Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels

Nils Christian, Alexander Skupin, Silvia Morante, Karl Jansen, Giancarlo Rossi, Oliver Ebenhoeh*

*Corresponding author for this work

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

A major challenge in biology is to understand how molecular processes determine phenotypic features. We address this fundamental problem in a class of model systems by developing a general mathematical framework that allows the calculation of mesoscopic properties from the knowledge of microscopic Markovian transition probabilities. We show how exact analytic formulae for the first and second moments of resident time distributions in mesostates can be derived from microscopic resident times and transition probabilities even for systems with a large number of microstates. We apply our formalism to models of the inositol trisphosphate receptor, which plays a key role in generating calcium signals triggering a wide variety of cellular responses. We demonstrate how experimentally accessible quantities, such as opening and closing times and the coefficient of variation of inter-spike intervals, and other, more elaborated, quantities can be analytically calculated from the underlying microscopic Markovian dynamics. A virtue of our approach is that we do not need to follow the detailed time evolution of the whole system, as we derive the relevant properties of its steady state without having to take into account the often extremely complicated transient features. We emphasize that our formulae fully agree with results obtained by stochastic simulations and approaches based on a full determination of the microscopic system's time evolution. We also illustrate how experiments can be devised to discriminate between alternative molecular models of the inositol trisphosphate receptor. The developed approach is applicable to any system described by a Markov process and, owing to the analytic nature of the resulting formulae, provides an easy way to characterize also rare events that are of particular importance to understand the intermittency properties of complex dynamic systems. (C) 2013 Elsevier Ltd. All rights reserved.

Original languageEnglish
Pages (from-to)102-112
Number of pages11
JournalJournal of Theoretical Biology
Volume343
Early online date21 Nov 2013
DOIs
Publication statusPublished - 21 Feb 2014

Keywords

  • calcium signaling
  • IP3 receptor
  • emergent properties of mesostates
  • Gillespie algorithm
  • inositol 1,4,5-trisphosphate receptors
  • IP3 receptors
  • kinetic-model
  • ion channels
  • single
  • simulations
  • cerebellum
  • reticulum
  • transport
  • clusters

Cite this

Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. / Christian, Nils; Skupin, Alexander; Morante, Silvia; Jansen, Karl; Rossi, Giancarlo; Ebenhoeh, Oliver.

In: Journal of Theoretical Biology, Vol. 343, 21.02.2014, p. 102-112.

Research output: Contribution to journalArticle

Christian, Nils ; Skupin, Alexander ; Morante, Silvia ; Jansen, Karl ; Rossi, Giancarlo ; Ebenhoeh, Oliver. / Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. In: Journal of Theoretical Biology. 2014 ; Vol. 343. pp. 102-112.
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AB - A major challenge in biology is to understand how molecular processes determine phenotypic features. We address this fundamental problem in a class of model systems by developing a general mathematical framework that allows the calculation of mesoscopic properties from the knowledge of microscopic Markovian transition probabilities. We show how exact analytic formulae for the first and second moments of resident time distributions in mesostates can be derived from microscopic resident times and transition probabilities even for systems with a large number of microstates. We apply our formalism to models of the inositol trisphosphate receptor, which plays a key role in generating calcium signals triggering a wide variety of cellular responses. We demonstrate how experimentally accessible quantities, such as opening and closing times and the coefficient of variation of inter-spike intervals, and other, more elaborated, quantities can be analytically calculated from the underlying microscopic Markovian dynamics. A virtue of our approach is that we do not need to follow the detailed time evolution of the whole system, as we derive the relevant properties of its steady state without having to take into account the often extremely complicated transient features. We emphasize that our formulae fully agree with results obtained by stochastic simulations and approaches based on a full determination of the microscopic system's time evolution. We also illustrate how experiments can be devised to discriminate between alternative molecular models of the inositol trisphosphate receptor. The developed approach is applicable to any system described by a Markov process and, owing to the analytic nature of the resulting formulae, provides an easy way to characterize also rare events that are of particular importance to understand the intermittency properties of complex dynamic systems. (C) 2013 Elsevier Ltd. All rights reserved.

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