论文标题
通过网络模型的复杂表型的合理设计
Rational design of complex phenotype via network models
论文作者
论文摘要
我们展示了一个建模和计算框架，该框架可以快速筛选数千种潜在的网络设计，以实现特定的动态行为。为了说明这种能力，我们考虑了滞后问题，这是构建可靠的双向开关的先决条件，因此是建造更复杂的合成电路的基石。我们根据其鲁棒表现出磁滞的能力来评估和对大多数三个节点网络进行对，其中在多种动态表型上测量了相对于参数的鲁棒性。关注排名最高的网络，我们演示了如何应用其他鲁棒性和设计约束。我们根据普通微分方程模型的特定参数化将结果与更传统的方法进行比较，并在计算成本的一小部分中证明了强烈的定性匹配。
We demonstrate a modeling and computational framework that allows for rapid screening of thousands of potential network designs for particular dynamic behavior. To illustrate this capability we consider the problem of hysteresis, a prerequisite for construction of robust bistable switches and hence a cornerstone for construction of more complex synthetic circuits. We evaluate and rank most three node networks according to their ability to robustly exhibit hysteresis where robustness is measured with respect to parameters over multiple dynamic phenotypes. Focusing on the highest ranked networks, we demonstrate how additional robustness and design constraints can be applied. We compare our results to more traditional methods based on specific parameterization of ordinary differential equation models and demonstrate a strong qualitative match at a small fraction of the computational cost.
