Lattice model for self-assembly with application to the formation of cytoskeletal-like structures

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 76, Issue 1, 2007, Pages

  Stewman, Shannon F ^a   Dinner, Aaron R ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEATION; PROTEINS; RANDOM PROCESSES; SELF ASSEMBLY;

ACTIN; COMPUTATIONAL COSTS; CYTOSKELETAL BEHAVIOR; LATTICE MODELS;

MOLECULAR STRUCTURE;

EID: 34547160253     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.76.016103     Document Type: Article

References (51)

1. J. B. Alberts and G. M. Odell, PLoS Biol. PBLIBG 1545-7885 2, 2054 (2004).
2. C. S. Peskin, G. M. Odell, and G. F. Oster, Biophys. J. BIOJAU 0006-3495 65, 316 (1993).
3. A. Mogilner and G. F. Oster, Eur. Biophys. J. EBJOE8 0175-7571 10.1007/s002490050016 25, 47 (1996).
4. A. Mogilner, Curr. Opin. Cell Biol. COCBE3 0955-0674 10.1016/j.ceb.2005. 11.001 18, 32 (2006).
5. M. Dogterom and B. Yurke, Science SCIEAS 0036-8075 10.1126/science.278. 5339.856 278, 856 (1997).
6. A. E. Carlsson, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.62.7082 62, 7082 (2000).
7. A. E. Carlsson, M. A. Wear, and J. A. Cooper, Biophys. J. BIOJAU 0006-3495 86, 1074 (2004).
8. E. Atilgan, D. Wirtz, and S. X. Sun, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.065383 89, 3589 (2005).
9. A. Zilman and S. A. Safran, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2003-00489-5 63, 139 (2003).
10. I. Borukhov, R. F. Bruinsma, W. M. Gelbart, and A. J. Liu, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0404140102 102, 3673 (2005).
11. J. Kierfeld, T. Kuhne, and R. Lipowsky, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.95.038102 95, 038102 (2005).
12. A. Mogilner and B. Y. Rubinstein, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.056515 89, 782 (2005).
13. E. Atilgan, D. Wirtz, and S. X. Sun, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.071480 90, 65 (2006).
14. L. Yang, D. Sept, and A. E. Carlsson, Biophys. J. BIOJAU 0006-3495 90, 4295 (2006).
15. G. H. Fredrickson and H. C. Andersen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.53.1244 53, 1244 (1984).
16. J. P. Garrahan and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.1233719100 100, 9710 (2003).
17. D. Vignjevic, D. Yarar, M. D. Welch, J. Peloquin, T. Svitkina, and G. G. Borisy, J. Cell Biol. JCLBA3 0021-9525 10.1083/jcb.200208059 160, 951 (2003).
18. T. M. Svitkina, E. A. Bulanova, O. Y. Chaga, D. M. Vignjevic, S. Kojima, J. M. Vasiliev, and G. G. Borisy, J. Cell Biol. JCLBA3 0021-9525 10.1083/jcb.200210174 160, 409 (2003).
19. R. J. Glauber, J. Math. Phys. JMAPAQ 0022-2488 10.1063/1.1703954 4, 294 (1963).
20. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, and A. H. Teller, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1699114 21, 1087 (1953).
21. J. V. Small, T. Stradal, E. Vignal, and K. Rottner, Trends Cell Biol. TCBIEK 0962-8924 12, 112 (2002).
22. S. Yamashiro-Matsumura and F. Matsumura, J. Biol. Chem. JBCHA3 0021-9258 260, 5087 (1985).
23. R. D. Mullins, J. A. Heuser, and T. D. Pollard, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.11.6181 95, 6181 (1998).
