Related papers: A two-state kinetic model for the unfolding of sin…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
We illustrate the Jarzynski equality on the exactly solvable model of a one-dimensional ideal gas in uniform expansion or compression. The analytical results for the probability density $P(W)$ of the work $W$ performed by the gas are…
The existence of two stationary solutions of the nonlinear Boltzmann equation for inelastic hard spheres or disks is investigated. They are restricted neither to weak dissipation nor to small gradients. The one-particle distribution…
We consider several multiscale-in-time kinetic Monte Carlo models, in which some variables evolve on a fast time scale, while the others evolve on a slow time scale. In the first two models we consider, a particle evolves in a…
We show how the presence of entanglement in a bipartite Gaussian state can be detected by the amount of work extracted by a continuos variable Szilard-like device, where the bipartite state serves as the working medium of the engine. We…
We describe here a model for inelastic collisions for electronic excitation and deexcitation processes in a general, multifluid plasma. The model is derived from kinetic theory, and applicable to any mixture and mass ratio. The principle of…
We study the statistics of the dissipated energy in the two-dimensional random fuse model for fracture under different imposed strain conditions. By means of extensive numerical simulations we compare different ways to compute the…
We develop an energy-landscape based elasto-plastic model to understand the behaviour of amorphous solids under uniform and cyclic shear. Amorphous solids are modeled as being composed of mesoscopic sub-volumes, each of which may occupy…
We report measurements of global dissipated power within a turbulent flow homogeneously forced at small scale by a new forcing technique. The forcing is random in both time and space within the fluid by using magnetic particles in an…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
We report on systematic measurements of the distribution of normal forces exerted by granular material under uniaxial compression onto the interior surfaces of a confining vessel. Our experiments on three-dimensional, random packings of…
A kinetic equation for a dilute gas of hard spheres confined between two parallel plates separated a distance smaller than two particle dimeters is derived. It is a Boltzmann-like equation, which incorporates the effect of the confinement…
We present a model of solids made from polygonal cells connected via beams. We calculate the macroscopic elastic moduli from the beam and cell parameters. This modellisation is particularly suited for the simulation of fragmentation…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
Irreversible drift-diffusion processes are very common in biochemical reactions. They have a non-equilibrium stationary state (invariant measure) which does not satisfy detailed balance. For the corresponding Fokker-Planck equation on a…
By combining methods of kinetic and density functional theory, we present a description of molecular fluids which accounts for their microscopic structure and thermodynamic properties as well as for the hydrodynamic behavior. We focus on…
Physical systems with non-reciprocal or dissipative forces evolve according to a generalization of Liouville's equation that accounts for the expansion and contraction of phase space volume. Here, we connect geometric descriptions of these…
We apply the general procedure presented by Jarzynski in [1] to the problem of dissipation in a voltage-driven single-electron box. We obtain the expression of dissipated work, and find its relation to the dissipation Q obtained in [2]. We…
We consider the change of entanglement of formation $\Delta E$ produced by a unitary transformation acting on a general (pure or mixed) state $\rho$ describing a system of two qubits. We study numerically the probabilities of obtaining…