Spectral characteristics for a spherically confined -1/r + br^2 potential

We consider the analytical properties of the eigenspectrum generated by a class of central potentials given by V(r) = -a/r + br^2, b>0. In particular, scaling, monotonicity, and energy bounds are discussed. The potential $V(r)$ is considered both in all space, and under the condition of spherical confinement inside an impenetrable spherical boundary of radius R. With the aid of the asymptotic iteration method, several exact analytic results are obtained which exhibit the parametric dependence of energy on a, b, and R, under certain constraints. More general spectral characteristics are identified by use of a combination of analytical properties and accurate numerical calculations of the energies, obtained by both the generalized pseudo-spectral method, and the asymptotic iteration method. The experimental significance of the results for both the free and confined potential V(r) cases are discussed.Comment: 16 pages, 4 figure

Perturbation expansions for a class of singular potentials

Harrell's modified perturbation theory [Ann. Phys. 105, 379-406 (1977)] is applied and extended to obtain non-power perturbation expansions for a class of singular Hamiltonians H = -D^2 + x^2 + A/x^2 + lambda/x^alpha, (A\geq 0, alpha > 2), known as generalized spiked harmonic oscillators. The perturbation expansions developed here are valid for small values of the coupling lambda > 0, and they extend the results which Harrell obtained for the spiked harmonic oscillator A = 0. Formulas for the the excited-states are also developed.Comment: 23 page

Discontinuous Molecular Dynamics for Rigid Bodies: Applications

Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous potentials are compared with simulations in which the molecules interact through standard continuous Lennard-Jones potentials. It is shown that under similar conditions of temperature and pressure, the rigid discontinuous molecular dynamics method reproduces the essential dynamical and structural features found in continuous-potential simulations at both gas and liquid densities. Moreover, the discontinuous molecular dynamics approach is demonstrated to be between 2 to 100 times more efficient than the standard molecular dynamics method depending on the specific conditions of the simulation. The rigid discontinuous molecular dynamics method is also applied to a discontinuous-potential model of a liquid composed of rigid benzene molecules, and equilibrium and dynamical properties are shown to be in qualitative agreement with more detailed continuous-potential models of benzene. Qualitative differences in the dynamics of the two models are related to the relatively crude treatment of variations in the repulsive interactions as one benzene molecule rotates by another.Comment: 14 pages, double column revte

The use of prevalence as a measure of lice burden: a case study of Lepeophtheirus salmonis on Scottish Atlantic salmon, Salmo salar L., farms

This study investigates the benefits of using prevalence as a summary measure of sea lice infestation on farmed Atlantic salmon, Salmo salar L. Aspects such as sampling effort, the relationship between abundance and prevalence arising from the negative binomial distribution, and how this relationship can be used to indicate the degree of aggregation of lice on a site at a given time point are discussed. As a case study, data were drawn from over 50 commercial Atlantic salmon farms on the west coast of Scotland between 2002 and 2006. Descriptive statistics and formal analysis using a linear modelling technique identified significant variations in sea lice prevalence across year class, region and season. Supporting evidence of a functional relationship between prevalence and abundance of sea lice is provided, which is explained through the negative binomial distribution

Evaluating the Applicability of the Fokker-Planck Equation in Polymer Translocation: A Brownian Dynamics Study

Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N=21-61. The rate of translocation is controlled by a tunable friction coefficient, gamma_{0p}, for monomers inside the nanopore. In the case of unforced translocation, the mean translocation time scales with polymer length N as ~ (N-N_p)^alpha, where N_p is the average number of monomers in the nanopore. The exponent approaches the value alpha=2 when the pore friction is sufficiently high, in accord with the prediction for the case of the quasi-static regime where pore friction dominates. In the case of forced translocation, the polymer chain is stretched and compressed on the cis and trans sides, respectively, for low gamma_{0p}. However, the chain approaches conformational quasi-equilibrium for sufficiently large gamma_{0p}. In this limit the observed scaling of with driving force and chain length supports the FP prediction that is proportional to N/f_d for sufficiently strong driving force. Monte Carlo simulations are used to calculate translocation free energy functions for the system. The free energies are used with the Fokker-Planck equation to calculate translocation time distributions. At sufficiently high gamma_{0p}, the predicted distributions are in excellent agreement with those calculated from the BD simulations. Thus, the FP equation provides a valid description of translocation dynamics for sufficiently high pore friction for the range of polymer lengths considered here. Increasing N will require a corresponding increase in pore friction to maintain the validity of the FP approach. Outside the regime of low N and high pore friction, the polymer is out of equilibrium, and the FP approach is not valid.Comment: 13 pages, 11 figure

