{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T09:33:07Z","timestamp":1742981587706,"version":"3.40.3"},"publisher-location":"New York, NY","reference-count":72,"publisher":"Springer New York","isbn-type":[{"type":"electronic","value":"9781461473206"}],"license":[{"start":{"date-parts":[[2014,1,1]],"date-time":"2014-01-01T00:00:00Z","timestamp":1388534400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014]]},"DOI":"10.1007\/978-1-4614-7320-6_196-2","type":"book-chapter","created":{"date-parts":[[2014,9,12]],"date-time":"2014-09-12T07:51:55Z","timestamp":1410508315000},"page":"1-10","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Stochastic Simulators"],"prefix":"10.1007","author":[{"given":"Wonryull","family":"Koh","sequence":"first","affiliation":[]},{"given":"Kim T.","family":"Blackwell","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,5,19]]},"reference":[{"key":"196-2_CR1","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1038\/nbt0606-667","volume":"24","author":"R Alves","year":"2006","unstructured":"Alves R, Antunes F, Salvador A (2006) Tools for kinetic modeling of biochemical networks. Nat Biotech 24:667\u2013672","journal-title":"Nat Biotech"},{"key":"196-2_CR2","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1049\/sb:20045017","volume":"1","author":"M Ander","year":"2004","unstructured":"Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M et al (2004) SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst Biol 1:129\u2013138","journal-title":"Syst Biol"},{"key":"196-2_CR3","doi-asserted-by":"publisher","first-page":"R523","DOI":"10.1016\/j.cub.2006.06.048","volume":"16","author":"SS Andrews","year":"2006","unstructured":"Andrews SS, Arkin AP (2006) Simulating cell biology. Curr Biol 16:R523\u2013R527","journal-title":"Curr Biol"},{"key":"196-2_CR4","doi-asserted-by":"publisher","first-page":"8730","DOI":"10.1007\/978-0-387-30440-3_524","volume-title":"Encyclopedia of complexity and systems science","author":"S Andrews","year":"2009","unstructured":"Andrews S, Dinh T, Arkin A (2009) Stochastic models of biological processes. In: Meyers RA (ed) Encyclopedia of complexity and systems science. Springer, New York, pp 8730\u20138749"},{"key":"196-2_CR5","doi-asserted-by":"publisher","first-page":"e1000705","DOI":"10.1371\/journal.pcbi.1000705","volume":"6","author":"SS Andrews","year":"2010","unstructured":"Andrews SS, Addy NJ, Brent R, Arkin AP (2010) Detailed simulations of cell biology with smoldyn 2.1. PLoS Comput Biol 6:e1000705","journal-title":"PLoS Comput Biol"},{"key":"196-2_CR6","doi-asserted-by":"publisher","first-page":"9288","DOI":"10.1523\/JNEUROSCI.5976-11.2012","volume":"32","author":"G Antunes","year":"2012","unstructured":"Antunes G, De Schutter E (2012) A stochastic signaling network mediates the probabilistic induction of cerebellar long-term depression. J Neurosci 32:9288\u20139300","journal-title":"J Neurosci"},{"key":"196-2_CR7","doi-asserted-by":"publisher","first-page":"S20","DOI":"10.1186\/1471-2105-7-S4-S20","volume":"7","author":"R Azuma","year":"2006","unstructured":"Azuma R, Kitagawa T, Kobayashi H, Konagaya A (2006) Particle simulation approach for subcellular dynamics and interactions of biological molecules. BMC Bioinform 7:S20","journal-title":"BMC Bioinform"},{"key":"196-2_CR8","doi-asserted-by":"publisher","first-page":"6139","DOI":"10.1103\/PhysRevE.54.6139","volume":"54","author":"F Baras","year":"1996","unstructured":"Baras F, Mansour MM (1996) Reaction\u2013diffusion master equation: a comparison with microscopic simulations. Phys Rev E 54:6139","journal-title":"Phys Rev E"},{"key":"196-2_CR9","doi-asserted-by":"publisher","first-page":"041103","DOI":"10.1103\/PhysRevE.71.041103","volume":"71","author":"D