Skip to main content
×
×
Home

Studying the Adsorption of Polymers and Biomolecules on Surfaces Using Enhanced Sampling Methods

  • Michael P. Allen (a1) and Adam D Swetnam (a1)
Abstract
ABSTRACT

We discuss how to use Wang-Landau simulations in an efficient manner to investigate the statistical mechanics of individual lattice polymers and peptides adsorbed at a planar surface. For nearest neighbor interactions, we show that a single Wang-Landau simulation, recording the density of states as a function of numbers of internal contacts and of surface beads, is sufficient to give a full description of the phase behavior of both adsorbed and desorbed states of single molecules. It is not necessary to introduce a second confining wall. Moreover, moves are never rejected due to overlap with the surface.

The proposed “wall-free” method has already been applied to homo-polymers and hetero-polymers (lattice peptides using the HP model) on a uniform surface, and on regularly patterned surfaces. We give here a specific example to indicate how the relative adsorption strengths of a given peptide on different surfaces may be calculated.

Copyright
References
Hide All
1. Lau K. F. and Dill K. A., Macromolecules 22, 3986 (1989).
2. Li Y. W., Wüst T. and Landau D. P., Comput. Phys. Commun. 182, 1896 (2011).
3. Lesh N., Mitzenmacher M. and Whitesides S., in Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology, RECOMB, edited by Vingron M., Istrail S., Pevzner P. and Waterman M. (ACM, New York, 2003) pp. 188195.
4. Bachmann M. and Janke W., J. Chem. Phys. 120, 6779 (2004).
5. Schiemann R., Bachmann M. and Janke W., Comput. Phys. Commun. 166, 8 (2005).
6. Bachmann M. and Janke W., Phys. Rev. Lett. 95, 058102 (2005).
7. Bachmann M. and Janke W., Phys. Rev. E 73, 020901 (2006).
8. Bachmann M. and Janke W., Phys. Rev. E 73 041802 (2006).
9. Rampf F., Binder K. and Paul W., J. Polym. Sci. B 44, 2542 (2006).
10. Zhang J. F., Kou S. C. and Liu J. S., J. Chem. Phys. 126, 225101 (2007).
11. Cheng Y., Liu G. R., Li Z. R., Lu C. and Mi D., J. Phys. D 41, 055308 (2008).
12. Luettmer-Strathmann J., Rampf F., Paul W. and Binder K., J. Chem. Phys. 128, 064903 (2008).
13. Owczarek A L, Rechnitzer A, Krawczyk J and Prellberg T, J. Phys. A 40, 13257 (2007).
14. Krawczyk J., Owczarek A. L., Prellberg T. and Rechnitzer A., Europhys. Lett. 70, 726 (2005).
15. Vrbová T. and Whittington S. G., J. Phys. A 31, 3989 (1998).
16. Singh Y., Giri D. and Kumar S., J. Phys. A 34, L67 (2001).
17. Wüst T. and Landau D. P., Comput. Phys. Commun. 179, 124 (2008).
18. Wüst T., Li Y. W. and Landau D. P., J. Stat. Phys. 144, 638 (2011).
19. Möddel M., Janke W. and Bachmann M., Macromolecules 44, 9013 (2011).
20. Radhakrishna M., Sharma S. and Kumar S. K., J Chem. Phys. 136, 114114 (2012).
21. Swetnam A. D. and Allen M. P., Phys. Chem. Chem. Phys. 11, 2046 (2009).
22. Swetnam A. D. and Allen M. P., J. Comput. Chem. 32, 816 (2011).
23. Swetnam A. D., Brett C. and Allen M. P., Phys. Rev. E 85, 031804 (2012).
24. Swetnam A. D. and Allen M. P., Physics Procedia. (to appear).
25. Wang F. G. and Landau D. P., Phys. Rev. Lett. 86, 2050 (2001).
26. Wang F. G. and Landau D. P., Phys. Rev. E 64, 056101 (2001).
27. Metropolis N., Rosenbluth A. W., Rosenbluth M. N., Teller A. H. and Teller E., J. Chem. Phys. 21, 1087 (1953).
28. Frenkel D. and Smit B., Understanding Molecular Simulation (2 nd edition, Academic Press, 2002).
29. Landau D. P. and Binder K., A Guide to Monte Carlo Simulations in Statistical Physics (3 rd edition, Cambridge University Press, 2009).
30. Allen M. P. and Tildesley D. J., Computer Simulation of Liquids (Clarendon Press, 1989).
31. Yue K. Z. and Dill K. A.. Phys. Rev. E 48, 2267 (1993).
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

MRS Online Proceedings Library (OPL)
  • ISSN: -
  • EISSN: 1946-4274
  • URL: /core/journals/mrs-online-proceedings-library-archive
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Keywords:

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 5 *
Loading metrics...

Abstract views

Total abstract views: 62 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 20th January 2018. This data will be updated every 24 hours.