On biological networks capable of robust adaptation in the presence of uncertainties: A systems-theoretic approach

Abstract

Biological adaptation, the tendency of every living organism to regulate its essential activities in environmental fluctuations, is a well-studied functionality in systems and synthetic biology. In this work, we present a generic methodology inspired by systems theory to discover the design principles for robust adaptation, perfect and imperfect, in two different contexts: (1) in the presence of deterministic external disturbance and (2) in a stochastic setting. In all the cases, firstly, we translate the necessary qualitative conditions for adaptation to mathematical constraints using the language of systems theory, which we then map back as design requirements for the underlying networks. Thus, contrary to the existing approaches, the proposed methodologies provide an exhaustive set of admissible network structures without resorting to computationally burdensome brute-force techniques. Further, the proposed frameworks do not assume prior knowledge about the particular rate kinetics, thereby validating the conclusions for a large class of biological networks. In the deterministic setting, we show that, unlike the incoherent feed-forward network structures (IFFLP), the modules containing negative feedback with buffer action (NFBLB) are robust to parametric fluctuations when a specific part of the network is assumed to remain unaffected. To this end, we propose a sufficient condition for imperfect adaptation and show that adding negative feedback in an IFFLP topology improves the robustness concerning parametric fluctuations. Further, we propose a stricter set of necessary conditions for imperfect adaptation. Turning to the stochastic scenario, we adopt a Wiener-Kolmogorov filter strategy to tune the parameters of a given network structure towards minimum output variance. We show that both NFBLB and IFFLP can be used as a reduced-order W-K filter. Further, we define the notion of nearest neighboring motifs to compare the output variances across different network structures. We argue that the NFBLB achieves adaptation at the cost of a variance higher than its nearest neighboring motifs, whereas the IFFLP topology produces locally minimum variance when compared with its nearest neighboring motifs. We present numerical simulations to support the theoretical results. Overall, our results present a generic, systematic, and robust framework for advancing the understanding of complex biological networks.

Homeostasis in Networks with Multiple Inputs

“…This notion of homeostasis has appeared under the names near-perfect adaptation [1, 17, 39] and imperfect adaptation [6, 7]. Despite some contribution in this direction [8], it has remained relatively unexplored.…”