Confined Lennard-Jones potential: a variational treatment

In this work, the energy eigenvalues for the confined Lennard-Jones potential are calculated through the Variational Method allied to the Super symmetric Quantum Mechanics. Numerical results are obtained for different energy levels, parameters of the potential and values of confinement radius. In the limit, where this radius assumes great values, the results for the non-confined case are recovered..

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Configuration-Dependent Diffusion Dynamics of Downhill and Two-State Protein Folding

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Particular solution for anomalous diffusion equation with source term

In literature the phenomenon of diffusion has been widely studied, however for nonextensive systems which are governed by a nonlinear stochastic dynamic, there are a few soluble models. The purpose of this study is to present the solution of the nonlinear Fokker-Planck equation for a model of potential with barrier considering a term of absorption. Systems of this nature can be observed in various chemical or biological processes and their solution enriches the studies of existing nonextensive systems.

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.

Symmetry analysis of an integrable reaction-diffusion equation

In this paper, we investigate the invariance and integrability properties of an integrable two-component reaction-diffusion equation. We perform Painleve analysis for both the reaction-diffusion equation modelled by a coupled nonlinear partial differential equations and its general similarity reduced ordinary differential equation and confirm its integrability. Further, we perform Lie symmetry analysis for this model. Interestingly our investigations reveals a rich variety of particular solutions, which have not been reported in the literature, for this model. (C) 2000 Elsevier B.V. Ltd. All rights reserved.

Mathematical models of generalized diffusion

We discuss in this paper equations describing processes involving non-linear and higher-order diffusion. We focus on a particular case (u(t) = 2 lambda (2)(uu(x))(x) + lambda (2)u(xxxx)), which is put into analogy with the KdV equation. A balance of nonlinearity and higher-order diffusion enables the existence of self-similar solutions, describing diffusive shocks. These shocks are continuous solutions with a discontinuous higher-order derivative at the shock front. We argue that they play a role analogous to the soliton solutions in the dispersive case. We also discuss several physical instances where such equations are relevant.

Critical temperature for first-order phase transitions in confined systems

We consider the Euclidean D-dimensional -lambda vertical bar phi vertical bar(4)+eta vertical bar rho vertical bar(6) (lambda,eta > 0) model with d (d <= D) compactified dimensions. Introducing temperature by means of the Ginzburg-Landau prescription in the mass term of the Hamiltonian, this model can be interpreted as describing a first-order phase transition for a system in a region of the D-dimensional space, limited by d pairs of parallel planes, orthogonal to the coordinates axis x(1), x(2),..., x(d). The planes in each pair are separated by distances L-1, L-2, ... , L-d. We obtain an expression for the transition temperature as a function of the size of the system, T-c({L-i}), i = 1, 2, ..., d. For D = 3 we particularize this formula, taking L-1 = L-2 = ... = L-d = L for the physically interesting cases d = 1 (a film), d = 2 (an infinitely long wire having a square cross-section), and for d = 3 (a cube). For completeness, the corresponding formulas for second-order transitions are also presented. Comparison with experimental data for superconducting films and wires shows qualitative agreement with our theoretical expressions.

Anomalous diffusion of pions at RHIC

After pointing out the difference between normal and anomalous diffusion, we consider a hadron resonance cascade (HRC) model simulation for particle emission at RHIC and point out that rescattering in an expanding hadron resonance gas leads to a heavy tail in the source distribution. The results are compared to recent PHENIX measurements of the tail of the particle emitting source in Au+Au collisions at RHIC. In this context, we show how can one distinguish experimentally the anomalous diffusion of hadrons from a second order QCD phase transition.

Blocking Radial Diffusion in a Double-Waved Hamiltonian Model

A non-twist Hamiltonian system perturbed by two waves with particular wave numbers can present Robust Tori, barriers created by the vanishing of the perturbing Hamiltonian at some defined positions. When Robust Tori exist, any trajectory in phase space passing close to them is blocked by emergent invariant curves that prevent the chaotic transport. We analyze the breaking up of the RT as well the transport dependence on the wave numbers and on the wave amplitudes. Moreover, we report the chaotic web formation in the phase space and how this pattern influences the transport.