24. T. M. Svitkina and G. G. Borisy, J. Biol. Chem. JBCHA3 0021-9258 145, 1009 (1999a).
25. L. Blanchoin, K. J. Amann, H. N. Higgs, J.-B. Marchand, D. A. Kaiser, and T. D. Pollard, Nature (London) NATUAS 0028-0836 10.1038/35010008 404, 1007 (2000).
26. J. R. Bartles, Curr. Opin. Cell Biol. COCBE3 0955-0674 10.1016/S0955-0674(99)00059-9 12, 72 (2000).
27. G. Borisy and T. Svitkina, Curr. Opin. Cell Biol. COCBE3 0955-0674 10.1016/S0955-0674(99)00063-0 12, 104 (2000).
28. T. D. Pollard, L. Blanchoin, and R. D. Mullins, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.29.1.545 29, 545 (2000).
29. N. Kureishy, V. Sapountzi, S. Prag, N. Anilkumar, and J. C. Adams, BioEssays BIOEEJ 0265-9247 24, 350 (2002).
30. S. J. Winder, Curr. Opin. Cell Biol. COCBE3 0955-0674 10.1016/S0955-0674(02)00002-9 15, 14 (2003).
31. H. N. Higgs and T. D. Pollard, Annu. Rev. Biochem. ARBOAW 0066-4154 70, 649 (2001).
32. J. Howard, Mechanics of Motor Proteins and the Cytoskeleton (Sinauer Associates, Sunderland, MA, 2001).
33. T. Svitkina and G. Borisy, Trends Biochem. Sci. TBSCDB 0167-7640 24, 432 (1999b).
34. D. Pantaloni, R. Boujemaa, D. Didry, P. Gounon, and M.-F. Carlier, Nat. Cell Biol. NCBIFN 1465-7392 10.1038/35017011 2, 385 (2000).
35. D. Vignjevic, S. Kojima, Y. Aratyn, O. Danciu, T. Svitkina, and G. G. Borisy, J. Biol. Chem. JBCHA3 0021-9258 174, 863 (2006).
36. A. Mogilner and G. F. Oster, Biophys. J. BIOJAU 0006-3495 84, 1591 (2003).
37. M. E. J. Newman and G. T. Barkema, Monte Carlo Methods in Statisical Physics (Clarendon Press, Oxford, 1999).
38. F. Lanni, D. L. Taylor, and B. R. Ware, Biophys. J. BIOJAU 0006-3495 35, 351 (1981).
39. J. L. McGrath, Y. Tardy, C. F. J. Dewey, J. J. Meister, and J. H. Hartwig, Biophys. J. BIOJAU 0006-3495 75, 2070 (1998).
40. A. van Oudenaarden and J. A. Theriot, Nat. Cell Biol. NCBIFN 1465-7392 10.1038/70281 1, 493 (1999).
41. G. B. Ermentrout and L. Edelstein-Keshet, J. Theor. Biol. JTBIAP 0022-5193 10.1006/jtbi.1993.1007 160, 97 (1993).
42. A. Troisi, V. Wong, and M. A. Ratner, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 102, 255 (2005).
43. H. Y. Lee and M. Kardar, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.64.056113 64, 056113 (2001).
44. I. V. Maly and G. G. Borisy, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.181338798 98, 11324 (2001).
45. A. B. Bortz, M. H. Kalos, and J. L. Lebowitz, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(75)90060-1 17, 10 (1975).
46. D. T. Gillespie, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100540a008 81, 2340 (1977).
47. M. Matsumoto and T. Nishimura, ACM Trans. Model. Comput. Simul. ATMCEZ 1049-3301 10.1145/272991.272995 8, 3 (1998).
48. D. C. Wylie, Y. Hori, A. R. Dinner, and A. K. Chakraborty, J. Phys. Chem. B JPCBFK 1089-5647 110, 12749 (2006).
49. M. A. Gibson and J. Bruck, J. Phys. Chem. A JPCAFH 1089-5639 10.1021/jp993732q 104, 1876 (2000).
50. J. Elf, A. Don, and M. Ehrenberg, Proc. SPIE PSISDG 0277-786X 5110, 114 (2003).
51. R. L. Kruse, B. P. Leung, and C. L. Tondo, Data Structures and Program Design in C, 2nd ed. (Prentice-Hall, Upper Saddle River, NJ, 1997).