MARKOV CHAIN MODELS OF COUPLED INTRACELLULAR CALCIUM CHANNELS: KRONECKER STRUCTURED REPRESENTATIONS AND BENCHMARK STATIONARY DISTRIBUTION CALCULATIONS

Pacific Symposium on Biocomputing 2008

HILARY DEREMIGIO ; PETER KEMPER ; M. DREW LAMAR ; GREGORY D. SMITH

Others  :  http://psb.stanford.edu/psb-online/proceedings/psb08/deremigio.pdf
PID  :  19803

来源: CEUR

【 摘 要 】

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). We present a Kronecker structured representationfor calcium release site models and perform benchmark stationary distribution calculations using numerical iterative solution techniques that leverage this structure. In this context we find multi-level methods and certain pre-conditioned projection methods superior to simple Gauss-Seidel type iterations. Response measures such as the number of channels in a particular state converge more quickly using these numerical iterative methods than occupation measures calculated via Monte Carlo simulation.