Bernstein","year":"2005","unstructured":"Bernstein D (2005) Simulating mesoscopic reaction\u2013diffusion systems using the Gillespie algorithm. Phys Rev E 71:041103","journal-title":"Phys Rev E"},{"key":"196-2_CR10","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1529\/biophysj.104.040469","volume":"87","author":"US Bhalla","year":"2004","unstructured":"Bhalla US (2004a) Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways. Biophys J 87:733\u2013744","journal-title":"Biophys J"},{"key":"196-2_CR11","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1529\/biophysj.104.040501","volume":"87","author":"US Bhalla","year":"2004","unstructured":"Bhalla US (2004b) Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties. Biophys J 87:745\u2013753","journal-title":"Biophys J"},{"key":"196-2_CR12","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/1752-0509-2-66","volume":"2","author":"L Boulianne","year":"2008","unstructured":"Boulianne L, Al Assaad S, Dumontier M, Gross W (2008) GridCell: a stochastic particle-based biological system simulator. BMC Syst Biol 2:66","journal-title":"BMC Syst Biol"},{"key":"196-2_CR13","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.pbiomolbio.2004.01.014","volume":"85","author":"K Burrage","year":"2004","unstructured":"Burrage K, Tian T, Burrage P (2004) A multi-scaled approach for simulating chemical reaction systems. Prog Biophys Mol Biol 85:217\u2013234","journal-title":"Prog Biophys Mol Biol"},{"key":"196-2_CR14","doi-asserted-by":"publisher","first-page":"014116","DOI":"10.1063\/1.1824902","volume":"122","author":"Y Cao","year":"2005","unstructured":"Cao Y, Gillespie DT, Petzold LR (2005a) The slow-scale stochastic simulation algorithm. J Chem Phys 122:014116","journal-title":"J Chem Phys"},{"key":"196-2_CR15","doi-asserted-by":"publisher","first-page":"054104","DOI":"10.1063\/1.1992473","volume":"123","author":"Y Cao","year":"2005","unstructured":"Cao Y, Gillespie DT, Petzold LR (2005b) Avoiding negative populations in explicit Poisson tau-leaping. J Chem Phys 123:054104","journal-title":"J Chem Phys"},{"key":"196-2_CR16","doi-asserted-by":"publisher","first-page":"044109","DOI":"10.1063\/1.2159468","volume":"124","author":"Y Cao","year":"2006","unstructured":"Cao Y, Gillespie DT, Petzold LR (2006) Efficient step size selection for the tau-leaping simulation method. J Chem Phys 124:044109","journal-title":"J Chem Phys"},{"key":"196-2_CR17","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/s10820-006-9042-9","volume":"14","author":"A Chatterjee","year":"2007","unstructured":"Chatterjee A, Vlachos D (2007) An overview of spatial microscopic and accelerated kinetic Monte Carlo methods. J Comput Aided Mater Des 14:253\u2013308","journal-title":"J Comput Aided Mater Des"},{"key":"196-2_CR18","doi-asserted-by":"publisher","first-page":"1969","DOI":"10.1093\/bioinformatics\/btm278","volume":"23","author":"M Dobrzynski","year":"2007","unstructured":"Dobrzynski M, Rodriguez JV, Kaandorp JA, Blom JG (2007) Computational methods for diffusion-influenced biochemical reactions. Bioinformatics 23:1969\u20131977","journal-title":"Bioinformatics"},{"key":"196-2_CR19","doi-asserted-by":"publisher","first-page":"074101","DOI":"10.1063\/1.3310809","volume":"132","author":"B Drawert","year":"2010","unstructured":"Drawert B, Lawson MJ, Petzold L, Khammash M (2010) The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction\u2013diffusion master equation. J Chem Phys 132:074101","journal-title":"J Chem Phys"},{"key":"196-2_CR20","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1186\/1752-0509-6-76","volume":"6","author":"B