Related papers: A two-state kinetic model for the unfolding of sin…
Granular systems confined in vertically vibrated shallow horizontal boxes (quasi two-dimensional geometry) present a liquid to solid phase transition when the frequency of the periodic forcing is increased. An effective model, where grains…
A simple model featuring a double well potential is used to represent a liquid that is quenched from an ergodic state into a history dependent glassy state. Issues surrounding the application of the Jarzynski Equality to glass formation are…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
This paper deals with the energy transport properties of charged particles with time-dependent damping force. Based on the proposed nonlinear dimensionless mapping,the stability and dynamical evolution of the particle system is analyzed…
We propose a thermodynamically consistent minimal model to study synchronization which is made of driven and interacting three-state units. This system exhibits at the mean-field level two bifurcations separating three dynamical phases: a…
A dilute gas of hard disks confined between two straight parallel lines is considered. The distance between the two boundaries is in between one and two particle diameters, so that the system is quasi-one-dimensional. A Boltzmann-like…
A model predicting the structure of repulsive, spherically symmetric, monodisperse particles confined between two walls is presented. We study the buckling transition of a single flat layer as the double layer state develops. Experimental…
Theoretical analysis, which maps single molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and…
Jarzynski's equality (JE) allows us to compute free energy differences from distributions of work. In molecular dynamics simulations, the traditional way of constructing work distributions is to perform as many pulling simulations as…
We propose a simple and straightforward method based on Wronskians for the calculation of bound--state energies and wavefunctions of one--dimensional quantum--mechanical problems. We explicitly discuss the asymptotic behavior of the…
We consider the process of diffusion scattering of a wave function given on the phase space. In this process the heat diffusion is considered only along momenta. We write down the modified Kramers equation describing this situation. In this…
Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…
A simple zipper model is introduced, representing in a simplified way, e.g., the folded DNA double helix or hairpin structures in RNA. The double stranded hairpin is connected to a heat bath at temperature $T$ and subject to an external…
Entangled states are a key resource in fundamental quantum physics, quantum cryp-tography, and quantum computation [1].To date, controlled unitary interactions applied to a quantum system, so-called "quantum gates", have been the most…
Nonequilibrium energetics of single molecule translational motor kinesin was investigated by measuring heat dissipation from the violation of the fluctuation-response relation of a probe attached to the motor using optical tweezers. The sum…
Time-dependent density functional theory, proposed recently in the context of atomic diffusion and non-equilibrium processes in solids, is tested against Monte Carlo simulation. In order to assess the basic approximation of that theory, the…
Motivated by a recent work on the metabolism of carbohydrates in bacteria, we study the kinetics and thermodynamics of two classic models for reversible polymerization, one preserving the total polymer concentration and the other one not.…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
We develop a formally exact technique for obtaining steady-state distributions of non-interacting active Brownian particles in a variety of systems. Our technique draws on results from the theory of two-way diffusion equations to solve the…
The estimate of free energy changes based on Bennett's acceptance ratio method is examined in several limiting cases and compared with other estimates based on the Jarzynski equality and on the Crooks relation. While the absolute amount of…