-
1
-
-
14844307095
-
Space as the _nal frontier in stochastic simulations of biological systems
-
Lemerle C, Di Ventura B, Serrano L, (2005) Space as the _nal frontier in stochastic simulations of biological systems. FEBS Letters 579: 1789-1794.
-
(2005)
FEBS Letters
, vol.579
, pp. 1789-1794
-
-
Lemerle, C.1
Di Ventura, B.2
Serrano, L.3
-
2
-
-
36949020617
-
The realistic modeling of biological systems: a workshop synopsis
-
Broderick G, Rubin E, (2006) The realistic modeling of biological systems: a workshop synopsis. Complexus 3: 217-230.
-
(2006)
Complexus
, vol.3
, pp. 217-230
-
-
Broderick, G.1
Rubin, E.2
-
3
-
-
77956277987
-
Interacting many-particle systems of di_erent particle types converge to a sorted state
-
Kokkendorff SL, Starke J, Hummel N, (2010) Interacting many-particle systems of di_erent particle types converge to a sorted state. SIAM Journal on Applied Mathematics 70: 2534.
-
(2010)
SIAM Journal on Applied Mathematics
, vol.70
, pp. 2534
-
-
Kokkendorff, S.L.1
Starke, J.2
Hummel, N.3
-
4
-
-
0000836206
-
Active walker model for the formation of human and animal trail systems
-
LP-2522539
-
Helbing D, Schweitzer F, Keltsch J, Molnár P, (1997) Active walker model for the formation of human and animal trail systems. Physical Review E 56: 2527 LP-2539.
-
(1997)
Physical Review E
, vol.56
, pp. 2527
-
-
Helbing, D.1
Schweitzer, F.2
Keltsch, J.3
Molnár, P.4
-
5
-
-
0035478374
-
Extracellular signals that regulate the tangential migration of olfactory bulb neuronal precursors: inducers, inhibitors, and repellents
-
Mason HA, Ito S, Corfas G, (2001) Extracellular signals that regulate the tangential migration of olfactory bulb neuronal precursors: inducers, inhibitors, and repellents. J Neurosci 21: 7654-7663.
-
(2001)
J Neurosci
, vol.21
, pp. 7654-7663
-
-
Mason, H.A.1
Ito, S.2
Corfas, G.3
-
6
-
-
0033595192
-
Directional guidance of neuronal migration in the olfactory system by the protein Slit
-
Wu W, Wong K, Chen Jh, Jiang Zh, Dupuis S, et al. (1999) Directional guidance of neuronal migration in the olfactory system by the protein Slit. Nature 400: 331-336.
-
(1999)
Nature
, vol.400
, pp. 331-336
-
-
Wu, W.1
Wong, K.2
Chen, J.3
Jiang, Z.4
Dupuis, S.5
-
7
-
-
0038790277
-
Distinguishing between directional guidance and motility regulation in neuronal migration
-
Ward M, McCann C, DeWulf M, Wu JY, Rao Y, (2003) Distinguishing between directional guidance and motility regulation in neuronal migration. J Neurosci 23: 5170-5177.
-
(2003)
J Neurosci
, vol.23
, pp. 5170-5177
-
-
Ward, M.1
McCann, C.2
DeWulf, M.3
Wu, J.Y.4
Rao, Y.5
-
8
-
-
33746635608
-
Modelling directional guidance and motility regulation in cell migration
-
Cai AQ, Landman Ka, Hughes BD, (2006) Modelling directional guidance and motility regulation in cell migration. Bulletin of mathematical biology 68: 25-52.
-
(2006)
Bulletin of Mathematical Biology
, vol.68
, pp. 25-52
-
-
Cai, A.Q.1
Landman, K.2
Hughes, B.D.3
-
9
-
-
33846542380
-
Agents in bioinformatics, computational and systems biology
-
Merelli E, Armano G, Cannata N, Corradini F, D'Inverno M, et al. (2007) Agents in bioinformatics, computational and systems biology. Briefings in bioinformatics 8: 45-59.
