Reduction of calcium release site models via fast/slow analysis and iterative aggregation/disaggregation.
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 calcium puffs and sparks. Such models often take the form of stochastic automata networks in which the transition probabilities of each channel depend on the local calcium concentration and thus the state of the other channels. In order to overcome the state-space explosion that occurs in such compositionally defined calcium release site models, we have implemented several automated procedures for model reduction using fast/slow analysis. After categorizing rate constants in the single channel model as either fast or slow, groups of states in the expanded release site model that are connected by fast transitions are lumped, and transition rates between reduced states are chosen consistent with the conditional probability distribution among states within each group. For small problems these conditional probability distributions can be numerically calculated from the full model without approximation. For large problems the conditional probability distributions can be approximated without the construction of the full model by assuming rapid mixing of states connected by fast transitions. Alternatively, iterative aggregation/disaggregation may be employed to obtain reduced calcium release site models in a memory-efficient fashion. Benchmarking of several different iterative aggregation/disaggregation-based fast/slow reduction schemes establishes the effectiveness of automated calcium release site reduction utilizing the Koury-McAllister-Stewart method.
Hao
Yan
Y
Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23187, USA.
Kemper
Peter
P
Smith
Gregory D
GD
D000465:Algorithms; D000818:Animals; D001683:Biological Clocks / Q000502:physiology*; D015220:Calcium Channels / Q000502:physiology*; D020013:Calcium Signaling / Q000502:physiology*; D003198:Computer Simulation; D006801:Humans; D015640:Ion Channel Gating / Q000502:physiology*; D008954:Models, Biological; D015233:Models, Statistical; D017711:Nonlinear Dynamics; D009991:Oscillometry / Q000379:methods*
D015220:Calcium Channels