scholarly journals Accelerating mono-domain cardiac electrophysiology simulations using OpenCL

2015 ◽  
Vol 1 (1) ◽  
pp. 413-417
Author(s):  
Eike M. Wülfers ◽  
Zhasur Zhamoliddinov ◽  
Olaf Dössel ◽  
Gunnar Seemann
Keyword(s):  
Cardiac Electrophysiology ◽  
Cardiac Tissue ◽  
Ionic Currents ◽  
Domain Model ◽  
Electrical Excitation ◽  
Simulation Domain ◽  
Speed Up ◽  
Cross Platform ◽  
Atrial Myocyte ◽  
Intel Xeon

AbstractUsing OpenCL, we developed a cross-platform software to compute electrical excitation conduction in cardiac tissue. OpenCL allowed the software to run parallelized and on different computing devices (e.g., CPUs and GPUs). We used the macroscopic mono-domain model for excitation conduction and an atrial myocyte model by Courtemanche et al. for ionic currents. On a CPU with 12 HyperThreading-enabled Intel Xeon 2.7 GHz cores, we achieved a speed-up of simulations by a factor of 1.6 against existing software that uses OpenMPI. On two high-end AMD FirePro D700 GPUs the OpenCL software ran 2.4 times faster than the OpenMPI implementation. The more nodes the discretized simulation domain contained, the higher speed-ups were achieved.

scholarly journals An integrated platform for intuitive mathematical programming modeling using LaTeX

2018 ◽  
Vol 4 ◽  
pp. e161 ◽  
Author(s):  
Charalampos P. Triantafyllidis ◽  
Lazaros G. Papageorgiou
Keyword(s):  
Mathematical Programming ◽  
Error Detection ◽  
Development Process ◽  
Optimization Problems ◽  
Scientific Work ◽  
Input Language ◽  
Speed Up ◽  
Cross Platform ◽  
Algebraic Modeling Language ◽  
Friendly Graphical User Interface

This paper presents a novel prototype platform that uses the same LaTeX mark-up language, commonly used to typeset mathematical content, as an input language for modeling optimization problems of various classes. The platform converts the LaTeX model into a formal Algebraic Modeling Language (AML) representation based on Pyomo through a parsing engine written in Python and solves by either via NEOS server or locally installed solvers, using a friendly Graphical User Interface (GUI). The distinct advantages of our approach can be summarized in (i) simplification and speed-up of the model design and development process (ii) non-commercial character (iii) cross-platform support (iv) easier typo and logic error detection in the description of the models and (v) minimization of working knowledge of programming and AMLs to perform mathematical programming modeling. Overall, this is a presentation of a complete workable scheme on using LaTeX for mathematical programming modeling which assists in furthering our ability to reproduce and replicate scientific work.

scholarly journals Numerical Simulations of Fractionated Electrograms and Pathological Cardiac Action Potential

2002 ◽  
Vol 4 (3) ◽  
pp. 167-181 ◽  
Author(s):  
Simona Sanfelici
Keyword(s):  
Numerical Simulations ◽  
Cardiac Tissue ◽  
Time Discretization ◽  
Ionic Currents ◽  
Bidomain Model ◽  
Approximation Process ◽  
Point Of Interest ◽  
Intracellular Conductivity ◽  
Membrane Ionic Currents ◽  
Fractionated Electrograms

The aim of this work is twofold. First we focus on the complex phenomenon of electrogram fractionation, due to the presence of discontinuities in the conduction properties of the cardiac tissue in a bidomain model. Numerical simulations of paced activation may help to understand the role of the membrane ionic currents and of the changes in cellular coupling in the formation of conduction blocks and fractionation of the electrogram waveform. In particular, we show that fractionation is independent ofINAalterations and that it can be described by the bidomain model of cardiac tissue. Moreover, some deflections in fractionated electrograms may give nonlocal information about the shape of damaged areas, also revealing the presence of inhomogeneities in the intracellular conductivity of the medium at a distance.The second point of interest is the analysis of the effects of space–time discretization on numerical results, especially during slow conduction in damaged cardiac tissue. Indeed, large discretization steps can induce numerical artifacts such as slowing down of conduction velocity, alteration in extracellular and transmembrane potential waveforms or conduction blocks, which are not predicted by the continuous bidomain model. Several possible numerical and physiological explanations of these effects are given. Essentially, the discrete system obtained at the end of the approximation process may be interpreted as a discrete model of the cardiac tissue made up of isopotential cells where the effective intracellular conductivity tensor depends on the space discretization steps; the increase of these steps results in an increase of the effective intracellular resistance and can induce conduction blocks if a certain critical value is exceeded.