-
(2007)
Briefings in Bioinformatics
, vol.8
, pp. 45-59
-
-
Merelli, E.1
Armano, G.2
Cannata, N.3
Corradini, F.4
D'Inverno, M.5
-
11
-
-
79951804820
-
Parallel particle-based reaction di_usion: A GPU implementation
-
In: Ballarini P, Barnat J, Weber M, editors, Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010
-
Dematté L, (2010) Parallel particle-based reaction di_usion: A GPU implementation. In: Ballarini P, Barnat J, Weber M, editors. pp. 67-77 Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010- Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010.
-
(2010)
, pp. 67-77
-
-
Dematté, L.1
-
12
-
-
72449169547
-
First-passage kinetic Monte Carlo method
-
Oppelstrup T, Bulatov VV, Donev A, Kalos MH, Gilmer GH, et al. (2009) First-passage kinetic Monte Carlo method. Physical Review E 80: 1-37.
-
(2009)
Physical Review E
, vol.80
, pp. 1-37
-
-
Oppelstrup, T.1
Bulatov, V.V.2
Donev, A.3
Kalos, M.H.4
Gilmer, G.H.5
-
13
-
-
77949327931
-
A First-Passage Kinetic Monte Carlo algorithm for complex diffusion-reaction systems
-
Donev A, Bulatov VV, Oppelstrup T, Gilmer GH, Sadigh B, et al. (2010) A First-Passage Kinetic Monte Carlo algorithm for complex diffusion-reaction systems. Journal of Computational Physics 229: 3214-3236.
-
(2010)
Journal of Computational Physics
, vol.229
, pp. 3214-3236
-
-
Donev, A.1
Bulatov, V.V.2
Oppelstrup, T.3
Gilmer, G.H.4
Sadigh, B.5
-
14
-
-
79952900494
-
Flexible single molecule simulation of reaction-diffusion processes
-
Hellander S, Ltstedt P, (2011) Flexible single molecule simulation of reaction-diffusion processes. Journal of Computational Physics 230: 3948-3965.
-
(2011)
Journal of Computational Physics
, vol.230
, pp. 3948-3965
-
-
Hellander, S.1
Ltstedt, P.2
-
15
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
-
(1977)
J Phys Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
16
-
-
0034225547
-
The chemical Langevin equation
-
Gillespie DT, (2000) The chemical Langevin equation. J Chem Phys 113: 297.
-
(2000)
J Chem Phys
, vol.113
, pp. 297
-
-
Gillespie, D.T.1
-
17
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
Gibson MA, Bruck J, (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 104: 1876-1889.
-
(2000)
J Phys Chem A
, vol.104
, pp. 1876-1889
-
-
Gibson, M.A.1
Bruck, J.2
-
18
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
Gillespie DT, (2001) Approximate accelerated stochastic simulation of chemically reacting systems. J Chem Phys 115: 1716.
-
(2001)
J Chem Phys
, vol.115
, pp. 1716
-
-
Gillespie, D.T.1
-
19
-
-
77951217960
-
Efficient parallelization of the stochastic simulation algorithm for chemically reacting systems on the graphics processing unit
-
Petzold L, Hong Li, (2010) Efficient parallelization of the stochastic simulation algorithm for chemically reacting systems on the graphics processing unit. International Journal of High Performance Computing Applications 24: 107-116.
-
(2010)
International Journal of High Performance Computing Applications
, vol.24
, pp. 107-116
-
-
Petzold, L.1
Hong, L.2
-
20
-
-
0041324718
-
Mesoscopic reaction-diffusion in intracellular signaling
-
In: Bezrukov SM, Frauenfelder H, Moss F, editors, Santa Fe, NM, USA, The International Society for Optical Engineering, volume 5110
-
Elf J, Doncic A, Ehrenberg M, (2003) Mesoscopic reaction-diffusion in intracellular signaling. In: Bezrukov SM, Frauenfelder H, Moss F, editors. Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems Santa Fe, NM, USA The International Society for Optical Engineering, volume 5110 pp. 114-124.
