Simplification of Reversible Markov Chains by Removal of States With Low Equilibrium Occupancy
dc.contributor.author | Ullah, Ghanim | |
dc.contributor.author | Bruno, William J. | |
dc.contributor.author | Pearson, John E. | |
dc.date.accessioned | 2017-06-16T21:10:55Z | |
dc.date.available | 2017-06-16T21:10:55Z | |
dc.date.issued | 2012-10-21 | |
dc.identifier.citation | Ullah, G., Bruno, W. J., & Pearson, J. E. (2012). Simplification of Reversible Markov Chains by Removal of States With Low Equilibrium Occupancy. Journal of Theoretical Biology, 311, 117–129. http://doi.org/10.1016/j.jtbi.2012.07.007 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/24527 | |
dc.description.abstract | We present a practical method for simplifying Markov chains on a potentially large state space when detailed balance holds. A simple and transparent technique is introduced to remove states with low equilibrium occupancy. The resulting system has fewer parameters. The resulting effective rates between the remaining nodes give dynamics identical to the original system’s except on very fast timescales. This procedure amounts to using separation of timescales to neglect small capacitance nodes in a network of resistors and capacitors. We illustrate the technique by simplifying various reaction networks, including transforming an acyclic four-node network to a three-node cyclic network. For a reaction step in which a ligand binds, the law of mass action implies a forward rate proportional to ligand concentration. The effective rates in the simplified network are found to be rational functions of ligand concentration | en_US |
dc.publisher | Elsevier | en_US |
dc.rights | This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 4.0 (CC BY-NC-ND 4.0), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. | en_US |
dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | en_US |
dc.subject | Reversible Markov Chains | en_US |
dc.subject | Model Simplification | en_US |
dc.subject | Ligand-binding | en_US |
dc.subject | Low-Occupancy States | en_US |
dc.subject | Nonlinear Chains | en_US |
dc.subject | MWC Model | en_US |
dc.title | Simplification of Reversible Markov Chains by Removal of States With Low Equilibrium Occupancy | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Bruno, William J. | |
kusw.kudepartment | Physics and Astronomy | en_US |
dc.identifier.doi | 10.1016/j.jtbi.2012.07.007 | en_US |
kusw.oaversion | Scholarly/refereed, author accepted manuscript | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.identifier.pmid | PMC3930476 | en_US |
dc.rights.accessrights | openAccess |
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Except where otherwise noted, this item's license is described as: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 4.0 (CC BY-NC-ND 4.0), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.