Related papers: Dissipation in non-steady state regulatory circuit…
In this paper, we present a collision model to stroboscopically simulate the dynamics of information in dissipative systems. In particular, an all-optical scheme is proposed to investigate the information scrambling of bosonic systems with…
The manner in which signals propagate through dense granular systems in both space and time is not well understood. In order to learn more about this process, we carry out discrete element simulations of the system response to excitations…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
The energy of the bosonic bath and the flow of quantum information are analyzed over short and long times in local dephasing channels for special correlated or factorized initial conditions, respectively, which involve thermal states. The…
We find that discrete noise of inhibiting (signal) molecules can greatly delay the extinction of plasmids in a plasmid replication system: a prototypical biochemical regulatory network. We calculate the probability distribution of the…
Spin chains with open boundaries, such as the transverse field Ising model, can display coherence times for edge spins that diverge with the system size as a consequence of almost conserved operators, the so-called strong zero modes. Here,…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…
A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
Fluctuations-driven complex oscillations are experimentally observed in cellular systems such as hepatocytes, cardiac cells, neuronal cells, etc. These systems are generally operating in regimes far from thermodynamic equilibrium. To study…
Open quantum many-body systems with controllable dissipation can exhibit novel features in their dynamics and steady states. A paradigmatic example is the dissipative transverse field Ising model. It has been shown recently that the steady…
Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady…
Here we numerically study a model of excitable media, namely, a network with occasionally quiet nodes and connection weights that vary with activity on a short-time scale. Even in the absence of stimuli, this exhibits unstable dynamics,…
Biological information processing is often carried out by complex networks of interconnected dynamical units. A basic question about such networks is that of reliability: if the same signal is presented many times with the network in…
Biological systems are known to communicate by diffusing chemical signals in the surrounding medium. However, most of the recent literature has neglected the electron transfer mechanism occurring amongst living cells, and its role in…
We carry out a detailed numerical investigation of stochastic resonance in underdamped systems in the non-perturbative regime. We point out that an important distinction between stochastic resonance in overdamped and underdamped systems…
In recent work, Baez, Fong and the author introduced a framework for describing Markov processes equipped with a detailed balanced equilibrium as open systems of a certain type. These `open Markov processes' serve as the building blocks for…
Active matter generates order or patterns through nonequilibrium dynamics. An open research challenge is to determine how efficiently a nonequilibrium self-organising system can convert consumed energy into macroscopic order. We study an…
In the past the study of reaction-diffusion systems has greatly contributed to our understanding of the behavior of many-body systems far from equilibrium. In this paper we aim at characterizing the properties of diffusion limited reactions…
Oscillations in nonequilibrium noisy systems are important physical phenomena. These oscillations can happen in autonomous biochemical oscillators such as circadian clocks. They can also manifest as subharmonic oscillations in periodically…
The prospect of a system possessing two or more stable states for a given excitation condition is of topical interest with applications in information processing networks. In this work, we establish the remote transfer of bistability from a…