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L. Dematte, "Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 3, pp. 655667, MayJune, 2012.  
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@article{ 10.1109/TCBB.2011.106, author = {L. Dematte}, title = {Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {9}, number = {3}, issn = {15455963}, year = {2012}, pages = {655667}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.106}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
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TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations IS  3 SN  15455963 SP655 EP667 EPD  655667 A1  L. Dematte, PY  2012 KW  stochastic processes KW  biochemistry KW  biodiffusion KW  Brownian motion KW  chemical reactions KW  fluctuations KW  graphics processing units KW  physiological models KW  computational demanding steps KW  Smoldyn KW  graphics processing units KW  massively parallel Brownian dynamics simulation KW  biochemical systems KW  single molecule movement KW  localized fluctuations KW  diffusion KW  spatial models KW  stochastic methods KW  high spatial resolution KW  parallel simulation algorithms KW  stochastic simulation KW  chemical reactions KW  GPU KW  Graphics processing unit KW  Biological system modeling KW  Computational modeling KW  Solid modeling KW  Adaptation models KW  Stochastic processes KW  Surface treatment KW  GPU. KW  Parallel KW  reactiondiffusion KW  particles KW  Brownian Dynamics VL  9 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] D. Fusco, N. Accornero, B. Lavoie, S. Shenoy, J. Blanchard, R. Singer, and E. Bertrand, "Single Mrna Molecules Demonstrate Probabilistic Movement in Living Mammallian Cells," Current Biology, vol. 13, pp. 161167, 2003.
[2] P. Takizawa, A. Sil, J. Swedlow, I. Herskowitz, and R.V. RD, "ActinDependent Localization of an RNA Encoding a CellFate Determinant in Yeast," Nature, vol. 389, no. 6646, pp. 9093, 1997.
[3] W. Driever and C. NüssleinVolhard, "A Gradient of Bicoid Protein in Drosophila Embryos," Cell, vol. 54, no. 1, pp. 8393, July 1988.
[4] T. Shimizu, S.V. Aksenov, and D. Bray, "A Spatially Extended Stochastic Model of the Bacterial Chemotaxis Signalling Pathway," J. Molecular Biology, vol. 329, pp. 291309, 2003.
[5] E.R. Kandel, "The Molecular Biology of Memory Storage: A Dialogue between Genes and Synapses," Science, vol. 294, pp. 10301038, 2001.
[6] A. CsikászNagy, B. Gyorffy, W. Alt, J. Tyson, and B. Novák, "Spatial Controls for Growth Zone Formation during the Fission Yeast Cell Cycle," Yeast, vol. 25, no. 1, pp. 5969, Jan. 2008.
[7] D. Gillespie, "Exact Stochastic Simulation of Coupled Chemical Reactions," J. Physical Chemistry, vol. 81, no. 25, pp. 23402361, Dec. 1977.
[8] P. Lecca, L. Dematté, and C. Priami, "Modeling and Simulating ReactionDiffusion Systems with StateDependent Diffusion Coefficients," Proc. Int'l Conf. Bioinformatics and Biomedicine, vol. 35, 2008.
[9] P. Lecca and L. Dematté, "Stochastic Simulation of ReactionDiffusion Systems," Int. J. Medical and Biological Eng., vol. 1, no. 4, pp. 211231, Dec. 2008.
[10] J. Elf and M. Ehrenberg, "Spontaneous Separation of BiStable Biochemical Systems into Spatial Domains of Opposite Phases," Proc. IEE Systems Biology, vol. 1, no. 2, pp. 230236, Dec. 2004.
[11] L. Dematté and T. Mazza, "On Parallel Stochastic Simulation of Diffusive Systems," Proc. Sixth Int'l Conf. Computational Methods in Systems Biology (CMSB '08), vol. 5307, pp. 191210, 2008.
[12] K. Takahashi, S. Arjunan, and M. Tomita, "Space in Systems Biology of Signaling Pathways—Towards Intracellular Molecular Crowding in Silico," FEBS Letters, vol. 579, no. 8, pp. 17831788, 2005.
[13] A. Fick, "Über Diffusion," Poggendorff's Annalen der Physik und Chemie, vol. 94, pp. 5986, 1855.