Drawert","year":"2012","unstructured":"Drawert B, Engblom S, Hellander A (2012) URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. BMC Syst Biol 6:76","journal-title":"BMC Syst Biol"},{"key":"196-2_CR21","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1049\/sb:20045021","volume":"1","author":"J Elf","year":"2004","unstructured":"Elf J, Ehrenberg M (2004) Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Syst Biol 1:230\u2013236","journal-title":"Syst Biol"},{"key":"196-2_CR22","doi-asserted-by":"publisher","first-page":"046001","DOI":"10.1088\/1478-3975\/6\/4\/046001","volume":"6","author":"R Erban","year":"2009","unstructured":"Erban R, Chapman SJ (2009) Stochastic modelling of reaction\u2013diffusion processes: algorithms for bimolecular reactions. Phys Biol 6:046001","journal-title":"Phys Biol"},{"key":"196-2_CR23","doi-asserted-by":"publisher","first-page":"e80","DOI":"10.1371\/journal.pcbi.0020080","volume":"2","author":"D Fange","year":"2006","unstructured":"Fange D, Elf J (2006) Noise-induced min phenotypes in E. coli. PLoS Comput Biol 2:e80","journal-title":"PLoS Comput Biol"},{"key":"196-2_CR24","doi-asserted-by":"publisher","first-page":"19820","DOI":"10.1073\/pnas.1006565107","volume":"107","author":"D Fange","year":"2010","unstructured":"Fange D, Berg OG, Sj\u00f6berg P, Elf J (2010) Stochastic reaction\u2013diffusion kinetics in the microscopic limit. Proc Natl Acad Sci 107:19820\u201319825","journal-title":"Proc Natl Acad Sci"},{"key":"196-2_CR25","doi-asserted-by":"publisher","first-page":"3155","DOI":"10.1093\/bioinformatics\/bts584","volume":"28","author":"D Fange","year":"2012","unstructured":"Fange D, Mahmutovic A, Elf J (2012) MesoRD 1.0: Stochastic reaction\u2013diffusion simulations in the microscopic limit. Bioinformatics 28:3155\u20133157","journal-title":"Bioinformatics"},{"key":"196-2_CR26","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/j.jcp.2009.09.030","volume":"229","author":"L Ferm","year":"2010","unstructured":"Ferm L, Hellander A, L\u00f6tstedt P (2010) An adaptive algorithm for simulation of stochastic reaction\u2013diffusion processes. J Comput Phys 229:343\u2013360","journal-title":"J Comput Phys"},{"key":"196-2_CR27","doi-asserted-by":"publisher","first-page":"1876","DOI":"10.1021\/jp993732q","volume":"104","author":"MA Gibson","year":"2000","unstructured":"Gibson MA, Bruck J (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 104:1876\u20131889","journal-title":"J Phys Chem A"},{"key":"196-2_CR28","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/0021-9991(76)90041-3","volume":"22","author":"DT Gillespie","year":"1976","unstructured":"Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22:403\u2013434","journal-title":"J Comput Phys"},{"key":"196-2_CR29","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"DT Gillespie","year":"1977","unstructured":"Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340\u20132361","journal-title":"J Phys Chem"},{"key":"196-2_CR30","doi-asserted-by":"publisher","first-page":"1716","DOI":"10.1063\/1.1378322","volume":"115","author":"DT Gillespie","year":"2001","unstructured":"Gillespie DT (2001) Approximate accelerated stochastic simulation of chemically reacting systems. J Chem Phys 115:1716","journal-title":"J Chem Phys"},{"key":"196-2_CR31","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1146\/annurev.physchem.58.032806.104637","volume":"58","author":"DT Gillespie","year":"2007","unstructured":"Gillespie DT (2007) Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 58:35\u201355","journal-title":"Annu Rev Phys Chem"},{"key":"196-2_CR32","doi-asserted-by":"publisher","first-page":"8229","DOI":"10.1063\/1.1613254","volume":"119","author":"DT