Detailed Simulations of Cell Biology with Smoldyn 2.1
暂无分享,去创建一个
[1] Roger Brent,et al. Automatic generation of cellular reaction networks with Moleculizer 1.0 , 2005, Nature Biotechnology.
[2] P. Merkey,et al. Beowulf: harnessing the power of parallelism in a pile-of-PCs , 1997, 1997 IEEE Aerospace Conference.
[3] Lee Bardwell,et al. A walk-through of the yeast mating pheromone response pathway , 2004, Peptides.
[4] Michel Dumontier,et al. GridCell: a stochastic particle-based biological system simulator , 2008, BMC Systems Biology.
[5] S. Plimpton,et al. ChemCell : a particle-based model of protein chemistry and diffusion in microbial cells. , 2003 .
[6] D. Finkelstein,et al. Metabolism of alpha-factor by a mating type cells of Saccharomyces cerevisiae. , 1979, The Journal of biological chemistry.
[7] S. Schnell,et al. A systematic investigation of the rate laws valid in intracellular environments. , 2006, Biophysical chemistry.
[8] Samuel A. Isaacson,et al. Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations , 2006, SIAM J. Sci. Comput..
[9] Rui Alves,et al. Tools for kinetic modeling of biochemical networks , 2006, Nature Biotechnology.
[10] David S. Wishart,et al. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli , 2004, Nucleic Acids Res..
[11] John Parkinson,et al. Cell++ - simulating biochemical pathways , 2006, Bioinform..
[12] Johan Hattne,et al. Stochastic reaction-diffusion simulation with MesoRD , 2005, Bioinform..
[13] Akihiro Kusumi,et al. Three-dimensional reconstruction of the membrane skeleton at the plasma membrane interface by electron tomography , 2006, The Journal of cell biology.
[14] Jaap A. Kaandorp,et al. Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli , 2006, Bioinform..
[15] M Ander,et al. SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. , 2004, Systems biology.
[16] Karen Lipkow,et al. Rapid Turnover of Stereocilia Membrane Proteins: Evidence from the Trafficking and Mobility of Plasma Membrane Ca2+-ATPase 2 , 2006, The Journal of Neuroscience.
[17] Ryuzo Azuma,et al. Particle simulation approach for subcellular dynamics and interactions of biological molecules , 2006, First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06).
[18] D. Gillespie. Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .
[19] Ned S. Wingreen,et al. Protease helps yeast find mating partners , 1998, Nature.
[20] Erik De Schutter,et al. Monte Carlo Methods for Simulating Realistic Synaptic Microphysiology Using MCell , 2000 .
[21] H. Berg. Random Walks in Biology , 2018 .
[22] G. L. Hazelbauer,et al. Cellular Stoichiometry of the Components of the Chemotaxis Signaling Complex , 2004, Journal of bacteriology.
[23] P. R. ten Wolde,et al. Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space. , 2005, The Journal of chemical physics.
[24] S. Plimpton,et al. Microbial cell modeling via reacting diffusive particles , 2005 .
[25] D. Bray,et al. Simulated Diffusion of Phosphorylated CheY through the Cytoplasm of Escherichia coli , 2005, Journal of bacteriology.
[26] Adam P. Arkin,et al. Stochastic Models of Biological Processes , 2009, Encyclopedia of Complexity and Systems Science.
[27] D. Bray,et al. Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. , 1993, Molecular biology of the cell.
[28] Adam P Arkin,et al. Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles , 2005, Physical biology.
[29] T. Manney,et al. Expression of the BAR1 gene in Saccharomyces cerevisiae: induction by the alpha mating pheromone of an activity associated with a secreted protein , 1983, Journal of bacteriology.
[30] D. Bray,et al. Stochastic simulation of chemical reactions with spatial resolution and single molecule detail , 2004, Physical biology.
[31] Paul A. Bates,et al. Probability-based model of protein-protein interactions on biological timescales , 2006, Algorithms for Molecular Biology.
[32] Luis Serrano,et al. Space as the final frontier in stochastic simulations of biological systems , 2005, FEBS letters.
[33] M. Saxton,et al. Lateral diffusion in an archipelago. The effect of mobile obstacles. , 1987, Biophysical journal.
[34] Byron Goldstein,et al. Diffusion Limited Reactions , 2007, SIAM J. Appl. Math..
[35] Makoto Matsumoto,et al. SIMD-Oriented Fast Mersenne Twister: a 128-bit Pseudorandom Number Generator , 2008 .
[36] Tianhai Tian,et al. A multi-scaled approach for simulating chemical reaction systems. , 2004, Progress in biophysics and molecular biology.
[37] Joel Keizer,et al. Diffusion effects on rapid bimolecular chemical reactions , 1987 .