[14] M. von Smoluchowski, "Versuch Einer Mathematischen Theorie Der Koagulationskinetik Kolloider Lösungen," J. Physical Chemistry, vol. 92, pp. 129168, 1917.
[15] K. Lipkow and D.J. Odde, "Model for Protein Concentration Gradients in the Cytoplasm," Cellular and Moleculer Bioeng., vol. 1, pp. 8492, 2008.
[16] K. Lipkow, "Changing Cellular Location of CheZ Predicted by Molecular Simulations," PLoS Computational Biology, vol. 2, pp. 03010310, 2006.
[17] S.S. Andrews, "Serial Rebinding of Ligands to Clustered Receptors as Exemplified by Bacterial Chemotaxis," Physical Biology, vol. 2, pp. 111122, 2005.
[18] K. Lipkow, S.S. Andrews, and D. Bray, "Simulated Diffusion of Phosphorylated CheY through the Cytoplasm of Escherichia Coli," J. Bacteriology, vol. 187, pp. 4553, 2005.
[19] S.S. Andrews and D. Bray, "Stochastic Simulation of Chemical Reactions with Spatial Resolution and Single Molecule Detail," Physical Biology, vol. 1, nos. 34, pp. 137151, 2004.
[20] H. Sutter and J. Larus, "Software and the Concurrency Revolution," Queue, vol. 3, no. 7, pp. 5462, 2005.
[21] E. Lindholm, J. Nickolls, S. Oberman, and J. Montrym, "Nvidia Tesla: A Unified Graphics and Computing Architecture," IEEE Micro, vol. 28, no. 2, pp. 3955, Mar./Apr. 2008.
[22] J. Nickolls, I. Buck, and M. Garland, "Scalable Parallel Programming with Cuda," Queue—GPU Computing , vol. 6, no. 2, pp. 4053, 2008.
[23] D. Prandi and L. Dematté, "Gpu Computing for Systems Biology," Briefings in Bioinformatics, vol. 11, no. 3, pp. 323333, 2010.
[24] S. Andrews, N. Addy, R. Brent, and A. Arkin, "Detailed Simulations of Cell Biology with Smoldyn 2.1," PLoS Computational Biology, vol. 6, no. 3, pp. e1000705, 2010.
[25] L. Dematté, "Parallel ParticleBased Reaction Diffusion: A gpu Implementation," Proc. Ninth Int'l Workshop Parallel and Distributed Methods in Verification, and Second Int'l Workshop High Performance Computational Systems Biology (PDMCHIBI '10), 2010.
[26] S.L. Grand, "BroadPhase Collision Detection with Cuda," GPU Gems 3, H. Nguyen, ed., ch. 32, AddisonWesley, 2007.
[27] S. Green, "Cuda Particles," NVIDIA Whitepaper, 2008.
[28] M. Matsumoto and T. Nishimura, "Mersenne Twister: A 623Dimensionally Equidistributed Uniform PseudoRandom Number Generator," ACM Trans. Modeling and Computer Simulation, vol. 8, no. 1, pp. 330, 1998.
[29] V. Podlozhnyuk, "Parallel Mersenne Twister," NVIDIA Whitepaper, 2007.
[30] G.E.P. Box and M.E. Muller, "A Note on the Generation of Random Normal Deviates," Annals of Math. Statistics, vol. 29, no. 2, pp. 610611, 1958.
[31] S.S. Andrews, "Accurate ParticleBased Simulation of Adsorption, Desorption, and Partial Transmission," Physical Biology, vol. 6, no. 4, p. 046015, 2009.
[32] N. Bell, Y. Yu, and P.J. Mucha, "ParticleBased Simulation of Granular Materials," Proc. ACM SIGGRAPH/Eurographics Symp. Computer Animation, p. 7786, 2005.
[33] S.S. Andrews, "Accurate ParticleBased Simulation of Adsorption, Desorption, and Partial Transmission," Physical Biology, vol. 6, no. 4 p. 046015, 2009.
[34] S. Sengupta, M. Harris, Y. Zhang, and J.D. Owens, "Scan Primitives for GPU Computing," GH '07: Proc. 22nd ACM SIGGRAPH/EUROGRAPHICS Symp. Graphics Hardware, pp. 97106. 2007,
[35] J.E. Stone, J.C. Phillips, P.L. Freddolino, D.J. Hardy, L.G. Trabuco, and K. Schulten, "Accelerating Molecular Modeling Applications with Graphics Processors," J. Computational Chemistry, vol. 16, pp. 26182640, 2007.
