Efficient approximation of the stationary solution to the chemical master equation

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University of Alabama Libraries

When studying chemical reactions on the cellular level, it is often helpful to model the system using the continuous-time Markov chain (CTMC) that results from the chemical master equation (CME). It is frequently instructive to compute the probability distribution of this CTMC at statistical equilibrium, thereby gaining insight into the stationary, or long-term, behavior of the system. Computing such a distribution directly is problematic when the state space of the system is large. To alleviate this difficulty, it has become popular to constrain the computational burden by using a finite state projection (FSP), which aims only to capture the most likely states of the system, rather than every possible state. We propose efficient methods to further narrow these states to those that remain highly probable in the long run, after the transient behavior of the system has dissipated. Our strategy is to quickly estimate the local maxima of the stationary distribution using the reaction rate formulation, which is of considerably smaller size than the full-blown chemical master equation, and from there develop adaptive schemes to profile the distribution around the maxima. The primary focus is on constructing an efficient FSP; however, we also examine how some of our initial estimates perform on their own and discuss how they might be applied to tensor-based methods. We include numerical tests that show the efficiency of our approaches.

Electronic Thesis or Dissertation
Mathematics, Applied mathematics, Computational chemistry