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Lin H, Nie Z, Shang E, Dai S. An Adaptive Local Iterative Method for Fast Calculation of Electrostatic Interactions between Charged Polymers in Dielectric Inhomogeneous System. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Hao Lin
- School of Mathematics and Statistics Wuhan University Wuhan 430072 P. R. China
| | - Zhiji Nie
- School of Mathematics and Statistics Wuhan University Wuhan 430072 P. R. China
| | - Enlong Shang
- School of Mathematics and Statistics Wuhan University Wuhan 430072 P. R. China
| | - Shuyang Dai
- School of Mathematics and Statistics Wuhan University Wuhan 430072 P. R. China
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Colman MA, Alvarez-Lacalle E, Echebarria B, Sato D, Sutanto H, Heijman J. Multi-Scale Computational Modeling of Spatial Calcium Handling From Nanodomain to Whole-Heart: Overview and Perspectives. Front Physiol 2022; 13:836622. [PMID: 35370783 PMCID: PMC8964409 DOI: 10.3389/fphys.2022.836622] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of intracellular calcium is a critical component of cardiac electrophysiology and excitation-contraction coupling. The calcium spark, the fundamental element of the intracellular calcium transient, is initiated in specialized nanodomains which co-locate the ryanodine receptors and L-type calcium channels. However, calcium homeostasis is ultimately regulated at the cellular scale, by the interaction of spatially separated but diffusively coupled nanodomains with other sub-cellular and surface-membrane calcium transport channels with strong non-linear interactions; and cardiac electrophysiology and arrhythmia mechanisms are ultimately tissue-scale phenomena, regulated by the interaction of a heterogeneous population of coupled myocytes. Recent advances in imaging modalities and image-analysis are enabling the super-resolution reconstruction of the structures responsible for regulating calcium homeostasis, including the internal structure of nanodomains themselves. Extrapolating functional and imaging data from the nanodomain to the whole-heart is non-trivial, yet essential for translational insight into disease mechanisms. Computational modeling has important roles to play in relating structural and functional data at the sub-cellular scale and translating data across the scales. This review covers recent methodological advances that enable image-based modeling of the single nanodomain and whole cardiomyocyte, as well as the development of multi-scale simulation approaches to integrate data from nanometer to whole-heart. Firstly, methods to overcome the computational challenges of simulating spatial calcium dynamics in the nanodomain are discussed, including image-based modeling at this scale. Then, recent whole-cell models, capable of capturing a range of different structures (such as the T-system and mitochondria) and cellular heterogeneity/variability are discussed at two different levels of discretization. Novel methods to integrate the models and data across the scales and simulate stochastic dynamics in tissue-scale models are then discussed, enabling elucidation of the mechanisms by which nanodomain remodeling underlies arrhythmia and contractile dysfunction. Perspectives on model differences and future directions are provided throughout.
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Affiliation(s)
- Michael A. Colman
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
- *Correspondence: Michael A. Colman,
| | | | - Blas Echebarria
- Departament de Fisica, Universitat Politècnica de Catalunya-BarcelonaTech, Barcelona, Spain
| | - Daisuke Sato
- Department of Pharmacology, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Henry Sutanto
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Jordi Heijman
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
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3
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Huber GA, Miao Y, Zhou S, Li B, McCammon JA. Hybrid finite element and Brownian dynamics method for charged particles. J Chem Phys 2016; 144:164107. [PMID: 27131531 DOI: 10.1063/1.4947086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented using a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species.
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Affiliation(s)
- Gary A Huber
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365, USA
| | - Yinglong Miao
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365, USA
| | - Shenggao Zhou
- Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Suzhou, 215006 Jiangsu, China
| | - Bo Li
- Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0112, USA
| | - J Andrew McCammon
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093, USA
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George UZ, Wang J, Yu Z. Numerical analysis of the effect of T-tubule location on calcium transient in ventricular myocytes. Biomed Mater Eng 2014; 24:1299-306. [PMID: 24212025 DOI: 10.3233/bme-130932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Intracellular calcium (Ca2+) signaling in cardiac myocytes is vital for proper functioning of the heart. Understanding the intracellular Ca2+ dynamics would give an insight into the functions of normal and diseased hearts. In the current study, spatiotemporal Ca2+ dynamics is investigated in ventricular myocytes by considering Ca2+ release and re-uptake via sarcolemma and transverse tubules (T-tubules), Ca2+ diffusion and buffering in the cytosol, and the blockade of Ca2+ activities associated with the sarcoplasmic reticulum. This study is carried out using a three dimensional (3D) geometric model of a branch of T-tubule extracted from the electron microscopy (EM) images of a partial ventricular myocyte. Mathematical modeling is done by using a system of partial differential equations involving Ca2+, buffers, and membrane channels. Numerical simulation results suggest that a lack of T-tubule structure at the vicinity of the cell surface could increase the peak time of Ca2+ concentration in myocytes. The results also show that T-tubules and mobile buffers play an important role in the regulation of Ca2+ transient in ventricular myocytes.
