Bounding the stationary distributions of the chemical master equation via mathematical programming
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Published version
Author(s)
Kuntz Nussio, juan
Thomas, philipp
Stan, guy bart
Barahona, Mauricio
Type
Journal Article
Abstract
The stochastic dynamics of biochemical networks are usually modelled with the chemical master equation (CME). The stationary distributions of CMEs are seldom solvable analytically, and numerical methods typically produce estimates with uncontrolled errors. Here, we introduce mathematical programming approaches that yield approximations of these distributions with computable error bounds which enable the verification of their accuracy. First, we use semidefinite programming to compute increasingly tighter upper and lower bounds on the moments of the stationary distributions for networks with rational propensities. Second, we use these moment bounds to formulate linear programs that yield convergent upper and lower bounds on the stationary distributions themselves, their marginals and stationary averages. The bounds obtained also provide a computational test for the uniqueness of the distribution. In the unique case, the bounds form an approximation of the stationary distribution with a computable bound on its error. In the non unique case, our approach yields converging approximations of the ergodic distributions. We illustrate our methodology through several biochemical examples taken from the literature: Schl¨ogl’s model for a chemical bifurcation, a two-dimensional toggle switch, a model for bursty gene expression, and a dimerisation model with multiple stationary distributions.
Date Issued
2019-07-21
Date Acceptance
2019-06-24
Citation
Journal of Chemical Physics, 2019, 151 (3)
ISSN
0021-9606
Publisher
AIP Publishing
Journal / Book Title
Journal of Chemical Physics
Volume
151
Issue
3
Copyright Statement
©2019 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license(http://creativecommons.org/licenses/by/4.0/)
Sponsor
Engineering & Physical Science Research Council (EPSRC)
Engineering & Physical Science Research Council (EPSRC)
Grant Number
EP/N014529/1
EP/M002187/1
Subjects
Science & Technology
Physical Sciences
Chemistry, Physical
Physics, Atomic, Molecular & Chemical
Chemistry
Physics
AUGMENTED TRUNCATION APPROXIMATIONS
MARKOV-CHAINS
EQUILIBRIUM DISTRIBUTION
ERROR-BOUNDS
SQUARES
IDENTIFICATION
OPTIMIZATION
STABILITY
SYSTEMS
MODELS
Cell Biology
Mathematical Computing
Models, Biological
Models, Chemical
Stochastic Processes
Stochastic Processes
Mathematical Computing
Models, Biological
Models, Chemical
Cell Biology
math.PR
math.PR
math.OC
q-bio.MN
q-bio.PE
q-bio.QM
Chemical Physics
02 Physical Sciences
03 Chemical Sciences
09 Engineering
Publication Status
Published
Article Number
034109
Date Publish Online
2019-07-18