Anatomically accurate high resolution modeling of human whole heart electromechanics: A strongly scalable algebraic multigrid solver method for nonlinear deformation.
Anatomically accurate high resolution modeling of human whole heart electromechanics: A strongly scalable algebraic multigrid solver method for nonlinear deformation.
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DOI：
10.1016/j.jcp.2015.10.045
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发表时间：
2016-01-15
影响因子：
4.1
通讯作者：
Plank G
中科院分区：
文献类型：
--
作者：
Augustin CM;Neic A;Liebmann M;Prassl AJ;Niederer SA;Haase G;Plank G
心脏机电 (EM) 模型已成功用于研究健康和疾病中心跳的基本机制。然而，在迄今为止报道的所有模型研究中，在表示细胞功能及其异质性的生物物理细节、大体解剖结构和组织微观结构以及电生理学（EP）和组织扩张之间的双向耦合方面进行了大量简化。一个限制因素是所采用的空间离散方法不够灵活，无法适应复杂的几何形状或解决异质性，但更重要的是，主流求解器技术的效率有限，在高时空分辨率下对心脏机电进行建模时，这些技术的可扩展性不足以应对自由度 (DOF) 的增加。这项研究报告了一种新方法的开发，该方法使用心脏机电的人体整个器官模型来求解有限弹性非线性方程，并以高细胞分辨率离散化。根据分辨率为 220 μm、440 μm 和 880 μm 的磁共振 (MR) 扫描重建了三个患者特异性、解剖学准确的全心脏 EM 模型，分别产生约 184.6、24.4 和 370 万个四面体单元以及 95.9、13.2 和 210 万个位移自由度的网格。使用相同的网格来离散电生理学 (EP) 和非线性弹性的控制方程。开发了一种用于迭代 Krylov 求解器的新型代数多重网格 (AMG) 预处理器来处理由此产生的计算负载。 AMG 预处理器的设计主要目标是为设置和解决方案运行时间实现有利的强大缩放特性，因为这是利用当前高性能计算硬件的关键。使用 220 μm、440 μm 和 880 μm 网格的基准测试结果表明，计算核心可有效扩展至 1024、4096 和 8192 个，从而分别在 44.3、87.8 和 235.3 分钟内模拟单次心跳。该方法的效率允许快速模拟周期，而不影响解剖或生物物理细节。
Electromechanical (EM) models of the heart have been used successfully to study fundamental mechanisms underlying a heart beat in health and disease. However, in all modeling studies reported so far numerous simplifications were made in terms of representing biophysical details of cellular function and its heterogeneity, gross anatomy and tissue microstructure, as well as the bidirectional coupling between electrophysiology (EP) and tissue distension. One limiting factor is the employed spatial discretization methods which are not sufficiently flexible to accommodate complex geometries or resolve heterogeneities, but, even more importantly, the limited efficiency of the prevailing solver techniques which are not sufficiently scalable to deal with the incurring increase in degrees of freedom (DOF) when modeling cardiac electromechanics at high spatio-temporal resolution. This study reports on the development of a novel methodology for solving the nonlinear equation of finite elasticity using human whole organ models of cardiac electromechanics, discretized at a high para-cellular resolution. Three patient-specific, anatomically accurate, whole heart EM models were reconstructed from magnetic resonance (MR) scans at resolutions of 220 μm, 440 μm and 880 μm, yielding meshes of approximately 184.6, 24.4 and 3.7 million tetrahedral elements and 95.9, 13.2 and 2.1 million displacement DOF, respectively. The same mesh was used for discretizing the governing equations of both electrophysiology (EP) and nonlinear elasticity. A novel algebraic multigrid (AMG) preconditioner for an iterative Krylov solver was developed to deal with the resulting computational load. The AMG preconditioner was designed under the primary objective of achieving favorable strong scaling characteristics for both setup and solution runtimes, as this is key for exploiting current high performance computing hardware. Benchmark results using the 220 μm, 440 μm and 880 μm meshes demonstrate efficient scaling up to 1024, 4096 and 8192 compute cores which allowed the simulation of a single heart beat in 44.3, 87.8 and 235.3 minutes, respectively. The efficiency of the method allows fast simulation cycles without compromising anatomical or biophysical detail.