Related papers: Non-equilibrium phase transitions in biomolecular …
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
We examine numerically the time-dependent properties of nonlinear bistable multilayer structures for constant wave illumination. We find that our system exhibits both steady-state and self-pulsing solutions. In the steady state regime, we…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological…
When studying out-of-equilibrium systems, one often excites the dynamics in some degrees of freedom while removing the excitation in others through damping. In order for the system to converge to a statistical steady state, the dynamics…
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…
Statistical models provide a powerful and useful class of approximations for calculating reaction rates by bypassing the need for detailed, and often difficult, dynamical considerations. Such approaches invariably invoke specific…
Time-dependently driven stochastic systems form a vast and manifold class of non-equilibrium systems used to model important applications on small length scales such as bit erasure protocols or microscopic heat engines. One property that…
A new approach to computing the equilibria and steady-states of biomolecular systems modelled by bond graphs is presented. The approach is illustrated using a model of a biomolecular cycle representing a membrane transporter and a model of…
Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters…
The goal of this paper is to understand if the property of adaptation, which is a typical property of many biochemical systems, can be achieved only by biological systems that actively consume energy or if it can be achieved also by passive…
The formation of polarized signaling domains on cell membranes is a fundamental example of biological pattern formation. While such patterns resemble structures from equilibrium phase separation, they are intrinsically non-equilibrium,…
We describe a phase transition in continuum limits of interacting particle systems that exhibits a vertical bifurcation diagram. The transition is mediated by a competition short-range repulsion and long-range attraction. As a consequence…
Active systems evade the rules of equilibrium thermodynamics by constantly dissipating energy at the level of their microscopic components. This energy flux stems from the conversion of a fuel, present in the environment, into sustained…
We study nonequilibrium phase transitions in a mass-aggregation model which allows for diffusion, aggregation on contact, dissociation, adsorption and desorption of unit masses. We analyse two limits explicitly. In the first case mass is…
Mass-conserving reaction-diffusion systems with bistable nonlinearity are useful models for studying cell polarity formation, which is a key process in cell division and differentiation. We rigorously show the existence and stability of…
Nonreciprocal interactions in many-body systems lead to time-dependent states, commonly observed in biological, chemical, and ecological systems. The stability of these states in the thermodynamic limit and the critical behavior of the…
The characterization of collective behavior and nonequilibrium phase transitions in quantum systems is typically rooted in the analysis of suitable system observables, so-called order parameters. These observables might not be known a…
Dynamical phase transitions are defined through non-analyticities of the survival probability of an out-of-equilibrium time-evolving state at certain critical times. They ensue from zeros of the corresponding survival amplitude. By…