-
(2003)
Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems
, pp. 114-124
-
-
Elf, J.1
Doncic, A.2
Ehrenberg, M.3
-
21
-
-
33748520215
-
Stochastic simulation of chemical reactions with spatial resolution and single molecule detail
-
Andrews SS, Bray D, (2004) Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Physical Biology 1: 137.
-
(2004)
Physical Biology
, vol.1
, pp. 137
-
-
Andrews, S.S.1
Bray, D.2
-
22
-
-
41349099680
-
Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm
-
Bernstein D, (2005) Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm. Physical Review E 71: 41103.
-
(2005)
Physical Review E
, vol.71
, pp. 41103
-
-
Bernstein, D.1
-
23
-
-
20844432892
-
Stochastic reaction-diffusion simulation with MesoRD
-
Hattne J, Fange D, Elf J, (2005) Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics 21: 2923-4.
-
(2005)
Bioinformatics
, vol.21
, pp. 2923-2924
-
-
Hattne, J.1
Fange, D.2
Elf, J.3
-
24
-
-
69949127857
-
Efficient stochastic simulation of reaction-diffusion processes via direct compilation
-
Lis M, Artyomov MN, Devadas S, Chakraborty AK, (2009) Efficient stochastic simulation of reaction-diffusion processes via direct compilation. Bioinformatics 25: 2289-91.
-
(2009)
Bioinformatics
, vol.25
, pp. 2289-2291
-
-
Lis, M.1
Artyomov, M.N.2
Devadas, S.3
Chakraborty, A.K.4
-
25
-
-
33747829956
-
Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli
-
Rodríguez JV, Kaandorp Ja, Dobrzyski M, Blom JG, (2006) Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. Bioinformatics 22: 1895-901.
-
(2006)
Bioinformatics
, vol.22
, pp. 1895-1901
-
-
Rodríguez, J.V.1
Kaandorp, J.2
Dobrzyski, M.3
Blom, J.G.4
-
26
-
-
62249111459
-
The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems
-
Lampoudi S, Gillespie DT, Petzold LR, (2009) The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems. J Chem Phys 130: 094104.
-
(2009)
J Chem Phys
, vol.130
, pp. 094104
-
-
Lampoudi, S.1
Gillespie, D.T.2
Petzold, L.R.3
-
27
-
-
78651417127
-
Accelerating reaction-diffusion simulations with generalpurpose graphics processing units
-
Vigelius M, Lane A, Meyer B, (2010) Accelerating reaction-diffusion simulations with generalpurpose graphics processing units. Bioinformatics 27: 288-290.
-
(2010)
Bioinformatics
, vol.27
, pp. 288-290
-
-
Vigelius, M.1
Lane, A.2
Meyer, B.3
-
28
-
-
0001518684
-
On the construction and comparison of difference schemes
-
Strang G, (1968) On the construction and comparison of difference schemes. SIAM Journal on Numerical Analysis 5: 506.
-
(1968)
SIAM Journal on Numerical Analysis
, vol.5
, pp. 506
-
-
Strang, G.1
-
29
-
-
61849164660
-
Simulation of stochastic reaction-diffusion processes on unstructured meshes
-
Engblom S, Ferm L, Hellander A, Lötstedt P, (2009) Simulation of stochastic reaction-diffusion processes on unstructured meshes. SIAM Journal on Scientific Computing 31: 1774.
-
(2009)
SIAM Journal on Scientific Computing
, vol.31
, pp. 1774
-
-
Engblom, S.1
Ferm, L.2
Hellander, A.3
Lötstedt, P.4
-
30
-
-
79251490718
-
Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells
-
Hellander A, Lötstedt P, (2010) Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells. Multiscale Modeling & Simulation 8: 1691.
-
(2010)
Multiscale Modeling & Simulation
, vol.8
, pp. 1691
-
-
Hellander, A.1
Lötstedt, P.2
-
33
-
-
70350729439
-
Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions
-
Erban R, Chapman SJ, (2009) Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions. Physical Biology 6: 46001.
