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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. ISSN 0167-2789. doi:10.1016/j.physd.2006.02.006
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Official URL: http://dx.doi.org/10.1016/j.physd.2006.02.006
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) | ||||||
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| Subjects: | Q Science > QA Mathematics Q Science > QC Physics |
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| Divisions: | Faculty of Science > Mathematics Faculty of Science > Physics |
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| Journal or Publication Title: | Physica D: Nonlinear Phenomena | ||||||
| Publisher: | Elsevier BV | ||||||
| ISSN: | 0167-2789 | ||||||
| Official Date: | 1 April 2006 | ||||||
| Dates: |
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| 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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