Observations on intramembrane charge movements in skeletal muscle

1975 ◽  
Vol 270 (908) ◽  
pp. 507-513 ◽  
Keyword(s):  
Ionic Currents ◽  
Charge Movement ◽  
Electrical Excitation ◽  
Signal Averaging ◽  
Gating Current ◽  
Residual Currents ◽  
Contraction Coupling ◽  
Intramembrane Charge Movement ◽  
Charge Movements ◽  
Averaging Techniques

Using signal-averaging techniques, one can record small membrane currents which remain even after blockage of the ionic currents which accompany electrical excitation in muscle. These residual currents probably represent the reorientation of charged molecules inside the membrane in response to a change in membrane potential. Two operationally separable types of intramembrane charge movement in muscle are described, one of which may play a role in excitation—contraction coupling. Studies of tetrodotoxin binding to muscle indicate that ‘sodium gating current’ is unlikely to contribute significantly to either type of charge movement.

scholarly journals Optimisation of a Generic Ionic Model of Cardiac Myocyte Electrical Activity

2013 ◽  
Vol 2013 ◽  
pp. 1-20 ◽  
Author(s):  
Tianruo Guo ◽  
Amr Al Abed ◽  
Nigel H. Lovell ◽  
Socrates Dokos
Keyword(s):  
Action Potential ◽  
Time Course ◽  
Cardiac Myocyte ◽  
Cardiac Tissue ◽  
Ionic Currents ◽  
Experimental Information ◽  
Electrical Stimulus ◽  
Right Atrial ◽  
Ionic Model ◽  
Multiple Datasets

A generic cardiomyocyte ionic model, whose complexity lies between a simple phenomenological formulation and a biophysically detailed ionic membrane current description, is presented. The model provides a user-defined number of ionic currents, employing two-gate Hodgkin-Huxley type kinetics. Its generic nature allows accurate reconstruction of action potential waveforms recorded experimentally from a range of cardiac myocytes. Using a multiobjective optimisation approach, the generic ionic model was optimised to accurately reproduce multiple action potential waveforms recorded from central and peripheral sinoatrial nodes and right atrial and left atrial myocytes from rabbit cardiac tissue preparations, under different electrical stimulus protocols and pharmacological conditions. When fitted simultaneously to multiple datasets, the time course of several physiologically realistic ionic currents could be reconstructed. Model behaviours tend to be well identified when extra experimental information is incorporated into the optimisation.

A computationally efficient electrophysiological model of human ventricular cells

2002 ◽  
Vol 282 (6) ◽  
pp. H2296-H2308 ◽  
Author(s):  
O. Bernus ◽  
R. Wilders ◽  
C. W. Zemlin ◽  
H. Verschelde ◽  
A. V. Panfilov
Keyword(s):  
Action Potential ◽  
Cardiac Tissue ◽  
Spiral Wave ◽  
Ionic Currents ◽  
Average Frequency ◽  
Computationally Efficient ◽  
Variable Model ◽  
Potential Shape ◽  
Ventricular Cells ◽  
Ventricular Tissue

Recent experimental and theoretical results have stressed the importance of modeling studies of reentrant arrhythmias in cardiac tissue and at the whole heart level. We introduce a six-variable model obtained by a reformulation of the Priebe-Beuckelmann model of a single human ventricular cell. The reformulated model is 4.9 times faster for numerical computations and it is more stable than the original model. It retains the action potential shape at various frequencies, restitution of action potential duration, and restitution of conduction velocity. We were able to reproduce the main properties of epicardial, endocardial, and M cells by modifying selected ionic currents. We performed a simulation study of spiral wave behavior in a two-dimensional sheet of human ventricular tissue and showed that spiral waves have a frequency of 3.3 Hz and a linear core of ∼50-mm diameter that rotates with an average frequency of 0.62 rad/s. Simulation results agreed with experimental data. In conclusion, the proposed model is suitable for efficient and accurate studies of reentrant phenomena in human ventricular tissue.

scholarly journals Stop the beat to see the rhythm: excitation-contraction uncoupling in cardiac research

2021 ◽  
Author(s):  
Luther M. Swift ◽  
Matthew W. Kay ◽  
Crystal M. Ripplinger ◽  
Nikki Gillum Posnack
Keyword(s):  
Electrical Activity ◽  
Cardiac Electrophysiology ◽  
Cardiac Tissue ◽  
Optical Mapping ◽  
Myocardial Contraction ◽  
Motion Artifacts ◽  
Secondary Effects ◽  
Metabolic Demand ◽  
Cardiovascular Research ◽  
Fluorescent Indicators

