Banerjee Soumyadip, Sen Shaunak
Department of Electrical Engineering, Indian Institute of Technology, New Delhi 110016, Delhi, India.
IET Syst Biol. 2020 Jun;14(3):127-132. doi: 10.1049/iet-syb.2019.0029.
Biomolecular oscillators can function robustly in the presence of environmental perturbations, which can either be static or dynamic. While the effect of different circuit parameters and mechanisms on the robustness to steady perturbations has been investigated, the scenario for dynamic perturbations is relatively unclear. To address this, the authors use a benchmark three protein oscillator design - the repressilator - and investigate its robustness to pulse perturbations, computationally as well as use analytical tools of Floquet theory. They found that the metric provided by direct computations of the time it takes for the oscillator to settle after pulse perturbation is applied, correlates well with the metric provided by Floquet theory. They investigated the parametric dependence of the Floquet metric, finding that the parameters that increase the effective delay enhance robustness to pulse perturbation. They found that the structural changes such as increasing the number of proteins in a ring oscillator as well as adding positive feedback, both of which increase effective delay, facilitates such robustness. These results highlight such design principles, especially the role of delay, for designing an oscillator that is robust to pulse perturbation.
生物分子振荡器在存在环境扰动的情况下仍能稳健运行，这些扰动可以是静态的，也可以是动态的。虽然已经研究了不同电路参数和机制对稳态扰动鲁棒性的影响，但动态扰动的情况相对不明确。为了解决这个问题，作者使用了一个基准的三蛋白振荡器设计——阻遏物振荡器，并通过计算以及使用弗洛凯理论的分析工具来研究其对脉冲扰动的鲁棒性。他们发现，通过直接计算振荡器在施加脉冲扰动后达到稳定所需的时间所提供的度量，与弗洛凯理论提供的度量具有很好的相关性。他们研究了弗洛凯度量的参数依赖性，发现增加有效延迟的参数会增强对脉冲扰动的鲁棒性。他们发现，诸如增加环形振荡器中蛋白质的数量以及添加正反馈等结构变化，这两者都会增加有效延迟，有助于提高这种鲁棒性。这些结果突出了此类设计原则，特别是延迟的作用，用于设计对脉冲扰动具有鲁棒性的振荡器。
