We present a computational framework for analyzing and simulating mitochondrial ATP synthesis using basic thermodynamic and kinetic principles. The framework invokes detailed descriptions of the thermodynamic driving forces associated with the processes of the electron transport chain, mitochondrial ATP synthetase, and phosphate and adenine nucleotide transporters. Assembling models of these discrete processes into an integrated model of mitochondrial ATP synthesis, we illustrate how to analyze and simulate in vitro respirometry experiments and how models identified from in vitro experimental data effectively explain cardiac respiratory control in vivo. Computer codes for these analyses are embedded as Python scripts in a Jupyter Book to facilitate easy adoption and modification of the concepts developed here. This accessible framework may also prove useful in supporting educational applications. All source codes are available on at https://beards-lab.github.io/QAMAS_book/.

我们提出了一个使用基本热力学和动力学原理分析和模拟线粒体 ATP 合成的计算框架。该框架详细描述了与电子传递链、线粒体 ATP 合成酶以及磷酸盐和腺嘌呤核苷酸转运蛋白的过程相关的热力学驱动力。将这些离散过程的模型组装成线粒体 ATP 合成的集成模型，我们说明了如何分析和模拟体外呼吸测定实验，以及从体外实验数据中确定的模型如何有效地解释体内心脏呼吸控制。用于这些分析的计算机代码作为 Python 脚本嵌入到 Jupyter Book 中，以便于轻松采用和修改此处开发的概念。这种可访问的框架也可能在支持教育应用方面证明是有用的。所有源代码都可以在 https://beards-lab.github.io/QAMAS_book/ 上找到。