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Affiliation(s)
- Uduak Z George
- Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, U.S.A
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Liu K, Yao G, Yu Z. Parallel acceleration for modeling of calcium dynamics in cardiac myocytes. Biomed Mater Eng 2013; 24:1417-24. [PMID: 24212039 DOI: 10.3233/bme-130946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Spatial-temporal calcium dynamics due to calcium release, buffering, and re-uptaking plays a central role in studying excitation-contraction (E-C) coupling in both healthy and defected cardiac myocytes. In our previous work, partial differential equations (PDEs) had been used to simulate calcium dynamics with realistic geometries extracted from electron microscopic imaging data. However, the computational costs of such simulations are very high on a single processor. To alleviate this problem, we have accelerated the numerical simulations of calcium dynamics by using graphics processing units (GPUs). Computational performance and simulation accuracy are compared with those based on a single CPU and another popular parallel computing technique, OpenMP.
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Affiliation(s)
- Ke Liu
- Department of Computer Science, University of Wisconsin-Milwaukee, WI, USA
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Sensitivity of rabbit ventricular action potential and Ca²⁺ dynamics to small variations in membrane currents and ion diffusion coefficients. BIOMED RESEARCH INTERNATIONAL 2013; 2013:565431. [PMID: 24222910 PMCID: PMC3814049 DOI: 10.1155/2013/565431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 08/19/2013] [Indexed: 12/19/2022]
Abstract
Little is known about how small variations in ionic currents and Ca²⁺ and Na⁺ diffusion coefficients impact action potential and Ca²⁺ dynamics in rabbit ventricular myocytes. We applied sensitivity analysis to quantify the sensitivity of Shannon et al. model (Biophys. J., 2004) to 5%-10% changes in currents conductance, channels distribution, and ion diffusion in rabbit ventricular cells. We found that action potential duration and Ca²⁺ peaks are highly sensitive to 10% increase in L-type Ca²⁺ current; moderately influenced by 10% increase in Na⁺-Ca²⁺ exchanger, Na⁺-K⁺ pump, rapid delayed and slow transient outward K⁺ currents, and Cl⁻ background current; insensitive to 10% increases in all other ionic currents and sarcoplasmic reticulum Ca²⁺ fluxes. Cell electrical activity is strongly affected by 5% shift of L-type Ca²⁺ channels and Na⁺-Ca²⁺ exchanger in between junctional and submembrane spaces while Ca²⁺-activated Cl⁻-channel redistribution has the modest effect. Small changes in submembrane and cytosolic diffusion coefficients for Ca²⁺, but not in Na⁺ transfer, may alter notably myocyte contraction. Our studies highlight the need for more precise measurements and further extending and testing of the Shannon et al. model. Our results demonstrate usefulness of sensitivity analysis to identify specific knowledge gaps and controversies related to ventricular cell electrophysiology and Ca²⁺ signaling.
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Yu Z, Wang J, Gao Z, Xu M, Hoshijima M. New software developments for quality mesh generation and optimization from biomedical imaging data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2013; 113:226-40. [PMID: 24252469 PMCID: PMC3836056 DOI: 10.1016/j.cmpb.2013.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 08/16/2013] [Accepted: 08/16/2013] [Indexed: 06/02/2023]
Abstract
In this paper we present a new software toolkit for generating and optimizing surface and volumetric meshes from three-dimensional (3D) biomedical imaging data, targeted at image-based finite element analysis of some biomedical activities in a single material domain. Our toolkit includes a series of geometric processing algorithms including surface re-meshing and quality-guaranteed tetrahedral mesh generation and optimization. All methods described have been encapsulated into a user-friendly graphical interface for easy manipulation and informative visualization of biomedical images and mesh models. Numerous examples are presented to demonstrate the effectiveness and efficiency of the described methods and toolkit.
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Affiliation(s)
- Zeyun Yu
- Department of Computer Science, University of Wisconsin at Milwaukee, USA.
