J-factors of short DNA molecules

The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair fluctuations with respect to the helix diameter are treated as path trajectories in the imaginary time path integral formalism. The partition function for the sub-ensemble of closed molecules is computed by imposing chain ends boundary conditions both on the radial fluctuations and on the angular degrees of freedom. The cyclization probability, the J-factor, proves to be highly sensitive to the stacking potential, mostly to its nonlinear parameters. We find that the J-factor generally decreases by reducing the sequence length ( N ) and, more significantly, below N = 100 base pairs. However, even for very small molecules, the J-factors remain sizeable in line with recent experimental indications. Large bending angles between adjacent base pairs and anharmonic stacking appear as the causes of the helix flexibility at short length scales.Comment: The Journal of Chemical Physics - May 2016 ; 9 page

A new representation for non--local operators and path integrals

We derive an alternative representation for the relativistic non--local kinetic energy operator and we apply it to solve the relativistic Salpeter equation using the variational sinc collocation method. Our representation is analytical and does not depend on an expansion in terms of local operators. We have used the relativistic harmonic oscillator problem to test our formula and we have found that arbitrarily precise results are obtained, simply increasing the number of grid points. More difficult problems have also been considered, observing in all cases the convergence of the numerical results. Using these results we have also derived a new representation for the quantum mechanical Green's function and for the corresponding path integral. We have tested this representation for a free particle in a box, recovering the exact result after taking the proper limits, and we have also found that the application of the Feynman--Kac formula to our Green's function yields the correct ground state energy. Our path integral representation allows to treat hamiltonians containing non--local operators and it could provide to the community a new tool to deal with such class of problems.Comment: 9 pages ; 1 figure ; refs added ; title modifie

Location- and observation time-dependent quantum-tunneling

We investigate quantum tunneling in a translation invariant chain of particles. The particles interact harmonically with their nearest neighbors, except for one bond, which is anharmonic. It is described by a symmetric double well potential. In the first step, we show how the anharmonic coordinate can be separated from the normal modes. This yields a Lagrangian which has been used to study quantum dissipation. Elimination of the normal modes leads to a nonlocal action of Caldeira-Leggett type. If the anharmonic bond defect is in the bulk, one arrives at Ohmic damping, i.e. there is a transition of a delocalized bond state to a localized one if the elastic constant exceeds a critical value $C_{crit}$. The latter depends on the masses of the bond defect. Superohmic damping occurs if the bond defect is in the site $M$ at a finite distance from one of the chain ends. If the observation time $T$ is smaller than a characteristic time $\tau_M \sim M$, depending on the location M of the defect, the behavior is similar to the bulk situation. However, for $T \gg \tau_M$ tunneling is never suppressed.Comment: 17 pages, 2 figure

Stability of quantum breathers

Using two methods we show that a quantized discrete breather in a 1-D lattice is stable. One method uses path integrals and compares correlations for a (linear) local mode with those of the quantum breather. The other takes a local mode as the zeroth order system relative to which numerical, cutoff-insensitive diagonalization of the Hamiltonian is performed.Comment: 4 pages, 3 figure

Discrete-time quantum walks: continuous limit and symmetries

The continuous limit of one dimensional discrete-time quantum walks with time- and space-dependent coefficients is investigated. A given quantum walk does not generally admit a continuous limit but some families (1-jets) of quantum walks do. All families (1-jets) admitting a continuous limit are identified. The continuous limit is described by a Dirac-like equation or, alternately, a couple of Klein-Gordon equations. Variational principles leading to these equations are also discussed, together with local invariance properties

Roughening transition, surface tension and equilibrium droplet shapes in a two-dimensional Ising system

The exact surface tension for all angles and temperatures is given for the two-dimensional square Ising system with anisotropic nearest-neighbour interactions. Using this in the Wulff construction, droplet shapes are computed and illustrated. Letting temperature approach zero allows explicit study of the roughening transition in this model. Results are compared with those of the solid-on-solid approximation

On hemispheric differences in evoked potentials to speech stimuli

Confirmation is provided for the belief that evoked potentials may reflect differences in hemispheric functioning that are marginal at best. Subjects were right-handed and audiologically normal men and women, and responses were recorded using standard EEG techniques. Subjects were instructed to listen for the targets while laying in a darkened sound booth. Different stimuli, speech and tone signals, were used. Speech sounds were shown to evoke a response pattern that resembles that to tone or clicks. Analysis of variances on peak amplitude and latency measures showed no significant differences between hemispheres, however, a Wilcoxon test showed significant differences in hemispheres for certain target tasks

Distributions of absolute central moments for random walk surfaces

We study periodic Brownian paths, wrapped around the surface of a cylinder. One characteristic of such a path is its width square, $w^2$, defined as its variance. Though the average of $w^2$ over all possible paths is well known, its full distribution function was investigated only recently. Generalising $w^2$ to $w^{(N)}$, defined as the $N$-th power of the {\it magnitude} of the deviations of the path from its mean, we show that the distribution functions of these also scale and obtain the asymptotic behaviour for both large and small $w^{(N)}$

Feynman's Path Integrals and Bohm's Particle Paths

Both Bohmian mechanics, a version of quantum mechanics with trajectories, and Feynman's path integral formalism have something to do with particle paths in space and time. The question thus arises how the two ideas relate to each other. In short, the answer is, path integrals provide a re-formulation of Schroedinger's equation, which is half of the defining equations of Bohmian mechanics. I try to give a clear and concise description of the various aspects of the situation.Comment: 4 pages LaTeX, no figures; v2 shortened a bi

Accelerating the convergence of path integral dynamics with a generalized Langevin equation

The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zero-point energy effects can be included comparatively cheaply in simulations of harmonic and quasi-harmonic systems by augmenting classical molecular dynamics with a generalized Langevin equation (GLE). Here we describe how a similar approach can be used to accelerate the convergence of path integral (PI) molecular dynamics to the exact quantum mechanical result in more strongly anharmonic systems exhibiting both zero point energy and tunnelling effects. The resulting PI-GLE method is illustrated with applications to a double-well tunnelling problem and to liquid water