Optical mapping is an imaging technique that is extensively used in cardiovascular research, wherein parameter-sensitive fluorescent indicators are used to study the electrophysiology and excitation-contraction coupling of cardiac tissues. Despite the many benefits of optical mapping, eliminating motion artifacts within the optical signals is a major challenge, as myocardial contraction interferes with the faithful acquisition of action potentials and intracellular calcium transients. As such, excitation-contraction uncoupling agents are frequently used to reduce signal distortion by suppressing contraction. Compared to other uncoupling agents, blebbistatin is the most frequently used as it offers increased potency with minimal direct effects on cardiac electrophysiology. Nevertheless, blebbistatin may exert secondary effects on electrical activity, metabolism, and coronary flow, and the incorrect administration of blebbistatin to cardiac tissue can prove detrimental, resulting in erroneous interpretation of optical mapping results. In this "Getting It Right" perspective, we briefly review the literature regarding the use of blebbistatin in cardiac optical mapping experiments, highlight potential secondary effects of blebbistatin on cardiac electrical activity and metabolic demand, and conclude with the consensus of the authors on best practices for effectively using blebbistatin in optical mapping studies of cardiac tissue.

scholarly journals An Auto-Programming Approach to Vulkan

2021 ◽  
Author(s):  
Vladimir Alexandrovich Frolov ◽  
Vadim Sanzharov ◽  
Vladimir Alexandrovich Galaktionov ◽  
Alexandr Scherbakov
Keyword(s):  
Performance Studies ◽  
General Purpose ◽  
Software Implementation ◽  
Programming Approach ◽  
Fine Grained ◽  
Speed Up ◽  
Cross Platform ◽  
Increase Productivity ◽  
And Performance ◽  
High Level

We propose a novel high-level approach for software development on GPU using Vulkan API. Our goal is to speed-up development and performance studies for complex algorithms on GPU, which is quite difficult and laborious for Vulkan due to large number of HW features low level details. The proposed approach uses auto programming to translate ordinary C++ to optimized Vulkan implementation with automatic shaders generation, resource binding and fine-grained barriers placement. Our model is not general-purpose programming, but is extendible and customer-focused. For a single C++ input our tool can generate multiple different implementations of algorithm in Vulkan for different cases or types of hardware. For example, we automatically detect reduction in C++ source code and then generate several variants of parallel reduction on GPU: with optimization for different warp size, with or without atomics, using or not subgroup operations. Another example is GPU ray tracing applications for which we can generate different variants: pure software implementation in compute shader, using hardware accelerated ray queries, using full RTX pipeline. The goal of our work is to increase productivity of developers who are forced to use Vulkan due to various required hardware features in their software but still do care about cross-platform ability of the developed software and want to debug their algorithm logic on the CPU. Therefore, we assume that the user will take generated code and integrate it with hand-written Vulkan code.

scholarly journals POD-Enhanced Deep Learning-Based Reduced Order Models for the Real-Time Simulation of Cardiac Electrophysiology in the Left Atrium

2021 ◽  
Vol 12 ◽  
Author(s):  
Stefania Fresca ◽  
Andrea Manzoni ◽  
Luca Dedè ◽  
Alfio Quarteroni
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Left Atrium ◽  
Real Time ◽  
Cardiac Electrophysiology ◽  
Front Propagation ◽  
Reduced Order Models ◽  
Reduced Order ◽  
Training Costs ◽  
Speed Up

The numerical simulation of multiple scenarios easily becomes computationally prohibitive for cardiac electrophysiology (EP) problems if relying on usual high-fidelity, full order models (FOMs). Likewise, the use of traditional reduced order models (ROMs) for parametrized PDEs to speed up the solution of the aforementioned problems can be problematic. This is primarily due to the strong variability characterizing the solution set and to the nonlinear nature of the input-output maps that we intend to reconstruct numerically. To enhance ROM efficiency, we proposed a new generation of non-intrusive, nonlinear ROMs, based on deep learning (DL) algorithms, such as convolutional, feedforward, and autoencoder neural networks. In the proposed DL-ROM, both the nonlinear solution manifold and the nonlinear reduced dynamics used to model the system evolution on that manifold can be learnt in a non-intrusive way thanks to DL algorithms trained on a set of FOM snapshots. DL-ROMs were shown to be able to accurately capture complex front propagation processes, both in physiological and pathological cardiac EP, very rapidly once neural networks were trained, however, at the expense of huge training costs. In this study, we show that performing a prior dimensionality reduction on FOM snapshots through randomized proper orthogonal decomposition (POD) enables to speed up training times and to decrease networks complexity. Accuracy and efficiency of this strategy, which we refer to as POD-DL-ROM, are assessed in the context of cardiac EP on an idealized left atrium (LA) geometry and considering snapshots arising from a NURBS (non-uniform rational B-splines)-based isogeometric analysis (IGA) discretization. Once the ROMs have been trained, POD-DL-ROMs can efficiently solve both physiological and pathological cardiac EP problems, for any new scenario, in real-time, even in extremely challenging contexts such as those featuring circuit re-entries, that are among the factors triggering cardiac arrhythmias.