Gillespie","year":"2003","unstructured":"Gillespie DT, Petzold LR (2003) Improved leap-size selection for accelerated stochastic simulation. J Chem Phys 119:8229","journal-title":"J Chem Phys"},{"key":"196-2_CR33","doi-asserted-by":"publisher","first-page":"6148","DOI":"10.1063\/1.441005","volume":"74","author":"P Hanusse","year":"1981","unstructured":"Hanusse P, Blanche A (1981) A Monte Carlo method for large reaction\u2013diffusion systems. J Chem Phys 74:6148","journal-title":"J Chem Phys"},{"key":"196-2_CR34","doi-asserted-by":"publisher","first-page":"144107","DOI":"10.1063\/1.2354085","volume":"125","author":"LA Harris","year":"2006","unstructured":"Harris LA, Clancy P (2006) A \u201cpartitioned leaping\u201d approach for multiscale modeling of chemical reaction dynamics. J Chem Phys 125:144107","journal-title":"J Chem Phys"},{"key":"196-2_CR35","doi-asserted-by":"publisher","first-page":"6959","DOI":"10.1063\/1.1505860","volume":"117","author":"EL Haseltine","year":"2002","unstructured":"Haseltine EL, Rawlings JB (2002) Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys 117:6959","journal-title":"J Chem Phys"},{"key":"196-2_CR36","doi-asserted-by":"publisher","first-page":"164115","DOI":"10.1063\/1.2062048","volume":"123","author":"EL Haseltine","year":"2005","unstructured":"Haseltine EL, Rawlings JB (2005) On the origins of approximations for stochastic chemical kinetics. J Chem Phys 123:164115","journal-title":"J Chem Phys"},{"key":"196-2_CR37","doi-asserted-by":"publisher","first-page":"2923","DOI":"10.1093\/bioinformatics\/bti431","volume":"21","author":"J Hattne","year":"2005","unstructured":"Hattne J, Fange D, Elf J (2005) Stochastic reaction\u2013diffusion simulation with MesoRD. Bioinformatics 21:2923\u20132924","journal-title":"Bioinformatics"},{"key":"196-2_CR38","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/1752-0509-6-36","volume":"6","author":"I Hepburn","year":"2012","unstructured":"Hepburn I, Chen W, Wils S, De Schutter E (2012) STEPS: efficient simulation of stochastic reaction\u2013diffusion models in realistic morphologies. BMC Syst Biol 6:36","journal-title":"BMC Syst Biol"},{"key":"196-2_CR39","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1137\/070705039","volume":"70","author":"S Isaacson","year":"2009","unstructured":"Isaacson S (2009) The reaction\u2013diffusion master equation as an asymptotic approximation of diffusion to a small target. SIAM J Appl Math 70:77\u2013111","journal-title":"SIAM J Appl Math"},{"key":"196-2_CR40","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1137\/040605060","volume":"28","author":"SA Isaacson","year":"2006","unstructured":"Isaacson SA, Peskin CS (2006) Incorporating diffusion in complex geometries into stochastic chemical kinetics simulations. SIAM J Sci Comput 28:47\u201374","journal-title":"SIAM J Sci Comput"},{"key":"196-2_CR41","doi-asserted-by":"publisher","first-page":"094101","DOI":"10.1063\/1.3310808","volume":"132","author":"KA Iyengar","year":"2010","unstructured":"Iyengar KA, Harris LA, Clancy P (2010) Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm. J Chem Phys 132:094101","journal-title":"J Chem Phys"},{"key":"196-2_CR42","doi-asserted-by":"publisher","first-page":"e1002084","DOI":"10.1371\/journal.pcbi.1002084","volume":"7","author":"M Kim","year":"2011","unstructured":"Kim M, Park AJ, Havekes R, Chay A, Guercio LA et al (2011) Colocalization of protein kinase A with adenylyl cyclase enhances protein kinase A activity during Induction of long-lasting long-term-potentiation. PLoS Comput Biol 7:e1002084","journal-title":"PLoS Comput Biol"},{"key":"196-2_CR43","doi-asserted-by":"publisher","first-page":"e1002953","DOI":"10.1371\/journal.pcbi.1002953","volume":"9","author":"B