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Ergodic pumping: A mechanism to drive biomolecular conformation changes

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MacKay, Robert S. and MacKay, D. J. C. (2006) Ergodic pumping: A mechanism to drive biomolecular conformation changes. In: Conference on Nonlinear Physics - Condensed Matter, Dynamical Systems and Biophysics, Inst Henri Poincare, Paris, FRANCE, MAY 30-31, 2005. Published in: Physica D: Nonlinear Phenomena, Volume 216 (Number 1). pp. 220-234. doi:10.1016/j.physd.2006.02.006 ISSN 0167-2789.

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Official URL: http://dx.doi.org/10.1016/j.physd.2006.02.006

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Abstract

We propose that a significant contribution to the power stroke of myosin and similar conformation changes in other biomolecules is the pressure of a single molecule (e.g. a phosphate ion) expanding a trap, a mechanism we call "ergodic pumping". We demonstrate the principle with a toy computer model and discuss the mathematics governing the evolution of slow degrees of freedom in large Hamiltonian systems. We indicate in detail how the mechanism could fit with known features of the myosin cycle. Many other biomolecular conformation changes could be driven in part by ergodic pumping. We suggest the use of ergodic pumping as a design principle in nanobiotechnology. (c) 2006 Elsevier B.V. All rights reserved.

Item Type: Conference Item (Paper)
Subjects: Q Science > QA Mathematics
Q Science > QC Physics
Divisions: Faculty of Science, Engineering and Medicine > Science > Mathematics
Faculty of Science, Engineering and Medicine > Science > Physics
Journal or Publication Title: Physica D: Nonlinear Phenomena
Publisher: Elsevier BV
ISSN: 0167-2789
Official Date: 1 April 2006
Dates:
DateEvent
30 March 2006Available
1 April 2006Published
Volume: Volume 216
Number: Number 1
Number of Pages: 15
Page Range: pp. 220-234
DOI: 10.1016/j.physd.2006.02.006
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Conference Paper Type: Paper
Title of Event: Conference on Nonlinear Physics - Condensed Matter, Dynamical Systems and Biophysics
Type of Event: Conference
Location of Event: Inst Henri Poincare, Paris, FRANCE
Date(s) of Event: MAY 30-31, 2005

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