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Homeostatic controllers compensating for growth and perturbations

机译:稳态控制器补偿增长和扰动

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摘要

Cells and organisms have developed homeostatic mechanisms which protect them against a changing environment. How growth and homeostasis interact is still not well understood, but of increasing interest to the molecular and synthetic biology community to recognize and design control circuits which can oppose the diluting effects of cell growth. In this paper we describe the performance of selected negative feedback controllers in response to different applied growth laws and time dependent outflow perturbations of a controlled variable. The approach taken here is based on deterministic mass action kinetics assuming that cell content is instantaneously mixed. All controllers behave ideal in the sense that they for step-wise perturbations in volume and a controlled compound A are able to drive A precisely back to the controllers’ theoretical set-points. The applied growth kinetics reflect experimentally observed growth laws, which range from surface to volume ratio growth to linear and exponential growth. Our results show that the kinetic implementation of integral control and the structure of the negative feedback loop are two properties which affect controller performance. Best performance is observed for controllers based on derepression kinetics and controllers with an autocatalytic implementation of integral control. Both are able to defend exponential growth and perturbations, although the autocatalytic controller shows an offset from its theoretical set-point. Controllers with activating signaling using zero-order or bimolecular (antithetic) kinetics for integral control behave very similar but less well. Their performance can be improved by implementing negative feedback structures having repression/derepression steps or by increasing controller aggressiveness. Our results provide a guide what type of feedback structures and integral control kinetics are suitable to oppose the dilution effects by different growth laws and time dependent perturbations on a deterministic level.
机译:细胞和生物体已经建立了体内平衡机制,可以保护它们免受环境变化的影响。生长与动态平衡如何相互作用尚不十分清楚,但是对于分子和合成生物学界来说,越来越认识到并设计出可以对抗细胞生长的稀释作用的控制电路,已经引起了越来越多的兴趣。在本文中,我们描述了响应于不同的应用增长规律和受控变量的时间依赖性流出扰动而选择的负反馈控制器的性能。此处采用的方法基于确定性的质量动力学,并假设细胞含量是即时混合的。所有控制器的性能都处于理想状态,因为它们可以逐步控制体积,并且受控化合物A可以将A精确地驱动回控制器的理论设定值。所应用的生长动力学反映了实验观察到的生长规律,其变化范围从表面到体积比的生长到线性和指数生长。我们的结果表明,积分控制的动力学实现和负反馈回路的结构是影响控制器性能的两个属性。对于基于减压动力学的控制器和具有整体控制的自动催化实现的控制器,可以观察到最佳性能。尽管自动催化控制器显示出偏离其理论设定值的能力,但两者都可以防御指数增长和扰动。具有使用零阶或双分子(对立)动力学进行积分控制的激活信号的控制器的行为非常相似,但效果较差。通过实施具有抑制/抑制步骤的负反馈结构或提高控制器的主动性,可以提高其性能。我们的结果提供了一种指导,即哪种类型的反馈结构和积分控制动力学适合于在确定性水平上抵制不同生长规律和时间相关扰动引起的稀释效应。

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