A mesoscopic simulation approach for modeling intracellular reactions

Journal of Statistical Physics

Volumn 128, Issue 1-2, 2007, Pages 139-164

  Grima, Ramon ^a   Schnell, Santiago ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Biological processes in organized media; Macromolecular crowding; Mesoscopic simulation; Modeling intracellular reactions

Indexed keywords

EID: 34249876893     PISSN: 00224715     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10955-006-9202-z     Document Type: Conference Paper

References (73)

1. A. R. Altenberger and M. Tirrell, J. Chem. Phys. 80: 2208 (1984).
2. S. S. Andrews and D. Bray Phys. Biol. 1: 137 (2004).
3. G. K. Batchelor J. Fluid Mech. 74: 1 (1976).
4. C. W. J. Beenakker and P. Mazur Physica A120: 388 (1983).
5. P. Bernado, J. G. de la Torre and M. Pons J. Mol. Recognit. 17: 397 (2004).
6. H. Berry Biophys. J. 83: 1891 (2002).
7. D. Bray Annu. Rev. Biophys. Biomol. Struct. 27: 59 (1998).
8. F. Brochard and P.-G. DeGennes, Macromolecules 10: 1157 (1977).
9. D. F. Calef and J. M. Deutch, Ann. Rev. Phys. Chem. 34: 493 (1983).
10. N. A. Campbell, Biology (The Benjamin/Cummings Publishing Company, California, 1996).
11. B. Cheng, R. L. Fournier, and P. A. Relue, Biotechnol. Bioeng. 70: 467 (2000).
12. R. I. Cukier Macromolecules 17: 252 (1984).
13. P.-G. DeGennes Macromolecules 9: 594 (1976).
14. P.-G. DeGennes Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, 1979).
15. J. M. Deutch and I. Oppenheim. J. Chem. Phys. 54: 3547 (1971).
16. M. Doi and S. F. Edwards The Theory of Polymer Dynamics (Oxford University Press, Oxford, 1986).
17. S. F. Edwards, J. Phys. A 8: 1670 (1975).
18. J. L. Eide and A. K. Chakraborty J. Phys. Chem. B. 110: 2318 (2006).
19. D. L. Ermak and J. A. McCammon J. Chem. Phys. 69: 1352 (1978).
20. B. U. Felderhof J. Phys. A 11: 929 (1978).
21. A. R. Fersht Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, (Freeman, New York, 1999).
22. U. Frisch, B. Hasslacher and Y. Pomeau Phys. Rev. Letts. 56: 1505 (1986).
23. A. B. Fulton Cell 30: 345 (1982).
24. C. W. Gardiner Handbook of Stochastic Methods, 2nd edition (Springer, Berlin, 1995).
25. N. D. Gershon, K. R. Porter and B. L. Trus Proc. Natl. Acad. Sci USA 82: 5030 (1985).
26. D. A. Wolf-Gladrow Lattice-Gas Cellular Automata and Lattice-Boltzmann Models: An Introduction (Springer, Berlin, 2000).
27. A. Goldbeter Biochemical oscillations and cellular rhythms (Cambridge University Press, 1996).
28. R. Grima and T. J. Newman Phys. Rev. E 70: 036703 (2004).
29. R. Grima and S. Schnell Biophysical Chemistry. DOI:10.1016/j.bpc.2006.04.019.
30. R. Grima and S. Schnell Chem. Phys. Chem. 7: 1422 (2006).
31. D. Hall and A. P. Minton BBA-Proteins Proteomics 1649: 127 (2003).
32. J. Hardy, Y. Pomeau and O. D. Pazzis J. Math. Phys. 14: 1746 (1973).
33. L. Johansson and J.-E Lofroth, J. Chem. Phys. 98: 7471 (1993).