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Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries. Front Physiol 2012; 3:351. [PMID: 23060801 PMCID: PMC3463892 DOI: 10.3389/fphys.2012.00351] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 08/16/2012] [Indexed: 12/26/2022] Open
Abstract
The transverse tubular system of rabbit ventricular myocytes consists of cell membrane invaginations (t-tubules) that are essential for efficient cardiac excitation-contraction coupling. In this study, we investigate how t-tubule micro-anatomy, L-type Ca2+ channel (LCC) clustering, and allosteric activation of Na+/Ca2+ exchanger by L-type Ca2+ current affects intracellular Ca2+ dynamics. Our model includes a realistic 3D geometry of a single t-tubule and its surrounding half-sarcomeres for rabbit ventricular myocytes. The effects of spatially distributed membrane ion-transporters (LCC, Na+/Ca2+ exchanger, sarcolemmal Ca2+ pump, and sarcolemmal Ca2+ leak), and stationary and mobile Ca2+ buffers (troponin C, ATP, calmodulin, and Fluo-3) are also considered. We used a coupled reaction-diffusion system to describe the spatio-temporal concentration profiles of free and buffered intracellular Ca2+. We obtained parameters from voltage-clamp protocols of L-type Ca2+ current and line-scan recordings of Ca2+ concentration profiles in rabbit cells, in which the sarcoplasmic reticulum is disabled. Our model results agree with experimental measurements of global Ca2+ transient in myocytes loaded with 50 μM Fluo-3. We found that local Ca2+ concentrations within the cytosol and sub-sarcolemma, as well as the local trigger fluxes of Ca2+ crossing the cell membrane, are sensitive to details of t-tubule micro-structure and membrane Ca2+ flux distribution. The model additionally predicts that local Ca2+ trigger fluxes are at least threefold to eightfold higher than the whole-cell Ca2+ trigger flux. We found also that the activation of allosteric Ca2+-binding sites on the Na+/Ca2+ exchanger could provide a mechanism for regulating global and local Ca2+ trigger fluxes in vivo. Our studies indicate that improved structural and functional models could improve our understanding of the contributions of L-type and Na+/Ca2+ exchanger fluxes to intracellular Ca2+ dynamics.
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Bauler P, Huber GA, McCammon JA. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions. J Chem Phys 2012; 136:164107. [PMID: 22559470 DOI: 10.1063/1.4704808] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetric diffusion systems.
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Affiliation(s)
- Patricia Bauler
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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Cheng Y, Kekenes-Huskey P, Hake J, Holst M, McCammon J, Michailova A. Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction. ACTA ACUST UNITED AC 2012; 5. [PMID: 23505398 DOI: 10.1088/1749-4699/5/1/015002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This article provides a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally-validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times with increasing ionic strength and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a non-linear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally-derived rodent ventricular myocyte geometries. Results reveal the important role for mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that the alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate subcellular Ca2+ signals. Model predicts that reduced off-rate in whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for integration of molecular-scale information into simulations of cellular-scale systems.
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Affiliation(s)
- Y Cheng
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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Yao G, Yu Z. A localized meshless approach for modeling spatial-temporal calcium dynamics in ventricular myocytes. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2012; 28:187-204. [PMID: 22408720 PMCID: PMC3294421 DOI: 10.1002/cnm.1453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Spatial–temporal calcium dynamics due to calcium release, buffering and re-uptaking plays a central role in studying excitation–contraction (E–C) coupling in both normal and diseased cardiac myocytes. In this paper, we employ a meshless method, namely, the local radial basis function collocation method (LRBFCM), to model such calcium behaviors by solving a nonlinear system of reaction–diffusion partial differential equations. In particular, a simplified structural unit containing a single transverse tubule (T-tubule) and its surrounding half sarcomeres is investigated using the meshless method. Numerical results are compared with those generated by finite element methods, showing the capability and efficiency of the LRBFCM in modeling calcium dynamics in ventricular myocytes. The single T-tubule model is also extended to the whole-cell scale with T-tubules excluded to demonstrate the scalability of the proposed meshless method in handling very large domains. The experiments have shown that the LRBFCM is suitable to multiscale modeling of calcium dynamics in ventricular myocytes with high accuracy and efficiency.