Diffusion and interface controlled reactions in alpha-(Cu-Al-Ag) alloys

The isothermal kinetics of Ag precipitation was studied in Cu-Al-Ag alloys with concentrations ranging from 2 to 8 wt.%Al and 2 to 12 wt.%Ag, using scanning electron microscopy (SEM), X-ray energy dispersive spectroscopy (EDX) and microhardness measurements. The results indicated a change in the precipitates growing mechanism from diffusion to interface controlled process, probably due to a change in the nature of the interface with the Ag and Al enrichment of the precipitates. (C) 2006 Elsevier B.V. All rights reserved.

NONLINEAR DIFFUSION PROCESS IN A BENARD SYSTEM AT THE CRITICAL-POINT FOR THE ONSET OF CONVECTION

The evolution equation governing surface perturbations of a shallow fluid heated from below at the critical Rayleigh number for the onset of convective motion, and with boundary conditions leading to zero critical wave number, is obtained. A solution for negative or cooling perturbations is explicitly exhibited, which shows that the system presents sharp propagating fronts.

Diffusion coefficients during osmotic dehydration of tomatoes in ternary solutions

The apparent diffusion coefficients for sucrose, NaCl and water during osmotic dehydration of tomatoes in ternary solutions were determined. Long time experiments (up to 60 h) were carried out in order to determine equilibrium concentrations inside tomatoes, whereas short time experiments (up to 4 h) were performed to provide detailed information on kinetics of water loss and solids gain at the beginning of osmotic treatment. The mass transfer rates for water and solutes showed to be dependent of NaCl and sucrose concentrations in osmotic solution and simple regression models as functions of solutes concentration were determined for diffusion coefficients. Salt and sucrose diffusivities showed to be interdependent, with increasing NaCl concentration causing the enhancement of water loss, at the same time that higher sucrose contents hindered the excessive salt penetration. (C) 2003 Elsevier Ltd. All rights reserved.

Supersymmetric variational energies of 3d confined potentials

Within the approach of supersymmetric quantum mechanics associated with the variational method a recipe to construct the superpotential of three-dimensional confined potentials in general is proposed. To illustrate the construction, the energies of the harmonic oscillator and the Hulthen potential, both confined in three dimensions are evaluated. Comparison with the corresponding results of other approximative and exact numerical results is presented. (C) 2003 Elsevier B.V. All rights reserved.

Moonlets wandering on a leash-ring

Since the Voyager flybys, embedded moonlets have been proposed to explain some of the surprising structures observed in Saturn's narrow F ring. Experiments conducted with the Cassini spacecraft support this suggestion. Images of the F ring show bright compact spots, and seven occultations of stars by the F ring, monitored by ultraviolet and infrared experiments, revealed nine events of high optical depth. These results point to a large number of such objects, but it is not clear whether they are solid moonlets or rather loose particle aggregates. Subsequent images suggested an irregular motion of these objects so that a determination of their orbits consistent with the F ring failed. Some of these features seem to cross the whole ring. Here we show that these observations are explained by chaos in the F ring driven mainly by the 'shepherd' moons Prometheus and Pandora. It is characterized by a rather short Lyapunov time of about a few hundred orbital periods. Despite this chaotic diffusion, more than 93 per cent of the F-ring bodies remain confined within the F ring because of the shepherding, but also because of a weak radial mobility contrasted by an effective longitudinal diffusion. This chaotic stirring of all bodies involved prevents the formation of 'propellers' typical of moonlets, but their frequent ring crossings explain the multiple radial 'streaks' seen in the F ring. The related 'thermal' motion causes more frequent collisions between all bodies which steadily replenish F-ring dust and allow for ongoing fragmentation and re-accretion processes (ring recycling).