文章基本信息

标题：Computational Framework for Design of a Pulse Generating Biomolecular Circuit
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作者：Abhilash Patel ; Shaunak Sen
期刊名称：IFAC PapersOnLine
印刷版ISSN：2405-8963
出版年度：2020
卷号：53
期号：1
页码：220-225
DOI：10.1016/j.ifacol.2020.06.038
语种：English
出版社：Elsevier
摘要：The design of dynamics according to the quantitative specifications is widespread throughout engineering, and may be important for synthetic biology. While there have been multiple instances, experimental and theoretical, of design of dynamics in biomolecular circuits, the design as per quantitative specifications is relatively less common. Here we address this issue, computationally, for the design of pulse dynamics in multiple biomolecular circuits. We map the pulse specifications of rise time, peak amplitude and decay timescale exactly to the solution of linearized dynamics of incoherent feedforward loops by exploiting the non-normal structure of these dynamics. We find that there can be an error between the pulse specifications and the pulse output of the full nonlinear model and propose a bias factor so that the output almost exactly matches the specifications. We note the degeneracy of solutions possible for a given specification and analyse how robustness to parametric perturbations can guide the choice of solutions. These results present a framework for specification-based design of biomolecular pulses that provides insight into the design process and is scalable.
关键词：biomolecular circuit;pulsing;feedforward loops;non-normality;circuit design