34. R. Kapral, A. Lawniczak and P. Masiar Phys. Rev. Lett. 66: 2539 (1991).
35. R. Kapral, A. Lawniczak and P. Masiar, J. Chem. Phys. 96: 2762 (1992).
36. L. B. Kier, C.-K. Cheng and P. G. Seybold Review's in Computational Chemistry Vol. 17 (John Wiley and Sons Inc., New York, 2001), pp. 205-254.
37. R. Kopelman J. Stat. Phys. 42: 185 (1986).
38. R. Kopelman Science 241: 1620 (1988).
39. H. Kuthan Prog. Biophys. Mol. Biol. 75: 1 (2001).
40. D. Langevin and F. Rondelez, Polymer 19: 875 (1978).
41. J. L. Lebowitz and E. Rubin Phys. Rev. 131: 2381 (1963).
42. R. J. LeVeque Numerical Methods for Conservation Laws (Birkhauser, Basel, 1990).
43. K. Lipkow, S. S. Andrews and D. Bray J. Bact. 187:45 (2005).
44. K. Luby-Phelps Int. Rev. Cytol. 192: 189 (2000).
45. P. Mazur and I. Oppenheim Physica 50: 241 (1970).
46. S. C. Merriam and G. D. J. Phillies J. Poly. Sci. Part B 42: 1663 (2004).
47. A. P. Minton Biopolymers 20: 2093 (1981).
48. A. P. Minton J. Biol. Chem. 276: 10577 (2001).
49. T. J. Murphy and J. L. Aguirre J. Chem. Phys. 57: 2098 (1972).
50. T. J. Newman and R. Grima Phys. Rev. E. 70: 051916 (2004).
51. P. A. Netz and T. Dorfmuller J. Chem. Phys. 107: 9221 (1997).
52. B. Novak, Z. Pataki, A. Ciliberto and J. J. Tyson Chaos 11: 277 (2001).
53. A. G. Ogston, B. N. Preston and J. D. Wells Proc. R. Soc. London, Ser. A 333: 297 (1973).
54. J. M. Petit, B. Roux, X. X. Zhu and P. M. Macdonald Macromolecules 29: 6031 (1996).
55. G. D. J. Phillies J. Phys. Chem. 93: 5029 (1989).
56. G. D. J. Phillies Macromolecules 20: 558 (1987).
57. G. D. J. Phillies Macromolecules 31: 2317 (1998).
58. G. D. J. Phillies Macromolecules 19: 2367 (1986).
59. G. D. J. Phillies J. Phys. Chem. 96: 10061 (1992).
60. C. G. Phillips and K. M. Jansons Macromolecules 23: 1717 (1990).
61. C. G. Phillips J. Chem. Phys. 95:4593 (1991).
62. D. C. Rapaport The Art of Molecular Dynamics Simulation, 2nd edition (Cambridge University Press, 2004).
63. H. Risken The Fokker-Planck Equation (Springer, Berlin, 1989).
64. J. M. Rohwer, P. W. Postma, B. N. Kholodenko, and H. V. Westerhoff Proc. Natl. Acad. Sci. U.S.A. 95: 10547 (1998).
65. J. Rottler and A. C. Maggs Phys. Rev. Lett. 93: 170201 (2004).
66. M. A. Savageau J. Theor. Biol. 176: 115 (1995).
67. S. Schnell and T. E. Turner Prog. Biophys. Mol. Biol. 85: 235 (2004).
68. M. Thellier, J.-C. Vincent, S. Alexandre, J.-P. Lassalles, B. Deschrevel, V. Morris and C. Ripoll C R. Biologies 326: 149 (2003).
69. M. Thellier, G. Legent, V. Norris, C. Baron and C. Ripoll C. R. Biologies 327: 1017 (2004).
70. M. Tokita, T. Miyoshi, K. Takegoshi and K. Hikichi Phys. Rev. E 53: 1823 (1996).
71. M. Tokuyama and I. Oppenheim Physica A 94: 501 (1978).
72. T. E. Turner, S. Schnell and K. Burrage Comp. Biol. Chem. 28: 165 (2004).
73. V. Zehnle and G. Searby J. Phys. Paris 50: 1083 (1989)