BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo, Spain.
Methods Mol Biol. 2021;2189:89-103. doi: 10.1007/978-1-0716-0822-7_8.
Synthetic biology aims at engineering synthetic circuits with pre-defined target functions. From a systems (model-based) perspective, the following problems are of central importance: (1) given the model of a biomolecular circuit, elucidate whether it is capable of a certain behavior/functionality; and (2) starting from a pre-defined required functionality and a library of biological parts, find the biomolecular circuit that, built as a combination of such parts, achieves the desired behavior. These two problems, framed, respectively, as nonlinear analysis and automated design problems, are tackled here by efficient optimization methods. We illustrate these methods with case studies considering the analysis and design of biocircuits capable of bistability (bistable switches). Bistability is of particular interest in the context of systems and synthetic biology because it endows cells with the capacity to make decisions.
合成生物学旨在设计具有预定目标功能的合成电路。从系统（基于模型）的角度来看，以下问题至关重要：（1）给定生物分子电路的模型，阐明它是否能够实现某种行为/功能；（2）从预定的所需功能和生物部件库开始，找到由这些部件组合而成的生物分子电路，以实现所需的行为。这两个问题分别被框定为非线性分析和自动化设计问题，这里通过有效的优化方法来解决。我们用能够实现双稳定性（双稳态开关）的生物电路的分析和设计的案例研究来说明这些方法。双稳定性在系统和合成生物学的背景下特别有趣，因为它赋予细胞做出决策的能力。
