{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T12:26:55Z","timestamp":1792672015973,"version":"4.5.0"},"reference-count":23,"publisher":"Society for Industrial & Applied Mathematics (SIAM)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["SIAM J. Sci. Comput."],"published-print":{"date-parts":[[2008,1]]},"abstract":"<jats:p>Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods.<\/jats:p>","DOI":"10.1137\/070692017","type":"journal-article","created":{"date-parts":[[2008,10,14]],"date-time":"2008-10-14T13:38:58Z","timestamp":1223991538000},"page":"3126-3149","source":"Crossref","is-referenced-by-count":328,"title":["Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces"],"prefix":"10.1137","volume":"30","author":[{"given":"Rex A.","family":"Kerr","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas M.","family":"Bartol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boris","family":"Kaminsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Dittrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jen-Chien Jack","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott B.","family":"Baden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terrence J.","family":"Sejnowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel R.","family":"Stiles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"351","published-online":{"date-parts":[[2008,10,13]]},"reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1088\/1478-3967\/1\/3\/001"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/0896-6273(94)90331-X"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(01)76033-X"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(91)82344-X"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(00)76275-8"},{"key":"R6","unstructured":"P. Cicotti and S. B. Baden,\n                      Asynchronous cellular microphysiology simulation\n                      , in Proceedings of the 12th Annual SIAM Conference on Parallel Processing for Scientific Computing (San Francisco, CA, 2006), SIAM, Philadelphia, 2006."},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1126\/science.1108239"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1021\/jp973371j"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1214\/aoms\/1177692644"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v005.i08"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1038\/msb4100014"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.97.230602"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1088\/1742-6596\/16\/1\/042"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1021\/jp010454y"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2005.11.017"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.105.073809"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0504953102"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.93.12.5747"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(99)76969-9"},{"key":"R20","doi-asserted-by":"crossref","unstructured":"J. R. Stiles and T. M. Bartol,\n                      Monte Carlo methods for simulating realistic synaptic microphysiology using MCell\n                      , in Computational Neuroscience: Realistic Modeling for Experimentalists, E. DeSchutter, ed., CRC Press, Boca Raton, FL, 2001, pp. 87\u2013127.","DOI":"10.1201\/9781420039290.ch4"},{"key":"R21","unstructured":"J. R. Stiles, T. M. Bartol, M. M. Salpeter, E. E. Salpeter, and T. J. Sejnowski,\n                      Synaptic variability: New insights from reconstructions and Monte Carlo simulations with MCell\n                      , in Synapses, W. M. Cowan, C. F. Stevens, and T. C. S\u00fcdhof, eds., The Johns Hopkins University Press, Baltimore, MD, 2001, pp. 681\u2013731."},{"key":"R22","doi-asserted-by":"crossref","unstructured":"J. R. Stiles, W. C. Ford, J. M. Pattillo, T. E. Deerinck, M. H. Ellisman, T. M. Bartol, and T. J. Sejnowski,\n                      Spatially realistic computational physiology: Past, present, and future\n                      , in Parallel Computing: Software Technology, Algorithms, Architectures & Applications, G. Joubert, ed., Elsevier, Amsterdam, 2004, pp. 685\u2013694.","DOI":"10.1016\/S0927-5452(04)80085-6"},{"key":"R23","doi-asserted-by":"crossref","unstructured":"E. Tajkhorshid, A. Aksimentiev, I. Balabin, M. Gao, B. Isralewitz, J. C. Phillips, F. Zhu, and K. Schulten,\n                      Large scale simulation of protein mechanics and function\n                      , in Advances in Protein Chemistry, Vol. 66, F. M. Richards, D. S. Eisenberg, and J. Kuriyan, eds., Elsevier Academic Press, New York, 2003, pp. 195\u2013247.","DOI":"10.1016\/S0065-3233(03)66006-7"}],"container-title":["SIAM Journal on Scientific Computing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/epubs.siam.org\/doi\/pdf\/10.1137\/070692017","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T17:54:21Z","timestamp":1787334861000},"score":1,"resource":{"primary":{"URL":"https:\/\/epubs.siam.org\/doi\/10.1137\/070692017"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,1]]},"references-count":23,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2008,1]]}},"alternative-id":["10.1137\/070692017"],"URL":"https:\/\/doi.org\/10.1137\/070692017","relation":{},"ISSN":["1064-8275","1095-7197"],"issn-type":[{"value":"1064-8275","type":"print"},{"value":"1095-7197","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1]]}}}