Kim","year":"2013","unstructured":"Kim B, Hawes SL, Gillani F, Wallace LJ, Blackwell KT (2013) Signaling pathways involved in striatal synaptic plasticity are sensitive to temporal pattern and exhibit spatial specificity. PLoS Comput Biol 9:e1002953","journal-title":"PLoS Comput Biol"},{"key":"196-2_CR44","doi-asserted-by":"publisher","first-page":"154103","DOI":"10.1063\/1.3572335","volume":"134","author":"W Koh","year":"2011","unstructured":"Koh W, Blackwell KT (2011) An accelerated algorithm for discrete stochastic simulation of reaction\u2013diffusion systems using gradient-based diffusion and tau-leaping. J Chem Phys 134:154103","journal-title":"J Chem Phys"},{"key":"196-2_CR45","doi-asserted-by":"publisher","first-page":"154111","DOI":"10.1063\/1.4758459","volume":"137","author":"W Koh","year":"2012","unstructured":"Koh W, Blackwell KT (2012) Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations. J Chem Phys 137:154111","journal-title":"J Chem Phys"},{"key":"196-2_CR46","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1038\/nrn2807","volume":"11","author":"JH Kotaleski","year":"2010","unstructured":"Kotaleski JH, Blackwell KT (2010) Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches. Nat Rev Neurosci 11:239\u2013251","journal-title":"Nat Rev Neurosci"},{"key":"196-2_CR47","doi-asserted-by":"publisher","first-page":"094104","DOI":"10.1063\/1.3074302","volume":"130","author":"S Lampoudi","year":"2009","unstructured":"Lampoudi S, Gillespie DT, Petzold LR (2009) The multinomial simulation algorithm for discrete stochastic simulation of reaction\u2013diffusion systems. J Chem Phys 130:094104","journal-title":"J Chem Phys"},{"key":"196-2_CR48","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1093\/bioinformatics\/17.6.575","volume":"17","author":"N Le Novere","year":"2001","unstructured":"Le Novere N, Shimizu TS (2001) STOCHSIM: modelling of stochastic biomolecular processes. Bioinformatics 17:575\u2013576","journal-title":"Bioinformatics"},{"key":"196-2_CR49","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1016\/j.febslet.2005.02.009","volume":"579","author":"C Lemerle","year":"2005","unstructured":"Lemerle C, Di Ventura B, Serrano L (2005) Space as the final frontier in stochastic simulations of biological systems. FEBS Lett 579:1789\u20131794","journal-title":"FEBS Lett"},{"key":"196-2_CR50","doi-asserted-by":"publisher","first-page":"104101","DOI":"10.1063\/1.2771548","volume":"127","author":"TT Marquez-Lago","year":"2007","unstructured":"Marquez-Lago TT, Burrage K (2007) Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics. J Chem Phys 127:104101","journal-title":"J Chem Phys"},{"key":"196-2_CR51","doi-asserted-by":"publisher","first-page":"044104","DOI":"10.1063\/1.2145882","volume":"124","author":"B Munsky","year":"2006","unstructured":"Munsky B, Khammash M (2006) The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys 124:044104","journal-title":"J Chem Phys"},{"key":"196-2_CR52","doi-asserted-by":"publisher","first-page":"e11725","DOI":"10.1371\/journal.pone.0011725","volume":"5","author":"RF Oliveira","year":"2010","unstructured":"Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W et al (2010) The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PLoS One 5:e11725","journal-title":"PLoS One"},{"key":"196-2_CR53","doi-asserted-by":"publisher","first-page":"e1002383","DOI":"10.1371\/journal.pcbi.1002383","volume":"8","author":"RF Oliveira","year":"2012","unstructured":"Oliveira RF, Kim M, Blackwell KT (2012) Subcellular location of PKA controls striatal plasticity: stochastic simulations in spiny dendrites. PLoS Comput Biol 8:e1002383","journal-title":"PLoS