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Journal of Chemical Physics / Volume 136 / Issue 2 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 136, 025101 (2012); http://dx.doi.org/10.1063/1.3675920 (9 pages)

Exploring the dynamics of dimer crossing over a Kramers type potential

Mesfin Asfaw and Yohannes Shiferaw

Department of Physics and Astronomy, California State University Northridge, California 91330, USA

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(Received 14 October 2011; accepted 20 December 2011; published online 10 January 2012)

We explore the escape rate of a dimer crossing a potential barrier using both analytical and numerical approaches. We find that for small coupling strength k, the barrier hopping can be well approximated by a two step reaction scheme where one monomer hops over the barrier and is then followed by the other. In this regime the escape rate increases with k showing that the cooperativity between monomers enhances the crossing rate. However, in the limit of large coupling strength, applying the method of adiabatic elimination, we find that the escape rate is a decreasing function of k. Thus, we find that the escape rate is a non-monotonic function of the spring constant which is peaked at an optimal coupling strength. Furthermore, in the presence of a weak periodic signal, we show that the system response to the periodic signal is pronounced at a particular spring constant showing the dimer can be transported rapidly across the reaction coordinate in a half period.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THE MODEL
  3. NUMERICAL SIMULATION AND COMPUTATIONAL MECHANICS
  4. QUANTITATIVE ANALYSIS FOR THE CROSSING RATE IN THE WEAK COUPLING REGIME
  5. EXPLORING THE THERMALLY ACTIVATED RATE VIA THE ADIABATIC ELIMINATION METHOD
  6. STOCHASTIC RESONANCE OF THE DIMER
  7. SUMMARY AND CONCLUSION

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KEYWORDS and PACS

Keywords

potential energy surfaces

PACS

  • 31.50.Gh

    Surface crossings, non-adiabatic couplings

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3675920

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990).

    P. J. Park and W. Sung, J. Chem. Phys. 111, 5259 (1999)JCPSA6000111000011005259000001.

    S. Lee and W. Sung, Phys. Rev. E 63, 021115 (2001).

    K. L. Sebastian and A. K. R. Paul, Phys. Rev. E 62, 927 (2000).

    J. F. Lindner, B. K. Meadows, W. L. Ditto, M. E. Inchiosa, and A. R. Bulsara, Phys. Rev. Lett. 75, 3 (1995)
    Phys. Rev. E 53, 2081 (1996).

    F. Marchesoni, L. Gammaitoni, and A. R. Bulsara, Phys. Rev. Lett. 76, 2609 (1996).

    I. E. Dikshtein, D. V. Kuznetsov, and L. Schimansky-Geier, Phys. Rev. E. 65, 061101 (1996).

    P. Jung, U. Behn, E. Pantazelou, and F. Moss, Phys. Rev. A 46, R1709 (1992).

    A. Pototsky, F. Marchesoni, and S. E. Savelevl, Phys. Rev. E 81, 031114 (2010).

    E. Heinsalu, M. Patriarca, and F. Marchesoni, Phys. Rev. E 77, 021129 (2008).

    O. M. Braun, R. Ferrando, and G. E. Tommei, Phys. Rev. E 68, 051101 (2003).

    P. S. Burada, G. Schmid, D. Reguera, M. H. Vainstein, J. M. Rubi, and P. Hänggi, Phys. Rev. Lett. 101, 130602 (2008).

    L. Gammaitoni, P. Hänggi, P. Jung, and F. Marchesoni, Rev. Mod. Phys. 70, 223 (1998).

    B. McNamara and K. Wiesenfeld, Phy. Rev. A 39, 4854 (1989).

    I. Goldhirsch and Y. Gefen, Phys. Rev. A 33, 2583 (1986).

    I. Goldhirsch and Y. Gefen, Phys. Rev. A 35, 1317 (1987).

    B. Schulze, A. Sljoka, and W. Whiteley, AIP Conf. Proc. 1368, 135 (2011)APCPCS001368000001000135000001.


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