petzold LR. Effect of reactant size on discrete stochastic chemical kinetics. J Chem Phys 2007, 126:034302. 10.1063/1.2424461, 17249866.
-
(2007)
J Chem Phys
, vol.126
, pp. 034302
-
-
Gillespie, D.T.1
Lampoudi, S.2
Petzold, L.R.3
-
58
-
-
62849097043
-
Effect of excluded volume on 2D discrete stochastic chemical kinetics
-
10.1016/j.jcp.2009.02.002, 2666880, 19360139
-
Lampoudi S, Gillespie DT, Petzold LR. Effect of excluded volume on 2D discrete stochastic chemical kinetics. J Comput Phys 2009, 228:3656-3668. 10.1016/j.jcp.2009.02.002, 2666880, 19360139.
-
(2009)
J Comput Phys
, vol.228
, pp. 3656-3668
-
-
Lampoudi, S.1
Gillespie, D.T.2
Petzold, L.R.3
-
59
-
-
80054814075
-
Adapting rule-based model descriptions for simulating in continuous and hybrid space
-
NY, USA: ACM New York
-
Bittig AT, Haack F, Maus C, Uhrmacher AM. Adapting rule-based model descriptions for simulating in continuous and hybrid space. In Proceedings of the 9th International Conference on Computational Methods in Systems Biology; 21-23 September 2011; Paris, France 2011, 161-170. NY, USA: ACM New York.
-
(2011)
In Proceedings of the 9th International Conference on Computational Methods in Systems Biology; 21-23 September 2011; Paris, France
, pp. 161-170
-
-
Bittig, A.T.1
Haack, F.2
Maus, C.3
Uhrmacher, A.M.4
-
60
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
Gillespie DT. Approximate accelerated stochastic simulation of chemically reacting systems. J Chem Phys 2001, 115:1716-1733.
-
(2001)
J Chem Phys
, vol.115
, pp. 1716-1733
-
-
Gillespie, D.T.1
-
61
-
-
77949409275
-
Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm
-
10.1063/1.3310808, 20210383
-
Iyengar KA, Harris LA, Clancy P. Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm. J Chem Phys 2010, 132:094101. 10.1063/1.3310808, 20210383.
-
(2010)
J Chem Phys
, vol.132
, pp. 094101
-
-
Iyengar, K.A.1
Harris, L.A.2
Clancy, P.3
-
62
-
-
79951511716
-
Exploring the performance of spatial stochastic simulation algorithms
-
Jeschke M, Ewald R, Uhrmacher AM. Exploring the performance of spatial stochastic simulation algorithms. J Comput Phys 2011, 230:2562-2574.
-
(2011)
J Comput Phys
, vol.230
, pp. 2562-2574
-
-
Jeschke, M.1
Ewald, R.2
Uhrmacher, A.M.3
-
63
-
-
0026784596
-
Rallpacks - a Set of Benchmarks for Neuronal Simulators
-
10.1016/0166-2236(92)90009-W, 1281353
-
Bhalla US, Bilitch DH, Bower JM. Rallpacks - a Set of Benchmarks for Neuronal Simulators. Trends Neurosci 1992, 15:453-458. 10.1016/0166-2236(92)90009-W, 1281353.
-
(1992)
Trends Neurosci
, vol.15
, pp. 453-458
-
-
Bhalla, U.S.1
Bilitch, D.H.2
Bower, J.M.3
-
64
-
-
3042554012
-
Structural basis of long-term potentiation in single dendritic spines
-
10.1038/nature02617, 15190253
-
Matsuzaki M, Honkura N, Ellis-Davies GCR, Kasai H. Structural basis of long-term potentiation in single dendritic spines. Nature 2004, 429:761-766. 10.1038/nature02617, 15190253.
-
(2004)
Nature
, vol.429
, pp. 761-766
-
-
Matsuzaki, M.1
Honkura, N.2
Ellis-Davies, G.C.R.3
Kasai, H.4
-
65
-
-
45949085855
-
Spine expansion and stabilization associated with long-term potentiation
-
10.1523/JNEUROSCI.3998-07.2008, 2561912, 18509035
-
Yang YL, Wang XB, Frerking M, Zhou Q. Spine expansion and stabilization associated with long-term potentiation. J Neurosci 2008, 28:5740-5751. 10.1523/JNEUROSCI.3998-07.2008, 2561912, 18509035.
-
(2008)
J Neurosci
, vol.28
, pp. 5740-5751
-
-
Yang, Y.L.1
Wang, X.B.2
Frerking, M.3
Zhou, Q.4
-
66
-
-
72049096926
-
A diffusional bimolecular propensity function
-
10.1063/1.3253798, 2780463, 19894929
-
Gillespie DT. A diffusional bimolecular propensity function. J Chem Phys 2009, 131:164109. 10.1063/1.3253798, 2780463, 19894929.
-
(2009)
J Chem Phys
, vol.131
, pp. 164109
-
-
Gillespie, D.T.1
-
67
-
-
4644266081
-
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
-
10.1063/1.1778376, 15332951
-
Cao Y, Li H, Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J Chem Phys 2004, 121:4059-4067. 10.1063/1.1778376, 15332951.
-
(2004)
J Chem Phys
, vol.121
, pp. 4059-4067
-
-
Cao, Y.1
Li, H.2
Petzold, L.3
|