scholarly journals Rotational Activity around an Obstacle in 2D Cardiac Tissue in Presence of Cellular Heterogeneity

Mathematics ◽  
2021 ◽  
Vol 9 (23) ◽  
pp. 3090
Author(s):  
Pavel Konovalov ◽  
Daria Mangileva ◽  
Arsenii Dokuchaev ◽  
Olga Solovyova ◽  
Alexander V. Panfilov
Keyword(s):  
Cardiac Tissue ◽  
Numerical Study ◽  
Cellular Heterogeneity ◽  
Gray Zone ◽  
Electrical Excitation ◽  
Minimal Period ◽  
Ionic Model ◽  
Human Cardiomyocytes ◽  
Wave Rotation ◽  
Dynamical Instabilities

Waves of electrical excitation rotating around an obstacle is one of the important mechanisms of dangerous cardiac arrhythmias occurring in the heart damaged by a post-infarction scar. Such a scar is also surrounded by the region of heterogeneity called a gray zone. In this paper, we perform the first comprehensive numerical study of various regimes of wave rotation around an obstacle surrounded by a gray zone. We use the TP06 cellular ionic model for human cardiomyocytes and study how the period and the pattern of wave rotation depend on the radius of a circular obstacle and the width of a circular gray zone. Our main conclusions are the following. The wave rotation regimes can be subdivided into three main classes: (1) functional rotation, (2) scar rotation and the newly found (3) gray zone rotation regimes. In the scar rotation regime, the wave rotates around the obstacle, while in the gray zone regime, the wave rotates around the gray zone. As a result, the period of rotation is determined by the perimeter of the scar, or gray zone perimeter correspondingly. The transition from the scar to the gray rotation regimes can be determined from the minimal period principle, formulated in this paper. We have also observed additional regimes associated with two types of dynamical instabilities which may affect or not affect the period of rotation. The results of this study can help to identify the factors determining the period of arrhythmias in post-infarction patients.

scholarly journals Mechanoelectric coupling and arrhythmogenesis in cardiomyocytes contracting under mechanical afterload in a 3D viscoelastic hydrogel

2021 ◽  
Vol 118 (31) ◽  
pp. e2108484118
Author(s):  
Bence Hegyi ◽  
Rafael Shimkunas ◽  
Zhong Jian ◽  
Leighton T. Izu ◽  
Donald M. Bers ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Action Potential ◽  
Cardiac Electrophysiology ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Ionic Currents ◽  
Adult Rabbit ◽  
Nitric Oxide Signaling ◽  
Mechanoelectric Coupling ◽  
The Individual

The heart pumps blood against the mechanical afterload from arterial resistance, and increased afterload may alter cardiac electrophysiology and contribute to life-threatening arrhythmias. However, the cellular and molecular mechanisms underlying mechanoelectric coupling in cardiomyocytes remain unclear. We developed an innovative patch-clamp-in-gel technology to embed cardiomyocytes in a three-dimensional (3D) viscoelastic hydrogel that imposes an afterload during regular myocyte contraction. Here, we investigated how afterload affects action potentials, ionic currents, intracellular Ca2+ transients, and cell contraction of adult rabbit ventricular cardiomyocytes. We found that afterload prolonged action potential duration (APD), increased transient outward K+ current, decreased inward rectifier K+ current, and increased L-type Ca2+ current. Increased Ca2+ entry caused enhanced Ca2+ transients and contractility. Moreover, elevated afterload led to discordant alternans in APD and Ca2+ transient. Ca2+ alternans persisted under action potential clamp, indicating that the alternans was Ca2+ dependent. Furthermore, all these afterload effects were significantly attenuated by inhibiting nitric oxide synthase 1 (NOS1). Taken together, our data reveal a mechano-chemo-electrotransduction (MCET) mechanism that acutely transduces afterload through NOS1–nitric oxide signaling to modulate the action potential, Ca2+ transient, and contractility. The MCET pathway provides a feedback loop in excitation–Ca2+ signaling–contraction coupling, enabling autoregulation of contractility in cardiomyocytes in response to afterload. This MCET mechanism is integral to the individual cardiomyocyte (and thus the heart) to intrinsically enhance its contractility in response to the load against which it has to do work. While this MCET is largely compensatory for physiological load changes, it may also increase susceptibility to arrhythmias under excessive pathological loading.

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