Related papers: Control principles of metabolic networks
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…
Observing and controlling complex networks are of paramount interest for understanding complex physical, biological and technological systems. Recent studies have made important advances in identifying sensor or driver nodes, through which…
The large-scale shape and function of metabolic networks are intriguing topics of systems biology. Such networks are on one hand commonly regarded as modular (i.e. built by a number of relatively independent subsystems), but on the other…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
The design and implementation of regulation motifs ensuring robust perfect adaptation are challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic pathways producing, for instance, drug precursors and…
The field of optimal control typically requires the assumption of perfect knowledge of the system one desires to control, which is an unrealistic assumption for biological systems, or networks, typically affected by high levels of…
This chapter provides a comprehensive overview of controlling collective behavior in complex systems comprising large ensembles of interacting dynamical agents. Building upon traditional control theory's foundation in individual systems, we…
Mathematical models of stem cell differentiation are commonly based upon the concept of subsequent cell fate decisions, each controlled by a gene regulatory network. These networks exhibit a multistable behavior and cause the system to…
Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants,…
The brain is an intricately structured organ responsible for the rich emergent dynamics that support the complex cognitive functions we enjoy as humans. With around $10^{11}$ neurons and $10^{15}$ synapses, understanding how the human brain…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
Perturbations are ubiquitous in metabolism. A central tool to understand and control their influence on metabolic networks is sensitivity analysis, which investigates how the network responds to external perturbations. We follow here a…
Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the…