Comput Biol"},{"key":"196-2_CR54","doi-asserted-by":"crossref","unstructured":"Plimpton SJ, Sleproy A (2003) ChemCell: a particle-based model of protein chemistry and diffusion in microbial cells. Sandia National Laboratories technical report 2003\u201345","DOI":"10.2172\/918231"},{"key":"196-2_CR55","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1142\/S0219720005001132","volume":"03","author":"S Ramsey","year":"2005","unstructured":"Ramsey S, Orrell D, Bolouri H (2005) Dizzy: Stochastic simulation of large-scale genetic regulatory networks. J Bioinform Comput Biol 03:415\u2013436","journal-title":"J Bioinform Comput Biol"},{"key":"196-2_CR56","doi-asserted-by":"publisher","first-page":"4999","DOI":"10.1063\/1.1545446","volume":"118","author":"CV Rao","year":"2003","unstructured":"Rao CV, Arkin AP (2003) Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. J Chem Phys 118:4999","journal-title":"J Chem Phys"},{"key":"196-2_CR57","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/nature01258","volume":"420","author":"CV Rao","year":"2002","unstructured":"Rao CV, Wolf DM, Arkin AP (2002) Control, exploitation and tolerance of intracellular noise. Nature 420:231\u2013237","journal-title":"Nature"},{"key":"196-2_CR58","doi-asserted-by":"publisher","first-page":"12784","DOI":"10.1063\/1.1627296","volume":"119","author":"M Rathinam","year":"2003","unstructured":"Rathinam M, Petzold LR, Cao Y, Gillespie DT (2003) Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method. J Chem Phys 119:12784","journal-title":"J Chem Phys"},{"key":"196-2_CR59","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1002\/wsbm.165","volume":"4","author":"DC Resasco","year":"2012","unstructured":"Resasco DC, Gao F, Morgan F, Novak IL, Schaff JC et al (2012) Virtual cell: computational tools for modeling in cell biology. Wiley Interdiscip Rev Syst Biol Med 4:129\u2013140","journal-title":"Wiley Interdiscip Rev Syst Biol Med"},{"key":"196-2_CR60","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1093\/bioinformatics\/btl271","volume":"22","author":"JV Rodriguez","year":"2006","unstructured":"Rodriguez JV, Kaandorp JA, Dobrzynski M, Blom JG (2006) Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. Bioinformatics 22:1895\u20131901","journal-title":"Bioinformatics"},{"key":"196-2_CR61","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.cplett.2007.11.055","volume":"451","author":"D Rossinelli","year":"2008","unstructured":"Rossinelli D, Bayati B, Koumoutsakos P (2008) Accelerated stochastic and hybrid methods for spatial simulations of reaction\u2013diffusion systems. Chem Phys Lett 451:136\u2013140","journal-title":"Chem Phys Lett"},{"key":"196-2_CR62","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.copbio.2008.06.011","volume":"19","author":"V Shahrezaei","year":"2008","unstructured":"Shahrezaei V, Swain PS (2008) The stochastic nature of biochemical networks. Curr Opin Biotechnol 19:369\u2013374","journal-title":"Curr Opin Biotechnol"},{"key":"196-2_CR63","doi-asserted-by":"publisher","first-page":"205101","DOI":"10.1063\/1.2919546","volume":"128","author":"A Slepoy","year":"2008","unstructured":"Slepoy A, Thompson AP, Plimpton SJ (2008) A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks. J Chem Phys 128:205101","journal-title":"J Chem Phys"},{"key":"196-2_CR64","doi-asserted-by":"publisher","first-page":"154109","DOI":"10.1063\/1.3580292","volume":"134","author":"R Srivastava","year":"2011","unstructured":"Srivastava R, Haseltine EL, Mastny E, Rawlings JB (2011) The stochastic quasi-steady-state assumption: reducing the model but not the noise. J Chem Phys 134:154109","journal-title":"J Chem