-
(2009)
Physical Biology
, vol.6
, pp. 46001
-
-
Erban, R.1
Chapman, S.J.2
-
34
-
-
67649365828
-
The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target
-
Isaacson S, (2009) The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target. SIAM Journal on Applied Mathematics 70: 77.
-
(2009)
SIAM Journal on Applied Mathematics
, vol.70
, pp. 77
-
-
Isaacson, S.1
-
35
-
-
65549164378
-
Taming the complexity of biological pathways through parallel computing
-
Ballarini P, Guido R, Mazza T, Prandi D, (2009) Taming the complexity of biological pathways through parallel computing. Briefings in Bioinformatics 10: 278-288.
-
(2009)
Briefings in Bioinformatics
, vol.10
, pp. 278-288
-
-
Ballarini, P.1
Guido, R.2
Mazza, T.3
Prandi, D.4
-
38
-
-
0034917420
-
The diffusion limit of transport equations derived from velocity-jump processes
-
Hillen T, Othmer HG, (2000) The diffusion limit of transport equations derived from velocity-jump processes. SIAM Journal on Applied Mathematics 61: 751-775.
-
(2000)
SIAM Journal on Applied Mathematics
, vol.61
, pp. 751-775
-
-
Hillen, T.1
Othmer, H.G.2
-
39
-
-
0036553052
-
The diffusion limit of transport equations II: chemotaxis equations
-
Othmer H, (2002) The diffusion limit of transport equations II: chemotaxis equations. SIAM Journal on Applied Mathematics 62: 1222.
-
(2002)
SIAM Journal on Applied Mathematics
, vol.62
, pp. 1222
-
-
Othmer, H.1
-
41
-
-
0037044534
-
Exactly solvable Ogston model of gel electrophoresis. IX. Generalizing the lattice model to treat high field intensities
-
Gauthier MG, Slater GW, Introduction I, (2002) Exactly solvable Ogston model of gel electrophoresis. IX. Generalizing the lattice model to treat high field intensities. Chemical Physics 117.
-
(2002)
Chemical Physics
, vol.117
-
-
Gauthier, M.G.1
Slater, G.W.2
Introduction, I.3
-
42
-
-
84859561894
-
Modelling a highly biased random walk: Application to gel electrophoresis
-
Master of science thesis, University of Ottawa
-
Gauthier M, (2003) Modelling a highly biased random walk: Application to gel electrophoresis. Master of science thesis, University of Ottawa.
-
(2003)
-
-
Gauthier, M.1
-
43
-
-
42749099229
-
Building reliable lattice Monte Carlo models for real drift and diffusion problems
-
Gauthier M, Slater G, (2004) Building reliable lattice Monte Carlo models for real drift and diffusion problems. Physical Review E 70: 6-9.
-
(2004)
Physical Review E
, vol.70
, pp. 6-9
-
-
Gauthier, M.1
Slater, G.2
-
46
-
-
0027398084
-
Theory of band broadening for DNA gel electrophoresis and sequencing
-
Slater GW, (1993) Theory of band broadening for DNA gel electrophoresis and sequencing. Electrophoresis 14: 1-7.
-
(1993)
Electrophoresis
, vol.14
, pp. 1-7
-
-
Slater, G.W.1
-
47
-
-
0035918068
-
One-dimensional drift-diffusion between two absorbing boundaries: application to granular segregation
-
Farkas Z, Fülöp T, (2001) One-dimensional drift-diffusion between two absorbing boundaries: application to granular segregation. Journal of Physics A: Mathematical and General 34: 3191.
-
(2001)
Journal of Physics A: Mathematical and General
, vol.34
, pp. 3191
-
-
Farkas, Z.1
Fülöp, T.2
-
51
-
-
55649109070
-
-
Boston, Addison-Wesley Professional
-
Nguyen H, (2007) GPU gems 3 Boston Addison-Wesley Professional.
-
(2007)
GPU Gems 3
-
-
Nguyen, H.1
-
52
-
-
77957743720
-
Diffusion about the mean drift location in a biased random walk
-
Codling EA, Bearon RN, Thorn GJ, (2010) Diffusion about the mean drift location in a biased random walk. Ecology 91: 3106-3113.
