Long time-scale simulations of in vivo diffusion using GPU hardware

IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium

Volumn , Issue , 2009, Pages

  Roberts, Elijah ^a   Stone, John E ^b   Sepúlveda, Leonardo ^a   Hwu, Wen Mei W ^c   Luthey Schulten, Zaida ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c United States of America   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHITECTURAL CONSTRAINTS; BIOCHEMICAL PATHWAY; CALCULATION CAPABILITY; CELLULAR CONDITIONS; CO-PROCESSORS; CORE SET; DIFFUSION OPERATORS; GRAPHICS PROCESSING UNIT; IN-VIVO; MATHEMATICAL CALCULATIONS; PARALLEL CALCULATION; REACTION-DIFFUSION MODELS; THREE-DIMENSIONAL MODEL; TIME SIMULATIONS; TIME-SCALE SIMULATION;

DIFFUSION; DISTRIBUTED PARAMETER NETWORKS; MATHEMATICAL OPERATORS; PROGRAM PROCESSORS; SIMULATORS; THREE DIMENSIONAL;

COMPUTER GRAPHICS EQUIPMENT;

EID: 70449877789     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2009.5160930     Document Type: Conference Paper

References (18)

1. D. Banks and C. Fradin. Anomalous diffusion of proteins due to molecular crowding. Biophys. J., 89(5):2960-2971, 2005.
2. B. Chopard and M. Droz. Cellular automata modeling of physical systems. Cambridge University Press, Cambridge, UK, 1998.
3. J. Dix, E. Hom, and A. Verkman. Fluorescence correlation spectroscopy simulations of photophysical phenomena and molecular interactions: a molecular dynamics/Monte Carlo approach. J. Phys. Chem. B, 110(4):1896, 2006.
4. J. Dix and A. Verkman. Crowding effects on diffusion in solutions and cells. Ann. Rev. Biophys., 37:247-263, 2008.
5. R. J. Ellis. Macromolecular crowding: obvious but underappreciated. Trends Biochem. Sci., 26(10):597-604, Oct 2001.
6. I. Golding and E. Cox. Physical nature of bacterial cytoplasm. Phys. Rev. Lett., 96(9):98102, 2006.
7. T. Karapiperis and B. Blankleider. Cellular automaton model of reaction-transport processes. Physica D, 78(1-2):30-64, 1994.
8. M. Konopka, I. Shkel, S. Cayley, M. Record, and J. Weisshaar. Crowding and confinement effects on protein diffusion in vivo. J. Bacteriol., 188(17):6115-6123, 2006.
9. P. L'Ecuyer and R. Simard. TestU01: A C library for empirical testing of random number generators. ACM Trans. Math. Software, 33(4):22, 2007.
10. J. Ortiz, F. Förster, J. Kürner, A. Linaroudis, and W. Baumeister. Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. J. Struct. Biol., 156(2):334-341, 2006.
11. W. Press. Numerical recipes: the art of scientific computing. Cambridge University Press, 2007.
12. D. Ridgway, G. Broderick, A. Lopez-Campistrous, M. Ru'aini, P. Winter, M. Hamilton, P. Boulanger, A. Kovalenko, and M. Ellison. Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys. J., 17(5):493-498, 2008.
13. M. Saxton. A biological interpretation of transient anomalous subdiffusion. I. Qualitative model. Biophys. J., 92(4):1178, 2007.
14. T. Toffoli and N. Margolus. Cellular automata machines: a new environment for modeling. The MIT Press, Cambridge, MA, 1987.
15. V. Volkov and J. Demmel. Benchmarking GPUs to tune dense linear algebra. In Proceedings of the 2008 ACM/IEEE conference on Supercomputing. IEEE Press Piscataway, NJ, USA, 2008.
16. M. Weiss, M. Elsner, F. Kartberg, and T. Nilsson. Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells. Biophys. J., 87(5):3518-3524, 2004.
17. S. Wolfram. Cellular automata and complexity: collected papers. Westview Press, Boulder, CO, 1994.
18. H. Zhou, G. Rivas, and A. Minton. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Ann. Rev. Biophys., 37(1), 2008.