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The dynamics of excitons in a one-dimensional ensemble with partial spatial order are studied. During optical excitation, cold Rydberg atoms spontaneously organize into regular spatial arrangements due to their mutual interactions. This…
We study quantum particle dynamics in a box and driven by PT-symmetric, delta-kicking complex potential. Such dynamical characteristics as the average kinetic energy as function of time and quasi-energy at different values of the kicking…
Many-body quantum-mechanical stationary states that have real valued wavefunctions are shown to satisfy a classical conservation of energy equation with a kinetic energy function. The terms in the equation depend on the probability…
We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high…
We study quantum dynamics of the rotationally driven Dicke model where the collective spin is rotated around the z axis with a finite velocity. In the absence of the rotating wave approximation we observe that for several physically…
We study a self-propelled particle moving in a solvent with the active Ornstein Uhlenbeck dynamics in the underdamped regime to evaluate the influence of the inertia. We focus on the properties of potential-free and harmonically confined…
In particle systems subject to a nonuniform drive, particle migration is observed from the driven to the non--driven region and vice--versa, depending on details of the hopping dynamics, leading to apparent violations of Fick's law and of…
Charge and heat transport through a single molecule tunnel-coupled to external normal electrodes have been studied. The molecule with sufficiently strong interaction between lectrons and vibrational internal degrees of freedom can be…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
A simple model with a novel type of dynamics is introduced in order to investigate the emergence of self-ordered motion in systems of particles with biologically motivated interaction. In our model particles are driven with a constant…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
In this article we examine the dynamics of a colloidal particle driven by a modulated force over a sinusoidal optical potential energy landscape. Coupling between the competing frequencies of the modulated drive and that of particle motion…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
The Aubry-Andr\'e 1D lattice model describes a particle hopping in a pseudo-random potential. Depending on its strength $\lambda$, all eigenstates are either localized ($\lambda>1$) or delocalized ($\lambda<1$). Near the transition, the…
We present a theoretical investigation of the stochastic dynamics of a damped particle in a tilted periodic potential with a double well per period. By applying the matrix continued fraction technique to the Fokker-Planck equation in…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
We combine particle-based simulations, mean-field rate equations, and Wertheim's theory to study the dynamics of patchy particles in and out of equilibrium, at different temperatures and densities. We consider an initial random distribution…
In this paper, we discuss the large--time behavior of solution of a simple kinetic model of Boltzmann--Maxwell type, such that the temperature is time decreasing and/or time increasing. We show that, under the combined effects of the…
Recent advances in non-equilibrium statistical mechanics and single molecule technologies make it possible to extract free energy differences from irreversible work measurements in pulling experiments. To date, free energy recovery has been…
We have developed a novel method to evaluate the potential profile of a molecular motor at each chemical state from only the probe's trajectory and applied it to a rotary molecular motor F$_1$-ATPase. By using this method, we could also…