Particle-based multiscale modeling of calcium puff dynamics

DOI10.1137/15M1015030MaRDI QIDQ5298149zbMATH OpenOpenAlexFDO

Authors U. Dobramysl, Radek Erban, S. Rüdiger

Publication date 13 December 2016

Published in Multiscale Modeling & Simulation (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/1504.00146

zbMATH Keywords

calcium puffsintracellular calciummultiscale modelingstochastic diffusion

Mathematics Subject Classification ID

Stochastic particle methods (65C35) Systems biology, networks (92C42)

Abstract: Intracellular calcium is regulated in part by the release of Ca${}^{2+}$ ions from the endoplasmic reticulum via inositol-4,5-triphosphate receptor (IP${}_3$R) channels (among other possibilities such as RyR and L-type calcium channels). The resulting dynamics are highly diverse, lead to local calcium "puffs" as well as global waves propagating through cells, as observed in {it Xenopus} oocytes, neurons, and other cell types. Local fluctuations in the number of calcium ions play a crucial role in the onset of these features. Previous modeling studies of calcium puff dynamics stemming from IP${}_3$R channels have predominantly focused on stochastic channel models coupled to deterministic diffusion of ions, thereby neglecting local fluctuations of the ion number. Tracking of individual ions is computationally difficult due to the scale separation in the Ca${}^{2+}$ concentration when channels are in the open or closed states. In this paper, a spatial multiscale model for investigating of the dynamics of puffs is presented. It couples Brownian motion (diffusion) of ions with a stochastic channel gating model. The model is used to analyze calcium puff statistics. Concentration time traces as well as channel state information are studied. We identify the regime in which puffs can be found and develop a mean-field theory to extract the boundary of this regime. Puffs are only possible when the time scale of channel inhibition is sufficiently large. Implications for the understanding of puff generation and termination are discussed.

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Cited in

(15)

• Multilevel and multi-index Monte Carlo methods for the McKean-Vlasov equation
• Modeling local and global intracellular calcium responses mediated by diffusely distributed inositol 1,4,5-trisphosphate receptors
• Calcium-dependent inactivation and the dynamics of calcium puffs and sparks
• Modelling calcium microdomains using homogenisation
• Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions
• Multiscale stochastic reaction-diffusion algorithms combining Markov chain models with stochastic partial differential equations
• Reactive boundary conditions as limits of interaction potentials for Brownian and Langevin dynamics
• Building oscillations bottom up: elemental time scales of intracellular calcium dynamics
• \(\mathrm{Ca}^{2+}\)-activation kinetics modulate successive puff/spark amplitude, duration and inter-event-interval correlations in a Langevin model of stochastic \(\mathrm{Ca}^{2+}\) release
• A model-based method for estimating \(\mathrm{Ca}^{2+}\) release fluxes from linescan images in \textit{Xenopus} oocytes
• Double-loop importance sampling for McKean-Vlasov stochastic differential equation
• Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling
• Multilevel importance sampling for rare events associated with the McKean-Vlasov equation
• A \(\text{Ca}^{2+}\) puff model based on integrodifferential equations
• Multi-index importance sampling for McKean-Vlasov stochastic differential equations

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Uses Software

• Tyche
• Smoldyn
• MesoRD

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