Related papers: Signal duration and the time scale dependence of s…
We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a…
Feedback circuits in biochemical networks which underly cellular signaling pathways are important elements in creating complex behavior. A specific aspect thereof is how stability of equilibrium points depends on model parameters. For…
The fundamental biological processes of development of tissues and organs in multicellular organisms is governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in concentration…
Biochemical networks can respond to temporal characteristics of time-varying signals. To understand how reliably biochemical networks can transmit information we must consider how an input signal as a function of time--the input…
Time-delay systems are an important class of dynamical systems which provide a solid mathematical framework to deal with many application domains of interest ranging from biology, chemical, electrical, and mechanical engineering, to…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
Many networks of physical and biological interest are characterized by a long-range coupling mediated by a chemical which diffuses through a medium in which oscillators are embedded. We considered a one-dimensional model for this effect for…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
The way in which different types of dynamics unfold in complex networks is intrinsically related to the propagation of activation along nodes, which is strongly affected by the network connectivity. In this work we investigate to which…
We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select…
We consider a heteroclinic network in the framework of winnerless competition of species. It consists of two levels of heteroclinic cycles. On the lower level, the heteroclinic cycle connects three saddles, each representing the survival of…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
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…
Time delay in general leads to instability in some systems, while a specific feedback with delay can control fluctuated motion in nonlinear deterministic systems to a stable state. In this paper, we consider a non-stationary stochastic…