Related papers: Non-equilibrium phase transitions in biomolecular …
This article is concerned with stability analysis and stabilization of randomly switched systems under a class of switching signals. The switching signal is modeled as a jump stochastic (not necessarily Markovian) process independent of the…
A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
In this paper we study how to shape temporal pulses to switch a bistable system between its stable steady states. Our motivation for pulse-based control comes from applications in synthetic biology, where it is generally difficult to…
The transient response of a stationary state of a quantum particle in a step potential to an instantaneous change in the step height (a simplified model for a sudden bias switch in an electronic semiconductor device) is solved exactly by…
We examine energy and particle exchange between finite-sized quantum systems and find a new form of nonequilibrium states. The exchange rate undergoes stepwise evolution in time, and its magnitude and sign dramatically change according to…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability,…
We demonstrate that absorbing phase transitions in one dimension may be induced by the dynamics of a single site. As an example we consider a one-dimensional model of diffusing particles, where a single site at the boundary evolves…
We study diffusion-controlled processes in nonequilibrium steady states, where standard rate theory assumptions break down. Using transition path theory, we generalize the relations between reactive probability fluxes and measures of the…
We pioneerly investigate the non-equilibrium transport near a quantum phase transition in a generic and relatively simple case model, the dissipative resonant level model, that has many ramifications in nanosystems. We formulate a rigorous…
We study numerically and analytically the dynamics of a sedimenting suspension of active, reproducing particles, such as growing bacteria in a gravitational field. In steady state we find a non-equilibrium phase transition between a…
We consider the general problem of determining the steady state of stochastic nonequilibrium systems such as those that have been used to model (among other things) biological transport and traffic flow. We begin with a broad overview of…
Reaction-diffusion systems driven far from thermodynamic equilibrium through the injection of energy can support multiple distinct spatial patterns that persist as long-lived dynamical phases. The stability of these metastable phases is not…
Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on…
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…
Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have…
We show that the thermodynamic limit of a bistable phosphorylation-dephosphorylation cycle has a selection rule for the "more stable" macroscopic steady state. The analysis is akin to the Maxwell construction. Based on the chemical master…
We study switching between period-two states of an underdamped quantum oscillator modulated at nearly twice its natural frequency. For all temperatures and parameter values switching occurs via quantum activation: it is determined by…
Multistationarity in biological systems is a mechanism of cellular decision making. In particular, signaling pathways regulated by protein phosphorylation display features that facilitate a variety of responses to different biological…
Bistability is considered wide-spread among bacteria and eukaryotic cells, useful e.g. for enzyme induction, bet hedging, and epigenetic switching. However, this phenomenon has mostly been described with deterministic dynamic or well-mixed…