相关论文: Non-equilibrium phase transitions in biomolecular …
Multistability is an inseparable feature of many physical, chemical and biological systems which are driven far from equilibrium. In these nonequilibrium systems, stochastic dynamics often induces switching between distinct states on…
Noise-induced transitions between metastable fixed points in systems evolving on multiple time scales are analyzed in situations where the time scale separation gives rise to a slow manifold with bifurcation. This analysis is performed…
We give an introduction to phase transitions in the steady states of systems that evolve stochastically with equilibrium and nonequilibrium dynamics, the latter defined as those that do not possess a time-reversal symmetry. We try as much…
The nonequilibrium phase transition in a system of diffusing, coagulating particles in the presence of a steady input and evaporation of particles is studied. The system undergoes a transition from a phase in which the average number of…
A rigorous mathematical framework for analyzing the chemical master equation (CME) with bistability, based on the theory of large deviation, is proposed. Using a simple phosphorylation-dephosphorylation cycle with feedback as an example, we…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
We investigate the transient nonequilibrium dynamics of a molecular junction biased by a finite voltage and strongly coupled to internal vibrational degrees of freedom. Using two different, numerical exact techniques, diagrammatic Monte…
Many biochemical processes can successfully be described by dynamical systems allowing some form of switching when, depending on their initial conditions, solutions of the dynamical system end up in different regions of state space…
We study the nonequilibrium dynamics of a many-body bosonic system on a lattice, subject to driving and dissipation. The time-evolution is described by a master equation, which we treat within a generalized Gutzwiller mean field…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely…
Nonequilibrium phase transitions are discussed with emphasis on general features such as the role of detailed balance violation in generating effective (long-range) interactions, the importance of dynamical anisotropies, the connection…
Multistable non-equilibrium systems are abundant outcomes of nonlinear dynamics with feedback but still relatively little is known about what determines the stability of the steady states and their switching rates in terms of entropy and…
Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics.…
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…
Dual phospho/dephosphorylation cycles, as well as covalent enzymatic-catalyzed modifications of substrates, are widely diffused within cellular systems and are crucial for the control of complex responses such as learning, memory and…
Living organisms are non-equilibrium, fluctuating, dynamic systems containing multi-step biological signaling cascades (BSC) with the ability to transduce changes in the concentration of extracellular molecules such as cytokines into…