Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces

SIAM Journal on Scientific Computing

Volumn 30, Issue 6, 2008, Pages 3126-3149

  Kerr, Rex A ^a,b   Bartol, Thomas M ^b,c   Kaminsky, Boris ^d   Dittrich, Markus ^d   Chang, Jen Chien Jack ^d   Baden, Scott B ^e   Sejnowski, Terrence J ^f   Stiles, Joel R ^d,g  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d PITTSBURGH SUPERCOMPUTING CENTER   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^g Carnegie Mellon University   (United States)

Author keywords

Cell simulation; Concentration clamp; DReAMM; MCell; Microscopic reversibility; Monte carlo; Reaction diffusion

Indexed keywords

BIOINFORMATICS; BIOLOGICAL SYSTEMS; COST EFFECTIVENESS; DIFFUSION IN LIQUIDS; INTELLIGENT SYSTEMS; MONTE CARLO METHODS; STOCHASTIC SYSTEMS;

BIOLOGICAL REACTION; CELL SIMULATION; CONCENTRATION CLAMP; CONTINUUM METHOD; DREAMM; MCELL; MICROSCOPIC REVERSIBILITY; MONTE CARLO; MONTE CARLO SIMULATION METHODS; REACTION-DIFFUSION;

SURFACE REACTIONS;

EID: 55149086309     PISSN: 10648275     EISSN: None     Source Type: Journal    
DOI: 10.1137/070692017     Document Type: Article

References (23)

1. S. S. ANDREWS AND D. BRAY, Stochastic simulation of chemical reactions with spatial resolution and single molecule detail, Phys. Biol., 1 (2004), pp. 137-151.
2. L. ANGLISTER, J. R. STILES, AND N. M. SALPETER, Acetylcholinesterase density and turnover number at frog neuromuscular junctions, with modeling of their role in synaptic function, Neuron, 12 (1994), pp. 783-794.
3. A. R. ATILGAN, S. R. DURRELL, R. L. JERNIGAN, M. C. DERNIREL, O. KESKIN, AND I. BAHAR, Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys. J., 80 (2001), pp. 505-515.
4. T. M. BARTOL, JR., B. R. LAND, E. E. SALPETER, AND M. M. SALPETER, Monte Carlo simulation of MEPC generation in the vertebrate neuromuscular junction, Biophys. J., 59 (1991), pp. 1290-1307.
5. A. E. CARDENAS, R. D. COALSON, AND M. G. KURNIKOVA, Three-dimensional Poisson-Nernst-Planck theory studies: Influence of membrane electrostatics on gramicidin A channel conductance, Biophys. J., 79 (2000), pp. 80-93.
6. P. CICOTTI AND S. B. BADEN, Asynchronous cellular microphysiology simulation, in Proceedings of the 12th Annual SIAM Conference on Parallel Processing for Scientific Computing (San Francisco, CA, 2006), SIAM, Philadelphia, 2006.
7. J. S. COGGAN, T. M. BARTOL, E. ESQUENAZI, J. R. STILES, S. LAMONT, M. E. MARTONE, D. K. BERG, M. H. ELLISMAN, AND T. J. SEJNOWSKI, Evidence for ectopic neurotransmission at a neuronal synapse, Science, 309 (2005), pp. 446-451.
8. A. KOLINSKI, L. JAROSZEWSKI, P. ROTKIEWICZ, AND J. SKOLNICK, An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side group centers of mass, J. Phys. Chem. B, 102 (1998), pp. 4628-4637.
9. G. MARSAGLIA, Choosing a point from the surface of a sphere, Ann. Math. Statist., 43 (1972), pp. 645-646.
10. G. MARSAGLIA AND W. W. TSANG, The ziggurat method for generating random variables, J. Statist. Softw., 5 (2000), pp. 1-7.
11. K. ODA, Y. MATSUOKA, A. FUNAHASHI, AND H. KITANO, A comprehensive pathway map of epidermal growth factor receptor signaling, Mol. Syst. Biol., 1 (2005), article 2005.0010.
12. T. OPPLESTRUP, V. V. BULATOV, G. H. GILMER, M. H. KALOS, AND B. SADIGH, First-passage Monte Carlo algorithm: Diffusion without all the hops, Phys. Rev. Lett., 97 (2006), article 230602.
13. S. J. PLIMPTON AND A. SLEPOY, Microbial cell modeling via reacting diffusive particles, J. Phys. Conf. Ser., 16 (2005), pp. 305-309.
14. W. ROCCHIA, E. ALEXOV, AND B. HONIG, Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalient ions, J. Phys. Chem. B, 105 (2001), pp. 6507-6514.
15. I. F. SBALZARINI, J. H. WALTHER, M. BERGDORF, S. E. HIEBER, E. M. KOTSALIS, AND P. KOUMOUTSAKOS, PPM: A highly efficient parallel particle mesh library for the simulation of continuum systems, J. Comput. Phys., 215 (2006), pp. 566-588.
16. I. F. SBALZARINI, A. HAYER, A. HELENIUS, AND P. KOUMOUTSAKOS, Simulations of (an)isotropic diffusion on curved biological surfaces, Biophys. J., 90 (2006), pp. 878-885.
17. P. SCHWARTZ, D. ADALSTEINSSON, P. COLELLA, A. P. ARKIN, AND M. ONSUM, Numerical computation of diffusion on a surface, Proc. Natl. Acad. Sci. USA, 102 (2005), pp. 11151-11156.
18. J. R. STILES, D. VAN HELDEN, T. M. BARTOL, JR., E. E. SALPETER, AND M. M. SALPETER, Miniature endplate current rise times < 100 μs from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle, Proc. Natl. Acad. Sci. USA, 93 (1996), pp. 5747-5752.
19. J. R. STILES, I. V. KOVYAZINA, E. E. SALPETER, AND M. M. SALPETER, The temperature sensitivity of miniature endplate currents is mostly governed by channel gating: Evidence from optimized recordings and Monte Carlo simulations, Biophys. J., 77 (1999), pp. 1177-1187.
20. J. R. STILES AND T. M. BARTOL, Monte Carlo methods for simulating realistic synaptic microphysiology using MCell, in Computational Neuroscience: Realistic Modeling for Experimentalists, E. DeSchutter, ed., CRC Press, Boca Raton, FL, 2001, pp. 87-127.
21. J. R. STILES, T. M. BARTOL, M. M. SALPETER, E. E. SALPETER, AND T. J. SEJNOWSKI, Synaptic variability: New insights from reconstructions and Monte Carlo simulations with MCell, in Synapses, W. M. Cowan, C. F. Stevens, and T. C. Südhof, eds., The Johns Hopkins University Press, Baltimore, MD, 2001, pp. 681-731.
22. J. R. STILES, W. C. FORD, J. M. PATTILLO, T. E. DEERINCK, M. H. ELLISMAN, T. M. BARTOL, AND T. J. SEJNOWSKI, Spatially realistic computational physiology: Past, present, and future, in Parallel Computing: Software Technology, Algorithms, Architectures & Applications, G. Joubert, ed., Elsevier, Amsterdam, 2004, pp. 685-694.
23. E. TAJKHORSHID, A. AKSIMENTIEV, I. BALABIN, M. GAO, B. ISRALEWITZ, J. C. PHILLIPS, F. ZHU, AND K. SCHULTEN, Large scale simulation of protein mechanics and function, in Advances in Protein Chemistry, Vol. 66, F. M. Richards, D. S. Eisenberg, and J. Kuriyan, eds., Elsevier Academic Press, New York, 2003, pp. 195-247.