Related papers: Dissipation in non-steady state regulatory circuit…
In biological systems, information is frequently transferred with Poisson like spike processes (shot noise) modulated in time by information-carrying signals. How then to quantify information transfer for the output for such nonstationary…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems…
The possible mechanisms of communications between distant bio-systems by means of optical and UV photons are studied. It is argued that their main production mechanism is owed to the biochemical reactions, occurring during the cell…
Gene expression and its regulation is a nonequilibrium stochastic process. Different molecules are involved in several biochemical steps in this process with low copies. It is observed that the stochasticity in biochemical processes is…
Sensory neurons give highly variable responses to stimulation, which can limit the amount of stimulus information available to downstream circuits. Much work has investigated the factors that affect the amount of information encoded in…
Biologically driven non-equilibrium fluctuations are often characterized by their non-Gaussianity or by an "effective temperature", which is frequency dependent and higher than the ambient temperature. We address these two measures…
This paper is concerned with conditions for the existence of oscillations in gene regulatory networks with negative cyclic feedback, where time delays in transcription, translation and translocation process are explicitly considered. The…
Complex systems can convert energy imparted by nonequilibrium forces to regulate how quickly they transition between long lived states. While such behavior is ubiquitous in natural and synthetic systems, currently there is no general…
Exchange of molecules allows cells to exchange information. How robust is the information to changes in cell parameters? We use a mapping between the stochastic dynamics of two cells sharing a stimulatory molecule, and parameters akin to an…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Living cells exhibit an important out-of-equilibrium mechanical activity, mainly due to the forces generated by molecular motors. These motor proteins, acting individually or collectively on the cytoskeleton, contribute to the violation of…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
This paper investigates the fundamental information-theoretic limits for the control and sensing of noiseless linear dynamical systems subject to a broad class of nonlinear observations. We analyze the interactions between the control and…
The work reported here aims to address the effects of time-dependent parameters and stochasticity on decision-making in biological systems. We achieve this by extending previous studies that resorted to simple normal forms. Yet, we focus…
When a system is perturbed by the variation of external parameters, a lag generally develops between the actual state of the system and the equilibrium state corresponding to the current parameter values. We establish a microscopic,…
We analyze how the amount of work dissipated by a fixed nonequilibrium process depends on the initial distribution over states. Specifically, we compare the amount of dissipation when the process is used with some specified initial…
This chapter provides a concise survey on different dissipativity conditions that have appeared in the literature on economic model predictive control and discusses their decisive role in this context.
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…