[36] W. Liu, B. Schmidt, G. Vossa, and W. MüllerWittiga, "Accelerating Molecular Dynamics Simulations Using Graphics Processing Units with Cuda," Computer Physics Comm., vol. 179, no. 9, pp. 634641, Nov. 2008.
[37] J.A. Anderson and A. Travesset, "Molecular Dynamics on Graphic Processing Units: Hoomd to the Rescue," Computing in Science and Eng., vol. 10, no. 6, pp. 610, 2008.
[38] K. Takahashi, "An Exact Brownian Dynamics Method for Cell Simulation," Proc. Sixth Int'l Conf. Computational Methods in Systems Biology (CMSB '08), vol. 5307, pp. 56, 2008.
[39] J.S. van Zon and P.R. Ten Wolde, "Green'sFunction Reaction Dynamics: A ParticleBased Approach for Simulating Biochemical Networks in Time and Space," J. Chemical Physics, vol. 123, no. 23, p. 234910, Dec. 2005.
[40] M. Januszewski and M. Kostur, "Accelerating Numerical Solution of Stochastic Differential Equations with Cuda," Computer Physics Comm., vol. 181, pp. 183188, 2010.
[41] M.J. Harris, G. Coombe, T. Scheuermann, and A. Lastra, "PhysicallyBased Visual Simulation on Graphics Hardware," Proc. ACM SIGGRAPH/EUROGRAPHICS Conf. Graphics Hardware (HWWS '02), pp. 109118, 2002.
[42] E. Roberts, J.E. Stone, L. Sepulveda, W.M.W. Hwu, and Z. LutheySchulten, "Long TimeScale Simulations of in Vivo Diffusion Using GPU Hardware," Proc. IEEE Int'l Symp. Parallel and Distributed Processing, pp. 18. 2009,
[43] S. Rybacki, J. Himmelspach, and A.M. Uhrmacher, "Experiments with Single Core, MultiCore, and GPU Based Computation of Cellular Automata," Proc. First Int'l Conf. Advances in System Simulation (SIMUL '09), pp. 6267, 2009.
[44] H. Li and L. Petzold, "Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit," Int'l J. High Performance Computing Applications, vol. 24, no. 2, pp. 107116, 2010.
[45] C. Dittamo and D. Cangelosi, "Optimized Parallel Implementation of Gillespie's First Reaction Method on Graphics Processing Units," Proc. Int'l Conf. Computer Modeling and Simulation (ICMMS '09), pp. 156161, 2009.
[46] S. Scarl, "Implications of the Turing Completeness of ReactionDiffusion Models, Informed by Gpgpu Simulations on An Xbox 360: Cardiac Arrhythmias, ReEntry and the Halting Problem," Computational Biology and Chemistry, vol. 33, no. 4, pp. 253260, Aug. 2009.
[47] E. Merelli, G. Armano, N. Cannata, F. Corradini, M. d'Inverno, A. Doms, P. Lord, A. Martin, L. Milanesi, S. Möller, M. Schroeder, and M. Luck, "Agents in Bioinformatics, Computational and Systems Biology," Proc. Briefings in Bioinformatics, pp. 4559, 2007.
[48] R.D. Chiara, U. Erra, and V. Scarano, "Massive Simulation Using gpu of a Distributed Behavioral Model of a Flock with Obstacle Avoidance," Proc. Vision, Modeling, and Visualization Conf., pp. 233240, 2004.
[49] K.S. Perumalla and B.G. Aaby, "Data Parallel Execution Challenges and Runtime Performance of Agent Simulations on Gpus," Proc. Spring Simulation Multiconf. (SpringSim '08) pp. 116123, 2008.
[50] P. Richmond, D. Walker, S. Coakley, and D.M. Romano, "High Performance Cellular Level AgentBased Simulation with Flame for the Gpu," Briefings in Bioinformatics, vol. 11, no. 3, pp. 334347, 2010.
[51] R.M. D'Souza, S. Marino, and D. Kirschner, "DataParallel Algorithms for AgentBased Model Simulation of Tuberculosis on Graphics Processing Units," Proc. Spring Simulation Multiconf. (SpringSim '09), 2009.