BIC: Collaborative Research: Rational Design of Synthetic Gene Networks using Formal Analysis of Hybrid Systems

合成生物学的新兴领域集中于创建小型合成遗传网络，将它们插入活细胞中以“编程”细胞行为。最近的原型包括一个拨动开关，振荡器，逻辑门，浓度带检测器，甚至脉冲发生器。合成基因网络在生物技术、医学和国防相关领域有着巨大的应用前景。这类工程生物设备将通过简单的计算和细胞间的通讯来诊断疾病、修复组织、检测和清除环境污染物以及制造生物材料。合成生物学的主要挑战是创建和调整基因网络以达到所需的规格。目前还没有正式的机制来保证这些系统的行为和调整他们的参数先验，以满足所需的性能。由于遗传网络的非线性、不确定性、动力学和调节参数的知识匮乏以及测量结果被噪声破坏，现有的形式分析工具不能成功地处理遗传网络。然而，采用合成基因网络的关键应用，如组织engineering requiresthat这些系统满足严格的安全guarantee.In这个项目中，我们提出了一个混合系统的方法来正向工程和分析syntheticgenetic networks。在这个框架中，基于区间的规范转化为形式化分析的核心问题--可达性分析和安全性验证。通过利用化学反应和协同规则引起的特殊非线性，我们首先通过构造离散抽象将这些无穷维问题转化为图上的有限搜索，然后将其映射到参数值区间。这个过程将允许foranalysis下的参数不确定性，并将提供一个可证明的正确的方法来调整theparameters，以实现所需的区间为基础的属性。我们将用两个实验系统验证我们的方法。我们将改进转录级联的稳态数字响应，并使用优化的级联来构建更鲁棒的切换开关。我们还将使用形式分析来微调脉冲发生器的动态行为，该脉冲发生器包含细胞间通信和前馈基序。

AbstractThe nascent field of synthetic biology is focused on creating small synthetic genetic networksinserting them into living cells in order to "program" cellular behavior. Recent prototypes includea toggle switch, an oscillator, logic gates, concentration band detectors, and even a pulsegenerator. Synthetic gene networks are foreseen to have tremendous applications inbiotechnology, medicine, and defense related areas. Such engineered biological devices willengage in simple computations and cell-cell communications to diagnose diseases, repair tissues,detect and clean up environmental pollutants, and manufacture biomaterials.The main challenge in synthetic biology is creating and tuning gene networks to desiredspecifications. There is currently no formal mechanism to guarantee the behavior of these systemsand to tune their parameters a-priori to satisfy desired performances. The existing tools for formalanalysis cannot handle genetic networks successfully due to nonlinearities, uncertainties, scarceknowledge of kinetic and regulatory parameters, and measurements corrupted by noise. However,the adoption of synthetic gene networks in critical applications such as tissue engineering requiresthat these systems meet strict safety guarantees.In this project, we propose a hybrid systems approach to forward engineer and analyze syntheticgenetic networks. In this framework, interval-based specifications translate to reachabilityanalysis and safety verification, which are the central problems of formal analysis. By exploitingthe particular nonlinearities induced by chemical reactions and cooperative regulations, we firstreduce these infinite dimensional problems to finite searches on graphs by constructing discreteabstractions, and then map them to parameter value intervals. This procedure will allow foranalysis under parameter uncertainty and will provide a provably correct methodology to tune theparameters to achieve desired interval-based properties. We will validate our approach with twoexperimental systems. We will improve the steady state digital response of a transcriptionalcascade and use the optimized cascades to build more robust toggle switches. We will also useformal analysis to fine-tune the dynamic behavior of a pulse generator that incorporates cell-cellcommunication and a feed-forward motif.