Related papers: Feedback Regulation and its Efficiency in Biochemi…
Feedback loops are major components of biochemical systems. Many systems show multiple such (positive or negative) feedback loops. Nevertheless, very few quantitative analyses address the question how such multiple feedback loops evolved.…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
Signal transduction in biological cells is effected by signaling pathways that typically include multiple feedback loops. Here we analyze information transfer through a prototypical signaling module with biochemical feedback. The module…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Feedback control is a renowned mechanism for attenuating intrinsic fluctuation in regulatory networks. However, its impact on the response sensitivity to external signals and the response timescale, which are also critical for signal…
We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of phosphotransfer mechanism between…
Self-organized network dynamics prevails for systems across physics, biology and engineering. How external signals generate distributed responses in networked systems fundamentally underlies their function, yet is far from fully understood.…
We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of bacterial two-component system. The proposed model takes into account post-translational…
Understanding computational capabilities of simple biological circuits, such as the regulatory circuits of single-cell organisms, remains an active area of research. Recent theoretical work has shown that a simple regulatory architecture…
We investigate the propagation of random fluctuations through biochemical networks in which the concentrations of species are large enough so that the unperturbed problem is well-described by ordinary differential equation. We characterize…
This paper develops a dynamical framework for adaptive coordination in systems of interacting agents referred to here as Feedback-Coupled Memory Systems (FCMS). Instead of framing coordination as equilibrium optimization or agent-centric…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
Networked dynamical systems, i.e., systems of dynamical units coupled via nontrivial interaction topologies, constitute models of broad classes of complex systems, ranging from gene regulatory and metabolic circuits in our cells to…
In distributed target-tracking sensor networks, efficient data gathering methods are necessary to save communication resources and assure information accuracy. This paper proposes a Feedback (FB) distributed data-gathering method which lets…
Information exchange is a critical process in all communication systems, including biological ones. The concept of retroactivity represents the loads that downstream modules apply to their upstream systems in biological circuits. This paper…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
We study the dynamics of dephasing in a quantum two-level system by modeling both 1/f and high-frequency noise by random telegraph processes. Our approach is based on a so-called spin-fluctuator model in which a noisy environment is modeled…
Stochastic fluctuations of molecular abundances are a ubiquitous feature of cellular processes and lead to significant cell-to-cell variability. Recent theoretical work established lower bounds for stochastic fluctuations in cells for broad…
Gene Regulatory Networks(GRNs) with feedback are essential components of many cellular processes and may exhibit oscillatory behavior. Analyzing such systems becomes increasingly complex as the number of components increases. Since gene…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…