Human heart simulation software for parallel computing systems

AbstractThis study demonstrates a software system for simulating the electrical and mechanical activity of the heart left ventricle (LV). The distinguishing feature of the system is the use of the heart anatomy model, which is based on an analytic description of the ventricular shape and fibre orientation. Another important system feature is that the simulation takes into account relationships between the mechanical and electrical activities that occur in the LV (cardiac mechano-electrical coupling). We describe our model integration design, the software system architecture, and the parallel implementation of the system using OpenMP technology. We evaluate the performance and scalability of the software system. In addition, we provide two examples of simulation results

Thermodynamically consistent orthotropic activation model capturing ventricular systolic wall thickening in cardiac electromechanics

The complex phenomena underlying mechanical contraction of cardiac cells and their influence in the dynamics of ventricular contraction are extremely important in understanding the overall function of the heart. In this paper we generalize previous contributions on the active strain formulation and propose a new model for the excitation-contraction coupling process. We derive an evolution equation for the active fiber contraction based on configurational forces, which is thermodynamically consistent. Geometrically, we link microscopic and macroscopic deformations giving rise to an orthotropic contraction mechanism that is able to represent physiologically correct thickening of the ventricular wall. A series of numerical tests highlights the importance of considering orthotropic mechanical activation in the heart and illustrates the main features of the proposed model

Computer modeling and signal analysis of cardiovascular physiology

This dissertation aims to study cardiovascular physiology from the cellular level to the whole heart level to the body level using numerical approaches. A mathematical model was developed to describe electromechanical interaction in the heart. The model integrates cardio-electrophysiology and cardiac mechanics through excitation-induced contraction and deformation-induced currents. A finite element based parallel simulation scheme was developed to investigate coupled electrical and mechanical functions. The developed model and numerical scheme were utilized to study cardiovascular dynamics at cellular, tissue and organ levels. The influence of ion channel blockade on cardiac alternans was investigated. It was found that the channel blocker may significantly change the critical pacing period corresponding to the onset of alternans as well as the alternans’ amplitude. The influence of electro-mechanical coupling on cardiac alternans was also investigated. The study supported the earlier assumptions that discordant alternans is induced by the interaction of conduction velocity and action potential duration restitution at high pacing rates. However, mechanical contraction may influence the spatial pattern and onset of discordant alternans. Computer algorithms were developed for analysis of human physiology. The 12-lead electrocardiography (ECG) is the gold standard for diagnosis of various cardiac abnormalities. However, disturbances and mistakes may modify physiological waves in ECG and lead to wrong diagnoses. This dissertation developed advanced signal analysis techniques and computer software to detect and suppress artifacts and errors in ECG. These algorithms can help to improve the quality of health care when integrated into medical devices or services. Moreover, computer algorithms were developed to predict patient mortality in intensive care units using various physiological measures. Models and analysis techniques developed here may help to improve the quality of health care

Enabling Detailed, Biophysics-Based Skeletal Muscle Models on HPC Systems

Realistic simulations of detailed, biophysics-based, multi-scale models often require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are typically designed to allow for high flexibility and generality in model development. Flexibility and model development, however, are often a limiting factor for large-scale simulations. Therefore, new models are typically tested and run on small-scale compute facilities. By using a detailed biophysics-based, chemo-electromechanical skeletal muscle model and the international open-source software library OpenCMISS as an example, we present an approach to upgrade an existing muscle simulation framework from a moderately parallel version toward a massively parallel one that scales both in terms of problem size and in terms of the number of parallel processes. For this purpose, we investigate different modeling, algorithmic and implementational aspects. We present improvements addressing both numerical and parallel scalability. In addition, our approach includes a novel visualization environment which is based on the MegaMol framework and is capable of handling large amounts of simulated data. We present the results of a number of scaling studies at the Tier-1 supercomputer HazelHen at the High Performance Computing Center Stuttgart (HLRS). We improve the overall runtime by a factor of up to 2.6 and achieve good scalability on up to 768 cores

A Novel Composite Material-based Computational Model for Left Ventricle Biomechanics Simulation

To model cardiac mechanics effectively, various mechanical characteristics of cardiac muscle tissue including anisotropy, hyperelasticity, and tissue active contraction characteristics must be considered. Some of these features cannot be implemented using commercial finite element (FE) solvers unless additional custom-developed computer codes/subroutines are appended. Such codes/subroutines are unavailable for the research community. Accordingly, the overarching objective of this research is to develop a novel LV mechanics model which is implementable in commercial FE solvers and can be used effectively within inverse FE frameworks towards cardiac disease diagnosis and therapy. This was broken down into a number of objectives. The first objective is to develop a novel cardiac tissue mechanical model. This model was constructed of microstructural cardiac tissue constituents while their associated volume contributions and mechanical properties were incorporated into the model. These constituents were organized in small FE tissue specimen models consistent with the normal/pathological cardiac tissue microstructure. In silico biaxial/uniaxial mechanical tests were conducted on the specimen models and corresponding stress-strain data were validated by comparing them with cardiac tissue data reported in the literature. Another objective of this research is developing a novel FE-based mechanical model of the LV which is fully implementable using commercial FE solvers without requiring further coding, potentially leading to a computationally efficient model which is easily adaptable to diverse pathological conditions. This was achieved through considering a novel composite material model of the cardiac tissue while all aspects of the cardiac mechanics including hyperelasticity, anisotropy, and active tissue responses were preserved. The model was applied to an in silico geometry of a canine LV under both normal and pathological conditions and systolic/diastolic responses of the model were compared with corresponding data of other LV mechanical models and LV contraction measurements. To test the suitability of the proposed cardiac model for FE inversion-based algorithms, the model was utilized for LV diastolic mechanical simulation to estimate the tissue stiffness and blood pressure using an ad-hoc optimization scheme. This led to reasonable tissue stiffness and blood pressure values falling within the range of LV measurements of healthy subjects, confirming the efficacy of this model for inversion-based diagnosis applications

A Fully Coupled Model for Electromechanics of the Heart

We present a fully coupled electromechanical model of the heart. The model integrates cardiac electrophysiology and cardiac mechanics through excitation-induced contraction and deformation-induced current. Numerical schemes based on finite element were implemented in a supercomputer. Numerical examples were presented using a thin cardiac tissue and a dog ventricle with realistic geometry. Performance of the parallel simulation scheme was studied. The model provides a useful tool to understand cardiovascular dynamics