Related papers: A non-equilibrium dynamic mechanism for the allost…
Driving an inertial many-body system out of equilibrium generates complex dynamics due to memory effects and the intricate relationships between the external driving force, internal forces, and transport effects. Understanding the…
A positive rate of entropy production at steady state is a distinctive feature of truly non-equilibrium processes. Exact results, while being often limited to simple models, offer a unique opportunity to explore the thermodynamic features…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
A new type of dynamical behavior of a multistable system is reported. We found that a simple non-equilibrium system can reduce its effective temperature autonomously at a global minimum if the residual frustration at a global minimum is…
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they…
Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide…
Self-propulsion allows living systems to display unusual collective behavior. Unlike passive systems in thermal equilibrium, active matter systems are not constrained by conventional thermodynamic laws. A question arises however as to what…
In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed…
Nonequilibrium thermodynamics formalism is proposed to derive the flux of grainy (bubbles-containing) matter, emerging in a nucleation growth process. Some power and non-power limits, due to the applied potential as well as owing to basic…
Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…
The driving force for active physical and biological systems is determined by both the underlying landscape and the non-equilibrium curl flux. While landscape can be quantified in the experiments by the histograms of the collecting…
Thermodynamic principles are often deceptively simple and yet surprisingly powerful. We show how a simple rule, such as the net flow of energy in and out of a moving atom under nonequilibrium steady state condition, can expose the…
A characteristic feature of the non--equilibrium dynamics of real spin glasses at low temperatures are strong aging effects. These phenomena can be manipulated by changing the external parameters in various ways: a thermo-cycling experiment…
A nonequilibrium thermodynamic theory demonstrating an induction effect of a statistical nature is presented. We have shown that this thermodynamic induction can arise in a class of systems that have variable kinetic coefficients (VKC). In…
We consider a chain of anharmonic oscillators immersed in a heat bath with a temperature gradient and a time varying tension applied to one end of the chain while the other side is fixed to a point. We prove that under diffusive space-time…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
In this paper, a non-autonomous stochastic logistic system is considered. An interesting result on the effect of stochastically perturbation for the dynamic behavior are obtained. That is, under certain conditions the stochastic system have…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
We present a dynamical model of lipoprotein metabolism derived by combining a cascading process in the blood stream and cellular level regulatory dynamics. We analyse the existence and stability of equilibria and show that this…