Exact on-event expressions for discrete potential systems

The properties of systems composed of atoms interacting though discrete potentials are dictated by a series of events which occur between pairs of atoms. There are only four basic event types for pairwise discrete potentials and the square-well/shoulder systems studied here exhibit them all. Closed analytical expressions are derived for the on-event kinetic energy distribution functions for an atom, which are distinct from the Maxwell-Boltzmann distribution function. Exact expressions are derived that directly relate the pressure and temperature of equilibrium discrete potential systems to the rates of each type of event. The pressure can be determined from knowledge of only the rate of core and bounce events. The temperature is given by the ratio of the number of bounce events to the number of disassociation/association events. All these expressions are validated with event-driven molecular dynamics simulations and agree with the data within the statistical precision of the simulations

Self-Similar Blowup Solutions to the 2-Component Camassa-Holm Equations

In this article, we study the self-similar solutions of the 2-component Camassa-Holm equations% \begin{equation} \left\{ \begin{array} [c]{c}% \rho_{t}+u\rho_{x}+\rho u_{x}=0 m_{t}+2u_{x}m+um_{x}+\sigma\rho\rho_{x}=0 \end{array} \right. \end{equation} with \begin{equation} m=u-\alpha^{2}u_{xx}. \end{equation} By the separation method, we can obtain a class of blowup or global solutions for $\sigma=1$ or $-1$. In particular, for the integrable system with $\sigma=1$, we have the global solutions:% \begin{equation} \left\{ \begin{array} [c]{c}% \rho(t,x)=\left\{ \begin{array} [c]{c}% \frac{f\left( \eta\right) }{a(3t)^{1/3}},\text{ for }\eta^{2}<\frac {\alpha^{2}}{\xi} 0,\text{ for }\eta^{2}\geq\frac{\alpha^{2}}{\xi}% \end{array} \right. ,u(t,x)=\frac{\overset{\cdot}{a}(3t)}{a(3t)}x \overset{\cdot\cdot}{a}(s)-\frac{\xi}{3a(s)^{1/3}}=0,\text{ }a(0)=a_{0}% >0,\text{ }\overset{\cdot}{a}(0)=a_{1} f(\eta)=\xi\sqrt{-\frac{1}{\xi}\eta^{2}+\left( \frac{\alpha}{\xi}\right) ^{2}}% \end{array} \right. \end{equation} where $\eta=\frac{x}{a(s)^{1/3}}$ with $s=3t;$ $\xi>0$ and $\alpha\geq0$ are arbitrary constants.\newline Our analytical solutions could provide concrete examples for testing the validation and stabilities of numerical methods for the systems.Comment: 5 more figures can be found in the corresponding journal paper (J. Math. Phys. 51, 093524 (2010) ). Key Words: 2-Component Camassa-Holm Equations, Shallow Water System, Analytical Solutions, Blowup, Global, Self-Similar, Separation Method, Construction of Solutions, Moving Boundar

Bound States of the Klein-Gordon Equation for Woods-Saxon Potential With Position Dependent Mass

The effective mass Klein-Gordon equation in one dimension for the Woods-Saxon potential is solved by using the Nikiforov-Uvarov method. Energy eigenvalues and the corresponding eigenfunctions are computed. Results are also given for the constant mass case.Comment: 13 page

Systematic perturbation calculation of integrals with applications to physics

In this paper we generalize and improve a method for calculating the period of a classical oscillator and other integrals of physical interest, which was recently developed by some of the authors. We derive analytical expressions that prove to be more accurate than those commonly found in the literature, and test the convergence of the series produced by the approach.Comment: 11 pages, 5 figure

Developing molecular genetic markers for grape breeding; using polymerase chain reaction procedures

Research Not

Exact Spin and Pseudo-Spin Symmetric Solutions of the Dirac-Kratzer Problem with a tensor potential via Laplace Transform Approach

Exact bound state solutions of the Dirac equation for the Kratzer potential in the presence of a tensor potential are studied by using the Laplace transform approach for the cases of spin- and pseudo-spin symmetry. The energy spectra is obtained in the closed form for the relativistic as well as non-relativistic cases including the Coulomb potential. It is seen that our analytical results are in agrement with the ones given in literature. The numerical results are also given in a table for different parameter values.Comment: 8 page

Diffusive transport in networks built of containers and tubes

We developed analytical and numerical methods to study a transport of non-interacting particles in large networks consisting of M d-dimensional containers C_1,...,C_M with radii R_i linked together by tubes of length l_{ij} and radii a_{ij} where i,j=1,2,...,M. Tubes may join directly with each other forming junctions. It is possible that some links are absent. Instead of solving the diffusion equation for the full problem we formulated an approach that is computationally more efficient. We derived a set of rate equations that govern the time dependence of the number of particles in each container N_1(t),N_2(t),...,N_M(t). In such a way the complicated transport problem is reduced to a set of M first order integro-differential equations in time, which can be solved efficiently by the algorithm presented here. The workings of the method have been demonstrated on a couple of examples: networks involving three, four and seven containers, and one network with a three-point junction. Already simple networks with relatively few containers exhibit interesting transport behavior. For example, we showed that it is possible to adjust the geometry of the networks so that the particle concentration varies in time in a wave-like manner. Such behavior deviates from simple exponential growth and decay occurring in the two container system.Comment: 21 pages, 18 figures, REVTEX4; new figure added, reduced emphasis on graph theory, additional discussion added (computational cost, one dimensional tubes

Coarse-grained model of entropic allostery

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand changes the intramolecular vibrational entropy, not just the mean static structure. We present a quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this effect. It also addresses the issue of how the signal information to bind or unbind is transmitted through the protein. The model may be applicable to a wide range of repressors and also to signaling in trans-membrane proteins