霍奇金-赫胥黎细胞模型的稳态近似:子宫平滑肌细胞模型的降阶。

IF 4.3 2区 生物学
PLoS Computational Biology Pub Date : 2023-08-30 eCollection Date: 2023-08-01 DOI:10.1371/journal.pcbi.1011359
Shawn A Means, Mathias W Roesler, Amy S Garrett, Leo Cheng, Alys R Clark
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引用次数: 1

摘要

子宫、胃或心脏等器官的多尺度数学生物电模型在准确性和计算可处理性方面都面临挑战。这些多尺度模型通常建立在源自经典Hodkgin-Huxley(HH)形式的生物细胞模型上。用表示电流激活或失活的动态变量来跟踪离子通道行为,这些电流松弛到对细胞膜电压的稳态依赖性。弛豫的时间尺度可以比伴随离子通道变量或整个细胞(如动作电位的爆发序列)或整个器官(如机电协调)的生理感兴趣的现象快几个数量级。将这些时间尺度与稳态近似用于相对快速作用的系统是一种众所周知但经常被忽视的方法,最近发表的模型证明了这一点。因此,我们研究了HH型细胞模型的大量降阶的可行性,该模型具有对全动态激活和失活离子通道变量的稳态近似。我们的工作利用了一个已发表的综合子宫平滑肌细胞模型,该模型包括19个常微分方程和105个配方。已发表的模型中的许多离子通道子模型表现出从10-1到105毫秒的弛豫时间。用稳态公式替换更快的动态变量表明,对于执行的测试用例,完整模型的准确再现和求解时间的显著改进。我们在这里展示了一种有效且相对简单的归约方法,强调了在开始大规模计算或参数扫描之前考虑模型简化的时间尺度的特殊重要性。作为对参数灵敏度和分叉分析等更密集的降阶方法的初步补充,该方法可以快速准确地提高具有挑战性的多尺度器官建模工作的计算可处理性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model.

Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model.

Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model.

Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model.

Multi-scale mathematical bioelectrical models of organs such as the uterus, stomach or heart present challenges both for accuracy and computational tractability. These multi-scale models are typically founded on models of biological cells derived from the classic Hodkgin-Huxley (HH) formalism. Ion channel behaviour is tracked with dynamical variables representing activation or inactivation of currents that relax to steady-state dependencies on cellular membrane voltage. Timescales for relaxation may be orders of magnitude faster than companion ion channel variables or phenomena of physiological interest for the entire cell (such as bursting sequences of action potentials) or the entire organ (such as electromechanical coordination). Exploiting these time scales with steady-state approximations for relatively fast-acting systems is a well-known but often overlooked approach as evidenced by recent published models. We thus investigate feasibility of an extensive reduction of order for an HH-type cell model with steady-state approximations to the full dynamical activation and inactivation ion channel variables. Our effort utilises a published comprehensive uterine smooth muscle cell model that encompasses 19 ordinary differential equations and 105 formulations overall. The numerous ion channel submodels in the published model exhibit relaxation times ranging from order 10-1 to 105 milliseconds. Substitution of the faster dynamic variables with steady-state formulations demonstrates both an accurate reproduction of the full model and substantial improvements in time-to-solve, for test cases performed. Our demonstration here of an effective and relatively straightforward reduction method underlines the particular importance of considering time scales for model simplification before embarking on large-scale computations or parameter sweeps. As a preliminary complement to more intensive reduction of order methods such as parameter sensitivity and bifurcation analysis, this approach can rapidly and accurately improve computational tractability for challenging multi-scale organ modelling efforts.

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来源期刊
PLoS Computational Biology
PLoS Computational Biology 生物-生化研究方法
CiteScore
7.10
自引率
4.70%
发文量
820
期刊介绍: PLOS Computational Biology features works of exceptional significance that further our understanding of living systems at all scales—from molecules and cells, to patient populations and ecosystems—through the application of computational methods. Readers include life and computational scientists, who can take the important findings presented here to the next level of discovery. Research articles must be declared as belonging to a relevant section. More information about the sections can be found in the submission guidelines. Research articles should model aspects of biological systems, demonstrate both methodological and scientific novelty, and provide profound new biological insights. Generally, reliability and significance of biological discovery through computation should be validated and enriched by experimental studies. Inclusion of experimental validation is not required for publication, but should be referenced where possible. Inclusion of experimental validation of a modest biological discovery through computation does not render a manuscript suitable for PLOS Computational Biology. Research articles specifically designated as Methods papers should describe outstanding methods of exceptional importance that have been shown, or have the promise to provide new biological insights. The method must already be widely adopted, or have the promise of wide adoption by a broad community of users. Enhancements to existing published methods will only be considered if those enhancements bring exceptional new capabilities.
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