相关论文: Strong current response to slow modulation: a meta…
This paper analyses of a stochastic model of a chemical reaction network with three types of chemical species ${\cal R}$, ${\cal M}$ and ${\cal U}$ that interact to transform a flow of external resources, the chemical species ${\cal Q}$, to…
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…
Understanding the asymptotic behavior of reaction-diffusion (RD) systems is crucial for modeling processes ranging from species coexistence in ecology to biochemical interactions within cells. In this work, we analyze RD systems in which…
We study the dynamical properties of small regulatory networks treated as non autonomous dynamical systems called modules when working inside larger networks or, equivalently when subject to external signal inputs. Particular emphasis is…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…
For most stochastic dynamical systems, variables which are tightly regulated tend to respond slowly to external changes. This idea is often discussed for applicable systems, within a linear response regime, through the Fluctuation…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
Symmetries are widespread in physical, technological, biological, and social systems and networks, including power grids. The swing equation is a classic model for the dynamics of powergrid networks. The main goal of this paper is to…
We study general linear transport-reaction systems on an arbitrary dimensional hypercube with periodic boundary conditions. Transport-reaction systems are often used to model the finite speed movement and interaction of particles, bacteria…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
We study the interplay of strong correlations and coherent driving by considering the strong-coupling Kondo model driven by a time-periodic bias voltage. Combining a recent nonequilibrium renormalization group method with Floquet theory, we…
Auto-regulation, a process wherein a protein negatively regulates its own production, is a common motif in gene expression networks. Negative feedback in gene expression plays a critical role in buffering intracellular fluctuations in…
We study the response of one dimensional diffusive systems, consisting of particles interacting via symmetric or asymmetric exclusion, to time-periodic driving from two reservoirs coupled to the ends. The dynamical response of the system…
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 consider steady states of dynamics that have an underlying network structure. We study how a steady state responds to small perturbations in the network parameters and how this sensitivity is connected to the network structure. We…
To study the impact of active systems on their surroundings, we introduce a model that couples an active nematic fluid to an isotropic substrate fluid via friction. We numerically show that as the active layer develops turbulence, the…
Dynamical systems theory provides powerful methods to extract effective macroscopic dynamics from complex systems with slow modes and fast modes. Here we derive and theoretically support a macroscopic, spatially discrete, model for a class…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
In this paper a theoretical model of functioning of a neural circuit during a behavioral response has been proposed. A neural circuit can be thought of as a directed multigraph whose each vertex is a neuron and each edge is a synapse. It…
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…