-
(2010)
Ecology
, vol.91
, pp. 3106-3113
-
-
Codling, E.A.1
Bearon, R.N.2
Thorn, G.J.3
-
54
-
-
0006087385
-
Solution of nonlinear Fokker-Planck equations
-
Drozdov A, Morillo M, (1996) Solution of nonlinear Fokker-Planck equations. Physical Review E 54: 931-937.
-
(1996)
Physical Review E
, vol.54
, pp. 931-937
-
-
Drozdov, A.1
Morillo, M.2
-
55
-
-
0031190076
-
Numerical method for the nonlinear Fokker-Planck equation
-
Zhang D, Wei G, Kouri D, Hoffman D, (1997) Numerical method for the nonlinear Fokker-Planck equation. Physical Review E 56: 1197-1206.
-
(1997)
Physical Review E
, vol.56
, pp. 1197-1206
-
-
Zhang, D.1
Wei, G.2
Kouri, D.3
Hoffman, D.4
-
57
-
-
0025805762
-
Diffusion models for chemotaxis: a statistical analysis of noninteractive unicellular movement
-
Watkins JC, Woessner B, (1991) Diffusion models for chemotaxis: a statistical analysis of noninteractive unicellular movement. Mathematical Biosciences 104: 271-303.
-
(1991)
Mathematical Biosciences
, vol.104
, pp. 271-303
-
-
Watkins, J.C.1
Woessner, B.2
-
58
-
-
0031207030
-
Aggregation, blowup, and collapse: the ABC's of taxis in reinforced random walks
-
Othmer HG, Stevens A, (1997) Aggregation, blowup, and collapse: the ABC's of taxis in reinforced random walks. SIAM Journal on Applied Mathematics 57: 1044.
-
(1997)
SIAM Journal on Applied Mathematics
, vol.57
, pp. 1044
-
-
Othmer, H.G.1
Stevens, A.2
-
61
-
-
77953539835
-
Keeping in touch with contact inhibition of locomotion
-
Mayor R, Carmona-Fontaine C, (2010) Keeping in touch with contact inhibition of locomotion. Trends in Cell Biology 20: 319-328.
-
(2010)
Trends in Cell Biology
, vol.20
, pp. 319-328
-
-
Mayor, R.1
Carmona-Fontaine, C.2
-
62
-
-
79955984497
-
An in vitro cell population dynamics model incorporating cell size, quiescence, and contact inhibition
-
Ducrot A, Le Foll F, Magal P, Murakawa H, Pasquier J, et al. (2011) An in vitro cell population dynamics model incorporating cell size, quiescence, and contact inhibition. Mathematical Models and Methods in Applied Sciences 21: 871-892.
-
(2011)
Mathematical Models and Methods in Applied Sciences
, vol.21
, pp. 871-892
-
-
Ducrot, A.1
Le, F.F.2
Magal, P.3
Murakawa, H.4
Pasquier, J.5
-
63
-
-
77958509217
-
An adaptive algorithm for simulation of stochastic reaction-diffusion processes
-
Ferm L, Hellander A, Ltstedt P, (2010) An adaptive algorithm for simulation of stochastic reaction-diffusion processes. Journal of Computational Physics 229: 343-360.
-
(2010)
Journal of Computational Physics
, vol.229
, pp. 343-360
-
-
Ferm, L.1
Hellander, A.2
Ltstedt, P.3
-
64
-
-
0033871649
-
High performance parametric modeling with Nimrod/G: killer application for the global grid?
-
In: Proceedings 14th International Parallel and Distributed Processing Symposium. IPDPS 2000. IEEE Comput. Soc
-
Abramson D, Giddy J, Kotler L, (2000) High performance parametric modeling with Nimrod/G: killer application for the global grid? pp. 520-528 In: Proceedings 14th International Parallel and Distributed Processing Symposium. IPDPS 2000. IEEE Comput. Soc.
-
(2000)
, pp. 520-528
-
-
Abramson, D.1
Giddy, J.2
Kotler, L.3
|