Sextic anharmonic oscillators and orthogonal polynomials

Under certain constraints on the parameters a, b and c, it is known that Schroedinger's equation -y"(x)+(ax^6+bx^4+cx^2)y(x) = E y(x), a > 0, with the sextic anharmonic oscillator potential is exactly solvable. In this article we show that the exact wave function y is the generating function for a set of orthogonal polynomials P_n^{(t)}(x) in the energy variable E. Some of the properties of these polynomials are discussed in detail and our analysis reveals scaling and factorization properties that are central to quasi-exact solvability. We also prove that this set of orthogonal polynomials can be reduced,by means of a simple scaling transformation, to a remarkable class of orthogonal polynomials, P_n(E)=P_n^{(0)}(E) recently discovered by Bender and Dunne.Comment: 11 page

Transmission of Renormalized Benzene Circuits

The renormalization equations emerge from a Greenian-matrix solution of the discretized Schrodinger equation. A by-product of these equations is the decimation process, which enables substituted-benzenes to be mapped onto corresponding dimers, that are used to construct the series and parallel circuits of single-, double- and triple-dimers. The transmittivities of these circuits are calculated by the Lippmann-Schwinger theory, which yields the transmission-energy function T(E). The average value of T(E) provides a measure of the electron transport in the circuit in question. The undulating nature of the T(E) profiles give rise to resonances (T=1) and anti-resonances (T=0) across the energy spectrum. Analysis of the structure of the T(E) graphs highlights the distinguishing features associated with the homo- and hetero-geneous series and parallel circuits. Noteworthy results include the preponderance of p-dimers in circuits with high T(E) values, and the fact that parallel circuits tend to be better transmitters than their series counterparts.Comment: 32 pages, 14 figures, 1 tabl

Polymer Translocation Dynamics in the Quasi-Static Limit

Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean translocation time scales with polymer length N according to \propto (N-N_p)^2, where N_p is the average number of monomers in the nanopore; this scaling is an indication of a quasi-static regime in which polymer-nanopore friction dominates. We use a multiple-histogram method to calculate the variation of the free energy with Q, a coordinate used to quantify the degree of translocation. The free energy functions are used with the Fokker-Planck formalism to calculate translocation time distributions in the quasi-static regime. These calculations also require a friction coefficient, characterized by a quantity N_{eff}, the effective number of monomers whose dynamics are affected by the confinement of the nanopore. This was determined by fixing the mean of the theoretical distribution to that of the distribution obtained from MC dynamics simulations. The theoretical distributions are in excellent quantitative agreement with the distributions obtained directly by the MC dynamics simulations for physically meaningful values of N_{eff}. The free energy functions for narrow-pore systems exhibit oscillations with an amplitude that is sensitive to the nanopore length. Generally, larger oscillation amplitudes correspond to longer translocation times.Comment: 13 pages, 13 figure

Construction of exact solutions to eigenvalue problems by the asymptotic iteration method

We apply the asymptotic iteration method (AIM) [J. Phys. A: Math. Gen. 36, 11807 (2003)] to solve new classes of second-order homogeneous linear differential equation. In particular, solutions are found for a general class of eigenvalue problems which includes Schroedinger problems with Coulomb, harmonic oscillator, or Poeschl-Teller potentials, as well as the special eigenproblems studied recently by Bender et al [J. Phys. A: Math. Gen. 34 9835 (2001)] and generalized in the present paper to higher dimensions.Comment: 10 page

Wave equation and dispersion relations for a compressible rotating fluid

A fundamental non-classical fourth-order partial differential equation to describe small amplitude linear oscillations in a rotating compressible fluid, is obtained. The dispersion relations for such a fluid, and the different regions of the group and phase velocity are analyzed.Comment: 9 page