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Simulation Strategies for Calcium Microdomains and Calcium Noise.
Adv Exp Med Biol 2020; 1131:771-797AE

Abstract

In this article, we present an overview of simulation strategies in the context of subcellular domains where calcium-dependent signaling plays an important role. The presentation follows the spatial and temporal scales involved and represented by each algorithm. As an exemplary cell type, we will mainly cite work done on striated muscle cells, i.e. skeletal and cardiac muscle. For these cells, a wealth of ultrastructural, biophysical and electrophysiological data is at hand. Moreover, these cells also express ubiquitous signaling pathways as they are found in many other cell types and thus, the generalization of the methods and results presented here is straightforward.The models considered comprise the basic calcium signaling machinery as found in most excitable cell types including Ca2+ ions, diffusible and stationary buffer systems, and calcium regulated calcium release channels. Simulation strategies can be differentiated in stochastic and deterministic algorithms. Historically, deterministic approaches based on the macroscopic reaction rate equations were the first models considered. As experimental methods elucidated highly localized Ca2+ signaling events occurring in femtoliter volumes, stochastic methods were increasingly considered. However, detailed simulations of single molecule trajectories are rarely performed as the computational cost implied is too large. On the mesoscopic level, Gillespie's algorithm is extensively used in the systems biology community and with increasing frequency also in models of microdomain calcium signaling. To increase computational speed, fast approximations were derived from Gillespie's exact algorithm, most notably the chemical Langevin equation and the τ-leap algorithm. Finally, in order to integrate deterministic and stochastic effects in multiscale simulations, hybrid algorithms are increasingly used. These include stochastic models of ion channels combined with deterministic descriptions of the calcium buffering and diffusion system on the one hand, and algorithms that switch between deterministic and stochastic simulation steps in a context-dependent manner on the other. The basic assumptions of the listed methods as well as implementation schemes are given in the text. We conclude with a perspective on possible future developments of the field.

Authors+Show Affiliations

Broad Institute of MIT and Harvard, Cambridge, MA, USA. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. Medical Biophysics Group, Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany.Medical Biophysics Group, Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany.Medical Biophysics Group, Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany. vonWegner@med.uni-frankfurt.de. Department of Neurology and Brain Imaging Center, Goethe University Frankfurt, Frankfurt am Main, Germany. vonWegner@med.uni-frankfurt.de.

Pub Type(s)

Journal Article
Review

Language

eng

PubMed ID

31646534

Citation

Wieder, Nicolas, et al. "Simulation Strategies for Calcium Microdomains and Calcium Noise." Advances in Experimental Medicine and Biology, vol. 1131, 2020, pp. 771-797.
Wieder N, Fink RHA, von Wegner F. Simulation Strategies for Calcium Microdomains and Calcium Noise. Adv Exp Med Biol. 2020;1131:771-797.
Wieder, N., Fink, R. H. A., & von Wegner, F. (2020). Simulation Strategies for Calcium Microdomains and Calcium Noise. Advances in Experimental Medicine and Biology, 1131, pp. 771-797. doi:10.1007/978-3-030-12457-1_31.
Wieder N, Fink RHA, von Wegner F. Simulation Strategies for Calcium Microdomains and Calcium Noise. Adv Exp Med Biol. 2020;1131:771-797. PubMed PMID: 31646534.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Simulation Strategies for Calcium Microdomains and Calcium Noise. AU - Wieder,Nicolas, AU - Fink,Rainer H A, AU - von Wegner,Frederic, PY - 2019/10/25/entrez PY - 2019/10/28/pubmed PY - 2019/10/30/medline KW - Calcium KW - Calcium noise KW - Calcium signaling KW - Chemical master equation KW - Colored noise KW - Gillespie’s algorithm KW - IP3R KW - Langevin equation KW - Microdomains KW - Stochastic modeling SP - 771 EP - 797 JF - Advances in experimental medicine and biology JO - Adv. Exp. Med. Biol. VL - 1131 N2 - In this article, we present an overview of simulation strategies in the context of subcellular domains where calcium-dependent signaling plays an important role. The presentation follows the spatial and temporal scales involved and represented by each algorithm. As an exemplary cell type, we will mainly cite work done on striated muscle cells, i.e. skeletal and cardiac muscle. For these cells, a wealth of ultrastructural, biophysical and electrophysiological data is at hand. Moreover, these cells also express ubiquitous signaling pathways as they are found in many other cell types and thus, the generalization of the methods and results presented here is straightforward.The models considered comprise the basic calcium signaling machinery as found in most excitable cell types including Ca2+ ions, diffusible and stationary buffer systems, and calcium regulated calcium release channels. Simulation strategies can be differentiated in stochastic and deterministic algorithms. Historically, deterministic approaches based on the macroscopic reaction rate equations were the first models considered. As experimental methods elucidated highly localized Ca2+ signaling events occurring in femtoliter volumes, stochastic methods were increasingly considered. However, detailed simulations of single molecule trajectories are rarely performed as the computational cost implied is too large. On the mesoscopic level, Gillespie's algorithm is extensively used in the systems biology community and with increasing frequency also in models of microdomain calcium signaling. To increase computational speed, fast approximations were derived from Gillespie's exact algorithm, most notably the chemical Langevin equation and the τ-leap algorithm. Finally, in order to integrate deterministic and stochastic effects in multiscale simulations, hybrid algorithms are increasingly used. These include stochastic models of ion channels combined with deterministic descriptions of the calcium buffering and diffusion system on the one hand, and algorithms that switch between deterministic and stochastic simulation steps in a context-dependent manner on the other. The basic assumptions of the listed methods as well as implementation schemes are given in the text. We conclude with a perspective on possible future developments of the field. SN - 0065-2598 UR - https://www.unboundmedicine.com/medline/citation/31646534/Simulation_Strategies_for_Calcium_Microdomains_and_Calcium_Noise_ L2 - https://dx.doi.org/10.1007/978-3-030-12457-1_31 DB - PRIME DP - Unbound Medicine ER -