Related papers: Kink motion in the Kramers problem for a chain mol…
The two-dimensional cage model for polymer motion is discussed with an emphasis on the effect of sideways motions, which cross the barriers imposed by the lattice. Using the Density Matrix Method as a solver of the Master Equation, the…
We have presented a simple approach to quantum theory of Brownian motion and barrier crossing dynamics. Based on an initial coherent state representation of bath oscillators and an equilibrium canonical distribution of quantum mechanical…
By means of computer simulations and solution of the equations of the Mode Coupling Theory (MCT), we investigate the role of the intramolecular barriers on several dynamic aspects of non-entangled polymers. The investigated dynamic range…
We present a theoretical treatment of energy transfer in a molecular motor described in terms of overdamped Brownian motion on a multidimensional tilted periodic potential. The tilt acts as a thermodynamic force driving the system out of…
We consider the thermally activated fragmentation of a homopolymer chain. In our simple model the dynamics of the intact chain is a Rouse one until a bond breaks and bond breakdown is considered as a first passage problem over a barrier to…
We consider the thermal breakage of a tethered polymer chain of discrete segments coupled by Morse potentials under constant tensile stress. The chain dynamics at the onset of fracture is studied analytically by Kramers-Langer…
Kramer's theory of activation over a potential barrier consists in computing the mean exit time from the boundary of a basin of attraction of a randomly perturbed dynamical system. Here we report that for some systems, crossing the boundary…
We theoretically analyse the equation of topological solitons in a chain of particles interacting via a repulsive power-law potential and confined by a periodic lattice. Starting from the discrete model, we perform a gradient expansion and…
We develop a model for charge trapping on conjugated polymer chains using a continuous representation of the polymer. By constraining the motion to along the chain, we find that kinks along the chain serve as points of attraction and can…
The Kramers turnover problem, that is obtaining a uniform expression for the rate of escape of a particle over a barrier for any value of the external friction was solved in the eighties. Two formulations were given, one by Melnikov and…
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of…
In the present study the interaction of a sine-Gordon kink with a localized inhomogeneity is considered. In the absence of dissipation, the inhomogeneity considered is found to impose a potential energy barrier. The motion of the kink for…
The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy…
We study the activated motion of adsorbed polymers which are driven over a structured substrate by a localized point force.Our theory applies to experiments with single polymers using, for example, tips of scanning force microscopes to drag…
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…
The theory of the dislocation motion in the periodic potential relief of the crystal lattice (the Peierls-Nabarro barriers) is reviewed. On the basis of the kink mechanism the temperature dependence of the flow stress is described for a…
The translocation time of a polymer chain through an interaction energy gradient nanopore was studied by Monte Carlo simulations and the Fokker-Planck equation with double-absorbing boundary conditions. Both the simulation and calculation…
The Frenkel-Kontorova chain with a free end is used to study initiation and propagation of crowdions (anti-kinks) caused by impact of a molecule consisting of K atoms. It is found that molecules with 1 < K < 10 are more efficient in…
We study the propagation of tension caused by an external force along a long polymeric molecule in two different settings, namely along a free polymer in 3d space being pulled from one end, and along a pre-stretched circular polymer,…
A time-dependent approach for the kinetic energy release (KER) spectrum is developed for a fragmentation of a diatomic molecule after an electronic decay process, e.g. Auger process. It allows one to simulate the time-resolved spectra and…