论文标题
具有多个输入节点和鲁棒性的网络中的稳态
Homeostasis in Networks with Multiple Input Nodes and Robustness in Bacterial Chemotaxis
论文作者
论文摘要
当有一个受调节量保持在狭窄的值范围内时，生物系统可以实现稳态。在这里，我们将体内平衡视为网络动力学的现象。在这种情况下，我们改善了一种一般理论，用于分析具有杰出输入和输出节点的网络动力学系统中的稳态，称为“输入输出输出网络”。该理论允许人们以“独立模型”方式定义给定网络的“体内平衡类型”，从某种意义上说，分类取决于网络拓扑而不是特定模型方程。每种“体内平衡类型”代表生成体内平衡的可能机制，并且与原始网络的合适的“子网络图案”相关联。我们的贡献是该理论扩展到具有多个输入节点的网络情况。为了展示我们的理论，我们将其应用于细菌趋化性，这是生化系统中稳态的范式。通过考虑大肠杆菌趋化性的代表性模型，我们验证了相应的抽象网络具有多个输入节点。因此，表明我们对理论的扩展允许包含以前无法触及的重要模型。此外，从我们的抽象角度来看，研究模型中体内平衡的发生是由一种新机制引起的，称为输入配重稳态。这种新的稳态机制是在我们调查过程中发现的，是由网络的几个输入节点之间的平衡产生的 - 因此，它需要至少存在两个输入节点。最后，这里开发的框架使人们可以根据理论动力学系统的“仿制”概念形式化稳态的“稳健性”概念。我们讨论趋化模型中体内平衡的这种鲁棒性如何。
A biological system achieve homeostasis when there is a regulated quantity that is maintained within a narrow range of values. Here we consider homeostasis as a phenomenon of network dynamics. In this context, we improve a general theory for the analysis of homeostasis in network dynamical systems with distinguished input and output nodes, called `input-output networks'. The theory allows one to define `homeostasis types' of a given network in a `model independent' fashion, in the sense that the classification depends on the network topology rather than on the specific model equations. Each `homeostasis type' represents a possible mechanism for generating homeostasis and is associated with a suitable `subnetwork motif' of the original network. Our contribution is an extension of the theory to the case of networks with multiple input nodes. To showcase our theory, we apply it to bacterial chemotaxis, a paradigm for homeostasis in biochemical systems. By considering a representative model of Escherichia coli chemotaxis, we verify that the corresponding abstract network has multiple input nodes. Thus showing that our extension of the theory allows for the inclusion of an important class of models that were previously out of reach. Moreover, from our abstract point of view, the occurrence of homeostasis in the studied model is caused by a new mechanism, called input counterweight homeostasis. This new homeostasis mechanism was discovered in the course of our investigation and is generated by a balancing between the several input nodes of the network -- therefore, it requires the existence of at least two input nodes to occur. Finally, the framework developed here allows one to formalize a notion of `robustness' of homeostasis based on the concept of `genericity' from the theory dynamical systems. We discuss how this kind of robustness of homeostasis appears in the chemotaxis model.
