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The stochastic quasi-steady-state assumption: Reducing the model but not the noise

Srivastava, Rishi and Haseltine, Eric L. and Mastny, Ethan and Rawlings, James B. (2011) The stochastic quasi-steady-state assumption: Reducing the model but not the noise. Journal of Chemical Physics, 134 (15). Art. No. 154109. ISSN 0021-9606.

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Highly reactive species at small copy numbers play an important role in many biological reaction networks. We have described previously how these species can be removed from reaction networks using stochastic quasi-steady-state singular perturbation analysis (sQSPA). In this paper we apply sQSPA to three published biological models: the pap operon regulation, a biochemical oscillator, and an intracellular viral infection. These examples demonstrate three different potential benefits of sQSPA. First, rare state probabilities can be accurately estimated from simulation. Second, the method typically results in fewer and better scaled parameters that can be more readily estimated from experiments. Finally, the simulation time can be significantly reduced without sacrificing the accuracy of the solution.

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Additional Information:© 2011 American Institute of Physics. Received 26 October 2010; accepted 24 March 2011; published online 20 April 2011. This work was supported by a National Institutes of Health (AI071197) award. E.L.H. gratefully acknowledges support from the National Institutes of Health under Ruth L. Kirschstein National Research Service Award 5F32CA120055. All simulations were performed using Octave ( Octave is freely distributed under the terms of the GNU General Public License.
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NIH Ruth L. Kirschstein National Research Service Award5F32CA120055
Subject Keywords:biochemistry; biology; cellular biophysics; genetics; microorganisms; perturbation techniques; stochastic processes
Issue or Number:15
Classification Code:PACS: 87.15.R-; 87.16.Yc; 87.17.Aa; 87.18.-h; 87.19.xd; 87.10.Mn
Record Number:CaltechAUTHORS:20110518-111220815
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:23717
Deposited By: Jason Perez
Deposited On:18 May 2011 18:49
Last Modified:03 Oct 2019 02:49

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