EPJ Nonlinear Biomed Phys
Volume 4, Number 1, December 2016
The Physics Behind Systems Biology
|Number of page(s)||21|
|Published online||04 June 2016|
Reduction of calcium release site models via optimized state aggregation
Math and Computer Science Department, Hobart and William Smith Colleges, 300 Pulteney St., Geneva, 14456, NY, USA
* e-mail: firstname.lastname@example.org
Accepted: 17 May 2016
Published online: 4 June 2016
Markov chain models of calcium release sites in living cells exhibit stochastic dynamics reminiscent of the experimentally observed phenomenon of calcium puffs and sparks. Such models often take the form of stochastic automata networks in which the transition probabilities for each of a large number of intercellular channel models depend on the local calcium concentration and thus the state of nearby channels. The state-space size in such compositionally defined calcium release site models increases exponentially as the number of channels increases, which is referred to as “state-space explosion”.
In order to overcome the state-space explosion problem, we utilized the idea of “coarse graining” and implemented an automated procedure that reduces the state space by aggregating and lumping states of the full release site model. For a given state aggregation scheme, the transition rates between reduced states are chosen consistent with the conditional probability distribution among states within each group. A genetic algorithm-based approach is then applied to select the state aggregation schemes that lead to reduced models that approximate the observable behaviors of the full model.
The genetic algorithm-based approach is implemented in Matlab®; and applied to two different release site models. The approach found reduced models that approximate the full model in the number of open channels, spark statistics, and the jump probability matrix as a function of time.
A novel automated genetic algorithm-based searching technique is implemented to find reduced calcium release site models that approximate observable behaviors of the full Markov chain models that possess intractable state-spaces. As compared to the full model, the reduced models produce quantitatively similar results using significantly less computational resources.
Key words: State space explosion / Genetic algorithms / Calcium signaling / Stochastic automata network / Set partition / Coarse graining strategies
© Hao., 2016
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