Markov chain models of coupled calcium channels: Kronecker representations and iterative solution methods.

Mathematical models of calcium release sites derived from Markov chain models of intracellular calcium channels exhibit collective gating reminiscent of the experimentally observed phenomenon of stochastic calcium excitability (i.e., calcium puffs and sparks). Calcium release site models are stochastic automata networks that involve many functional transitions, that is, the transition probabilities of each channel depend on the local calcium concentration and thus the state of the other channels. We present a Kronecker-structured representation for calcium release site models and perform benchmark stationary distribution calculations using both exact and approximate iterative numerical solution techniques that leverage this structure. When it is possible to obtain an exact solution, response measures such as the number of channels in a particular state converge more quickly using the iterative numerical methods than occupation measures calculated via Monte Carlo simulation. In particular, multi-level methods provide excellent convergence with modest additional memory requirements for the Kronecker representation of calcium release site models. When an exact solution is not feasible, iterative approximate methods based on the power method may be used, with performance similar to Monte Carlo estimates. This suggests approximate methods with multi-level iterative engines as a promising avenue of future research for large-scale calcium release site models.