[38] S. Andrews. Accurate particle-based simulation of adsorption, desorption and partial transmission , 2009, Physical biology.
[39] P. R. ten Wolde,et al. Spatio-temporal correlations can drastically change the response of a MAPK pathway , 2009, Proceedings of the National Academy of Sciences.
[40] C. Lumsden,et al. Stochastic Simulation of Coupled Reaction-Diffusion Processes , 1996 .
[41] Karen Lipkow,et al. Model for Protein Concentration Gradients in the Cytoplasm , 2008, Cellular and molecular bioengineering.
[42] N Le Novère,et al. Conformational spread in a ring of proteins: a stochastic approach to allostery. , 2001, Journal of molecular biology.
[43] F. Frances Yao,et al. Computational Geometry , 1991, Handbook of Theoretical Computer Science, Volume A: Algorithms and Complexity.
[44] Masaru Tomita,et al. A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation , 2009, Systems and Synthetic Biology.
[45] M. Smoluchowski. Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen , 1918 .
[46] Michael A. Gibson,et al. Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .
[47] Francine Berman,et al. Distributing MCell Simulations on the Grid , 2001, Int. J. High Perform. Comput. Appl..
[48] L. Hartwell,et al. Courtship in Saccharomyces cerevisiae: an early cell-cell interaction during mating , 1990, Molecular and cellular biology.
[49] H. Berg,et al. Chemotaxis in Escherichia coli analysed by Three-dimensional Tracking , 1972, Nature.
[50] Erik De Schutter,et al. Computational neuroscience : realistic modeling for experimentalists , 2000 .
[51] C. Pesce,et al. Regulated cell-to-cell variation in a cell-fate decision system , 2005, Nature.
[52] Steven S Andrews,et al. Spatial and stochastic cellular modeling with the Smoldyn simulator. , 2012, Methods in molecular biology.
[53] S. Andrews. Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis , 2005, Physical biology.
[54] R. Erban,et al. Stochastic modelling of reaction–diffusion processes: algorithms for bimolecular reactions , 2009, Physical biology.
[55] Scott B. Baden,et al. Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces , 2008, SIAM J. Sci. Comput..
[56] Karen Lipkow,et al. Changing Cellular Location of CheZ Predicted by Molecular Simulations , 2006, PLoS Comput. Biol..
[57] H. Kitano,et al. A quantitative characterization of the yeast heterotrimeric G protein cycle , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[58] Karen Lipkow,et al. Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy. , 2009, Progress in biophysics and molecular biology.
[59] Leland H. Hartwell,et al. Courtship in S. cerevisiae: Both cell types choose mating partners by responding to the strongest pheromone signal , 1990, Cell.
[60] Ismaïl Moukadiri,et al. Identification of Two Mannoproteins Released from Cell Walls of a Saccharomyces cerevisiae mnn1 mnn9 Double Mutant by Reducing Agents , 1999, Journal of bacteriology.
[61] T. Bartol,et al. Monte Carlo simulation of miniature endplate current generation in the vertebrate neuromuscular junction. , 1991, Biophysical journal.
[62] Erik Lindholm,et al. NVIDIA Tesla: A Unified Graphics and Computing Architecture , 2008, IEEE Micro.
[63] Jin Yang,et al. 'On-the-fly' or 'generate-first' modeling? , 2005, Nature Biotechnology.
[64] M. DELBRtrCK. THE BURST SIZE DISTRIBUTION IN THE GROWTH OF BACTERIAL VIRUSES ( BACTERIOPHAGES ) , 2022 .
[65] D. Bray,et al. Origins of individual swimming behavior in bacteria. , 1998, Biophysical journal.
[66] R. Erban,et al. Reactive boundary conditions for stochastic simulations of reaction–diffusion processes , 2007, Physical biology.
[67] A. Arkin,et al. Simulating cell biology , 2006, Current Biology.
[68] Drew Endy,et al. Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range , 2011, Proceedings of the National Academy of Sciences.
[69] Adam P Arkin,et al. Deviant effects in molecular reaction pathways , 2006, Nature Biotechnology.
[70] A. Mastro,et al. Diffusion of a small molecule in the cytoplasm of mammalian cells. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[71] Jaap A. Kaandorp,et al. Computational methods for diffusion-influenced biochemical reactions , 2007, Bioinform..
[72] J. Segall,et al. Polarization of yeast cells in spatial gradients of alpha mating factor. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[73] C. J. Morton-firth. Stochastic simulation of cell signaling pathways , 1998 .
[74] Maryann E Martone,et al. Evidence for Ectopic Neurotransmission at a Neuronal Synapse , 2005, Science.