生化网络的层次键合图建模
Hierarchical Bond Graph Modelling of Biochemical Networks
摘要：
键合图的方法来建模生化网络的扩展，允许复杂的模型从简单的组件分层建设。这是通过将更简单的组件表示为通过端口交换质量和能量的开放系统来实现的。这种方法的一个关键特征是，所得到的模型是鲁棒的热力学顺应性：热力学顺应性不依赖于参数的精确数值。此外，由于能量端口提供了定义良好的接口，因此模型可重复使用。为了从文献中找到的参数中提取键合图模型参数，开发了与自由能常数和平衡常数相关的通用和紧凑的公式。根据化学计量矩阵的基本性质，讨论了解的存在唯一性。通过建立骨骼肌糖原分解的层次键合图模型说明了该方法。
英文摘要：
The bond graph approach to modelling biochemical networks is extended to allow hierarchical construction of complex models from simpler components. This is made possible by representing the simpler components as thermodynamically open systems exchanging mass and energy via ports. A key feature of this approach is that the resultant models are robustly thermodynamically compliant: the thermodynamic compliance is not dependent on precise numerical values of parameters. Moreover, the models are reusable due to the well-defined interface provided by the energy ports. To extract bond graph model parameters from parameters found in the literature, general and compact formulae are developed to relate free-energy constants and equilibrium constants. The existence and uniqueness of solutions is considered in terms of fundamental properties of stoichiometric matrices. The approach is illustrated by building a hierarchical bond graph model of glycogenolysis in skeletal muscle.
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