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Affiliation(s)
| | - Zeyun Yu
- Correspondence to: Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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Yu Z, Yao G, Hoshijima M, Michailova A, Holst M. Multiscale modeling of calcium dynamics in ventricular myocytes with realistic transverse tubules. IEEE Trans Biomed Eng 2011; 58:2947-51. [PMID: 21632291 DOI: 10.1109/tbme.2011.2158316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spatial-temporal Ca(2+) dynamics due to Ca(2+) release, buffering, and reuptaking plays a central role in studying excitation-contraction (E-C) coupling in both normal and diseased cardiac myocytes. In this paper, we employ two numerical methods, namely, the meshless method and the finite element method, to model such Ca(2+) behaviors by solving a nonlinear system of reaction-diffusion partial differential equations at two scales. In particular, a subcellular model containing several realistic transverse tubules (or t-tubules) is investigated and assumed to reside at different locations relative to the cell membrane. To this end, the Ca(2+) concentration calculated from the whole-cell modeling is adopted as part of the boundary constraint in the subcellular model. The preliminary simulations show that Ca(2+) concentration changes in ventricular myocytes are mainly influenced by calcium release from t-tubules.
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Affiliation(s)
- Zeyun Yu
- Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP. Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput Biol 2010; 6:e1000972. [PMID: 21060856 PMCID: PMC2965743 DOI: 10.1371/journal.pcbi.1000972] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 09/23/2010] [Indexed: 12/21/2022] Open
Abstract
The t-tubules of mammalian ventricular myocytes are invaginations of the cell membrane that occur at each Z-line. These invaginations branch within the cell to form a complex network that allows rapid propagation of the electrical signal, and hence synchronous rise of intracellular calcium (Ca2+). To investigate how the t-tubule microanatomy and the distribution of membrane Ca2+ flux affect cardiac excitation-contraction coupling we developed a 3-D continuum model of Ca2+ signaling, buffering and diffusion in rat ventricular myocytes. The transverse-axial t-tubule geometry was derived from light microscopy structural data. To solve the nonlinear reaction-diffusion system we extended SMOL software tool (http://mccammon.ucsd.edu/smol/). The analysis suggests that the quantitative understanding of the Ca2+ signaling requires more accurate knowledge of the t-tubule ultra-structure and Ca2+ flux distribution along the sarcolemma. The results reveal the important role for mobile and stationary Ca2+ buffers, including the Ca2+ indicator dye. In agreement with experiment, in the presence of fluorescence dye and inhibited sarcoplasmic reticulum, the lack of detectible differences in the depolarization-evoked Ca2+ transients was found when the Ca2+ flux was heterogeneously distributed along the sarcolemma. In the absence of fluorescence dye, strongly non-uniform Ca2+ signals are predicted. Even at modest elevation of Ca2+, reached during Ca2+ influx, large and steep Ca2+ gradients are found in the narrow sub-sarcolemmal space. The model predicts that the branched t-tubule structure and changes in the normal Ca2+ flux density along the cell membrane support initiation and propagation of Ca2+ waves in rat myocytes. In cardiac muscle cells, calcium (Ca2+) is best known for its role in contraction activation. A remarkable amount of quantitative data on cardiac cell structure, ion-transporting protein distributions and intracellular Ca2+ dynamics has been accumulated. Various alterations in the protein distributions or cell ultra-structure are now recognized to be the primary mechanisms of cardiac dysfunction in a diverse range of common pathologies including cardiac arrhythmias and hypertrophy. Using a 3-D computational model, incorporating more realistic transverse-axial t-tubule geometry and considering geometric irregularities and inhomogeneities in the distribution of ion-transporting proteins, we analyze several important spatial and temporal features of Ca2+ signaling in rat ventricular myocytes. This study demonstrates that the computational models could serve as powerful tools for prediction and analyses of how the Ca2+ dynamics and cardiac excitation-contraction coupling are regulated under normal conditions or certain pathologies. The use of computational and mathematical approaches will help also to better understand aspects of cell functions that are not currently amenable to experimental investigation.
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Affiliation(s)
- Yuhui Cheng
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Zeyun Yu
- Department of Computer Science, University of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Masahiko Hoshijima
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Michael J. Holst
- Department of Mathematics, University of California San Diego, La Jolla, California, United States of America
| | - Andrew D. McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Anushka P. Michailova
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Fink M, Niederer SA, Cherry EM, Fenton FH, Koivumäki JT, Seemann G, Thul R, Zhang H, Sachse FB, Beard D, Crampin EJ, Smith NP. Cardiac cell modelling: observations from the heart of the cardiac physiome project. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 104:2-21. [PMID: 20303361 DOI: 10.1016/j.pbiomolbio.2010.03.002] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 12/06/2009] [Accepted: 03/04/2010] [Indexed: 10/19/2022]
Abstract
In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field.
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Affiliation(s)
- Martin Fink
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3JP, United Kingdom
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