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On the Properties of the Reaction Counts Chemical Master Equation

Computational Medicine, Zuse Institute Berlin, 14195 Berlin, Germany
Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
Entropy 2019, 21(6), 607;
Received: 28 February 2019 / Revised: 10 June 2019 / Accepted: 13 June 2019 / Published: 19 June 2019
PDF [908 KB, uploaded 26 June 2019]


The reaction counts chemical master equation (CME) is a high-dimensional variant of the classical population counts CME. In the reaction counts CME setting, we count the reactions which have fired over time rather than monitoring the population state over time. Since a reaction either fires or not, the reaction counts CME transitions are only forward stepping. Typically there are more reactions in a system than species, this results in the reaction counts CME being higher in dimension, but simpler in dynamics. In this work, we revisit the reaction counts CME framework and its key theoretical results. Then we will extend the theory by exploiting the reactions counts’ forward stepping feature, by decomposing the state space into independent continuous-time Markov chains (CTMC). We extend the reaction counts CME theory to derive analytical forms and estimates for the CTMC decomposition of the CME. This new theory gives new insights into solving hitting times-, rare events-, and a priori domain construction problems. View Full-Text
Keywords: chemical master equation; jump continuous-time Markov chains; reaction counts chemical master equation; jump continuous-time Markov chains; reaction counts

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Sunkara, V. On the Properties of the Reaction Counts Chemical Master Equation. Entropy 2019, 21, 607.

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