Phys"},{"key":"196-2_CR65","first-page":"87","volume-title":"Computational neuroscience: realistic modeling for experimentalists","author":"JR Stiles","year":"2001","unstructured":"Stiles JR, Bartol TM Jr (2001) Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In: De Schutter E (ed) Computational neuroscience: realistic modeling for experimentalists. CRC Press, Boca Raton, pp 87\u2013127"},{"key":"196-2_CR66","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1006\/jcph.1996.0168","volume":"127","author":"AB Stundzia","year":"1996","unstructured":"Stundzia AB, Lumsden CJ (1996) Stochastic simulation of coupled reaction\u2013diffusion processes. J Comput Phys 127:196\u2013207","journal-title":"J Comput Phys"},{"key":"196-2_CR67","doi-asserted-by":"publisher","first-page":"1783","DOI":"10.1016\/j.febslet.2005.01.072","volume":"579","author":"K Takahashi","year":"2005","unstructured":"Takahashi K, Arjunan SNV, Tomita M (2005) Space in systems biology of signaling pathways \u2013 towards intracellular molecular crowding in silico. FEBS Lett 579:1783\u20131788","journal-title":"FEBS Lett"},{"key":"196-2_CR68","doi-asserted-by":"publisher","first-page":"10356","DOI":"10.1063\/1.1810475","volume":"121","author":"T Tian","year":"2004","unstructured":"Tian T, Burrage K (2004) Binomial leap methods for simulating stochastic chemical kinetics. J Chem Phys 121:10356","journal-title":"J Chem Phys"},{"key":"196-2_CR69","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/1752-0509-4-24","volume":"4","author":"D Tolle","year":"2010","unstructured":"Tolle D, Le Novere N (2010) Meredys, a multi-compartment reaction\u2013diffusion simulator using multistate realistic molecular complexes. BMC Syst Biol 4:24","journal-title":"BMC Syst Biol"},{"key":"196-2_CR70","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/j.compbiolchem.2004.05.001","volume":"28","author":"TE Turner","year":"2004","unstructured":"Turner TE, Schnell S, Burrage K (2004) Stochastic approaches for modelling in vivo reactions. Comput Biol Chem 28:165\u2013178","journal-title":"Comput Biol Chem"},{"key":"196-2_CR71","doi-asserted-by":"publisher","first-page":"e33384","DOI":"10.1371\/journal.pone.0033384","volume":"7","author":"M Vigelius","year":"2012","unstructured":"Vigelius M, Meyer B (2012) Multi-dimensional, mesoscopic Monte Carlo simulations of inhomogeneous reaction-drift-diffusion systems on graphics-processing units. PLoS One 7:e33384","journal-title":"PLoS One"},{"key":"196-2_CR72","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1093\/bioinformatics\/btq622","volume":"27","author":"M Vigelius","year":"2011","unstructured":"Vigelius M, Lane A, Meyer B (2011) Accelerating reaction\u2013diffusion simulations with general-purpose graphics processing units. Bioinformatics 27:288\u2013290","journal-title":"Bioinformatics"}],"container-title":["Encyclopedia of Computational Neuroscience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4614-7320-6_196-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,8]],"date-time":"2023-02-08T03:03:16Z","timestamp":1675825396000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-4614-7320-6_196-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014]]},"ISBN":["9781461473206"],"references-count":72,"URL":"https:\/\/doi.org\/10.1007\/978-1-4614-7320-6_196-2","relation":{},"subject":[],"published":{"date-parts":[[2014]]},"assertion":[{"value":"15 April 2014, 10:07:34","order":1,"name":"received","label":"Received","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"15 April 2014, 10:07:34","order":2,"name":"accepted","label":"Accepted","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"19 May 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}