An agent-based approach for modeling molecular self-organization

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 2, 2005, Pages 255-260

  Troisi, Alessandro ^a   Wong, Vance ^b   Ratner, Mark A ^b  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Agent based simulation; Molecular self assembly; Nanostructure prediction

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER; MOLECULAR MODEL; MONTE CARLO METHOD; PRIORITY JOURNAL; SELF CONCEPT; SOCIOLOGY;

ALGORITHMS; COMPUTER SIMULATION; MODELS, MOLECULAR; STOCHASTIC PROCESSES;

EID: 12244264446     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0408308102     Document Type: Article

References (37)

1. Pinpinelli, A. & Villain, J. (1999) Physics of Crystal Growth (Cambridge Univ. Press, Cambridge, U.K.).
2. Camazine, S., Deneubourg, J.-L., Franks, N. R., Theraulaz, G. & Bonabeau, E. (2003) Self-Organization in Biological Systems (Princeton Univ. Press, Princeton).
3. Krugman, P. R. (1996) The Self-Organizing Economy (Blackwell, Cambridge, MA).
4. Albert, R. & Barabasi, A.-L. (2002) Rev. Mod. Phys. 74, 47-97.
5. Bonabeau, E., Dorigo, M. & Theraulaz, G. (1999) Swarm Intelligence: From Natural to Artificial Systems (Oxford Univ. Press, New York).
6. Wooldridge, M. (2002) An Introduction to MultiAgent Systems (Wiley, Chichester, U.K.).
7. Weiss, G., ed. (2000) Multiagent Systems: A Modern Approach to Distributed Artificial Intelligence (MIT Press, Cambridge, MA).
8. Davidson, P. (2001) Lect. Notes Artif. Int. 1979, 97-107.
9. Bonabeau, E. (2002) Proc. Natl. Acad. Sci. USA 99, 7280-7287.
10. Danielson, P. (2002) Proc. Natl. Acad. Sci. USA 99, 7237-7242.
11. Holland, J. H. (1995) Hidden Order: How Adaptation Builds Complexity (Addison-Wesley, Reading, MA).
12. Russel, S. J. & Norvig, P. (2003) Artificial Intelligence: A Modern Approach (Prentice-Hall, Upper Saddle River, NJ).
13. Axelrod, R. (1997) The Complexity of Cooperation (Princeton Univ. Press, Princeton).
14. Epstein, E. M. (2002) Proc. Natl. Acad. Sci. USA 99, 7243-7250.
15. Helbing, D., Farkas, I. & Vicsek, T. (2000) Nature 407, 487-490.
16. Chopard, B. & Droz, M. (1998) Cellular Automata Modeling of Physical Systems (Cambridge Univ. Press, Cambridge, U.K.).
17. Frisch, U., Hasslacher, B. & Pomeau, Y. (1986) Phys. Rev. Lett. 56, 1505-1508.
18. Wolfram, S. (1986) J. Stat. Phys. 45, 471-526.
19. Kadanoff, L. P., McNamara, G. R. & Zanetti, G. (1989) Phys. Rev. A 40, 4527-4541.
20. Taleb, A., Chausse, A., Dymitrowska, M., Stafiej, J. & Badiali, J. P. (2004) J. Phys. Chem. B 108, 952-958.
21. Kier, L. B., Cheng, C. K. & Testa, B. (2003) J. Chem. Inf. Comput. Sci. 43, 255-258.
22. Mao, L. Y., Harris, H. H. & Stine, K. J. (2002) J. Chem. Inf. Comput. Sci. 42, 1179-1184.
23. Kier, L. B., Cheng, C. K. & Testa, B. (1999) J. Chem. Inf. Comput. Sci. 39, 326-332.
24. Tsangaris, D. M. & de Pablo, J. J. (1994) J. Chem. Phys. 101, 1477-1489.
25. Busch, N. A., Wertheim, M. S. & Yarmush, M. L. (1996) J. Chem. Phys. 104, 3962-3975.
26. Chen, B. & Siepmann, J. I. (2000) J. Phys. Chem. B 104, 8725-8734.
27. Wierzchowski, S. & Kofke, D. A. (2001) J. Chem. Phys. 114, 8752-8762.
28. Wu, D., Chandler, D. & Smit, B. (1992) J. Phys. Chem. 96, 4077-4083.
29. Winfree, E. (2000) J. Biomol. Struct. Dyn. 11, 263-270.
30. Mao, C. D., LaBean, T. H., Reif, J. H. & Seeman, N. C. (2000) Nature 407, 493-496.
31. Klavins, E., Ghrist, R. & Lipsky, D. (2003) Graph Grammars for Self Assembling Robotic Systems, http://sveiks.ee.washington.edu/papers/icra04-sa. pdf.
32. Seeman, N. C. (2003) Nature 421, 427-431.
33. Troisi, A., Wong, V. & Ratner, M., J. Chem. Phys., in press.
34. Gilks, W. R., Roberts, R. O. & George, E. I. (1994) The Statistician 43, 179-189.
35. Ciccotti, G., Ferrario, M. & Ryckaert, J.-P. (1982) Mol. Phys. 47, 1253-1264.
36. Ikeguchi, M. (2004) J. Comput. Chem. 25, 529-541.
37. Shinoda, W. & Mikami, M. (2003) J. Comput. Chem. 24, 920-930.