Home | About Journal | Web Links | E-mail Alerts | RSS RSS Icon | Browse
Previous Article Next Article

Spatial averaging for small molecule diffusion in condensed phase environments

Source: J. Chem. Phys. 133, 044506 (2010); doi:10.1063/1.3458639

Published 26 July 2010

KEYWORDS and PACS
Keywords
PACS
  • 87.15.ak
    Monte Carlo simulations in molecular biophysics
  • 66.30.-h
    Diffusion in solids
  • YEAR: 2010
RELATED DATABASES

To view database links for this article,
you need to log in.
To view database links for this article,
you need to log in.
PUBLICATION DATA
ISSN:
1553-9628 (online)
Publisher:
AIP is a member of CrossRef AIP
Nuria Plattner,1 J. D. Doll,2 and Markus Meuwly1,2
1Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
2Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
Spatial averaging is a new approach for sampling rare-event problems. The approach modifies the importance function which improves the sampling efficiency while keeping a defined relation to the original statistical distribution. In this work, spatial averaging is applied to multidimensional systems for typical problems arising in physical chemistry. They include (I) a CO molecule diffusing on an amorphous ice surface, (II) a hydrogen molecule probing favorable positions in amorphous ice, and (III) CO migration in myoglobin. The systems encompass a wide range of energy barriers and for all of them spatial averaging is found to outperform conventional Metropolis Monte Carlo. It is also found that optimal simulation parameters are surprisingly similar for the different systems studied, in particular, the radius of the point cloud over which the potential energy function is averaged. For H2 diffusing in amorphous ice it is found that facile migration is possible which is in agreement with previous suggestions from experiment. The free energy barriers involved are typically lower than 1 kcal/mol. Spatial averaging simulations for CO in myoglobin are able to locate all currently characterized metastable states. Overall, it is found that spatial averaging considerably improves the sampling of configurational space. ©2010 American Institute of Physics
History: Received 16 March 2010; accepted 9 June 2010; published 26 July 2010
Permalink: http://link.aip.org/link/?JCPSA6/133/044506/1

REFERENCES (42)

For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
  2. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
  3. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998).
  4. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. 68, 9 (1992).
  5. J. D. Doll, J. E. Gubernatis, N. Plattner, M. Meuwly, P. Dupuis, and H. Wang, J. Chem. Phys. 131, 104107 (2009).
  6. A. Al-Halabi, H. J. Fraser, G. J. Kroes, and E. F. van Dishoeck, Astron. Astrophys. 422, 777 (2004).
  7. A. Kouchi and T. Kuroda, Nature (London) 344, 134 (1990).
  8. E. Mayer and R. Pletzer, Nature (London) 319, 298 (1986).
  9. R. Elber and M. Karplus, J. Am. Chem. Soc. 112, 9161 (1990).
  10. J. S. Olson and G. N. Phillips, Jr., J. Biol. Chem. 271, 17593 (1996).
  11. E. E. Scott, Q. H. Gibson, and J. S. Olson, J. Biol. Chem. 276, 5177 (2001).
  12. J. Cohen, A. Arkhipov, R. Braun, and K. Schulten, Biophys. J. 91, 1844 (2006).
  13. J. Z. Ruscio, D. Kumar, M. Shukla, M. G. Prisant, T. M. Murali, and A. V. Onufriev, Proc. Natl. Acad. Sci. U.S.A. 105, 9204 (2008).
  14. S. Mishra and M. Meuwly, Biophys. J. 96, 2105 (2009).
  15. O. Carrillo and M. Orozco, Proteins 70, 892 (2008).
  16. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
  17. S. Nosé and M. L. Klein, Mol. Phys. 50, 1055 (1983).
  18. W. G. Hoover, Phys. Rev. A 31, 1695 (1985).
  19. H. J. C. Berendsen, J. P. M. Postma, W. F. VanGunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
  20. J. Kuriyan, S. Wilz, M. Karplus, and G. A. Petsko, J. Mol. Biol. 192, 133 (1986).
  21. W. L. Jorgensen, J. D. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
  22. W. van Gunsteren and H. Berendsen, Mol. Phys. 34, 1311 (1977).
  23. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. E. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Fo resman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople (2004).
  24. A. J. Stone, J. Chem. Theory Comput. 1, 1128 (2005).
  25. N. Plattner and M. Meuwly, Biophys. J. 94, 2505 (2008).
  26. A. J. Stone, The Theory of Intermolecular Forces (Clarendon, Oxford, 1996).
  27. K. Kuczera, J. Kuriyan, and M. Karplus, J. Mol. Biol. 213, 351 (1990).
  28. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. E. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 102, 3586 (1998).
  29. D. J. Earl and M. W. Deem, Phys. Chem. Chem. Phys. 7, 3910 (2005).
  30. A. R. Dinner, “Monte Carlo simulations of protein folding,” Ph.D. thesis, Harvard University, Cambridge, 1999.
  31. D. M. Ceperley and M. Dewing, J. Chem. Phys. 110, 9812 (1999).
  32. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953).
  33. G. E. P. Box and M. E. Muller, Ann. Math. Stat. 29, 610 (1958).
  34. N. Plattner and M. Meuwly, ChemPhysChem 9, 1271 (2008).
  35. P. A. Gerakines, W. A. Schutte, J. M. Greenberg, and E. F. van Dishoeck, Astron. Astrophys. 296, 810 (1995).
  36. J. Bouwman, W. Ludwig, Z. Awad, K. I. Oeberg, G. W. Fuchs, E. F. van Dishoeck, and H. Linnartz, Astron. Astrophys. 476, 995 (2007).
  37. S. E. Bisschop, H. J. Fraser, K. I. Oberg, E. F. van Dishoeck, and S. Schlemmer, Astron. Astrophys. 449, 1297 (2006).
  38. R. W. Dissly, M. Allen, and V. G. Anicich, Astrophys. J. 435, 685 (1994).
  39. J. E. Roser, S. Swords, G. Vidali, G. Manico, and V. Pirronello, Astrophys. J. 596, L55 (2003).
  40. H. L. Strauss and Z. Chen, J. Chem. Phys. 101, 7177 (1994).
  41. R. F. Tilton, I. D. Kuntz, and G. A. Petsko, Biochemistry 23, 2849 (1984).
  42. C. Bossa, M. Anselmi, D. Roccatano, A. Amadei, B. Vallone, M. Brunori, and A. Di Nola, Biophys. J. 86, 3855 (2004).

CITING ARTICLES
For access to citing articles, you need to log in.
For access to citing articles, you need to Log in.
ADVERTISEMENT