Multicanonical Methods vs. Molecular Dynamics vs. Monte Carlo: Comparison for Lennard-Jones Glasses

We applied a multicanonical algorithm (entropic sampling) to a two-dimensional and a three-dimensional Lennard-Jones system with quasicrystalline and glassy ground states. Focusing on the ability of the algorithm to locate low lying energy states, we compared the results of the multicanonical simulations with standard Monte Carlo simulated annealing and molecular dynamics methods. We find slight benefits to using entropic sampling in small systems (less than 80 particles), which disappear with larger systems. This is disappointing as the multicanonical methods are designed to surmount energy barriers to relaxation. We analyze this failure theoretically, and show (1) the multicanonical method is reduced in the thermodynamic limit (large systems) to an effective Monte Carlo simulated annealing with a random temperature vs. time, and (2) the multicanonical method gets trapped by unphysical entropy barriers in the same metastable states whose energy barriers trap the traditional quenches. The performance of Monte Carlo and molecular dynamics quenches were remarkably similar.Comment: 12 pages, 6 figures, REVTEX, epsf.st

Saddles on the potential energy landscape of a Lennard-Jones liquid

By means of molecular dynamics simulations, we study the stationary points of the potential energy in a Lennard-Jones liquid, giving a purely geometric characterization of the energy landscape of the system. We find a linear relation between the degree of instability of the stationary points and their potential energy, and we locate the energy where the instability vanishes. This threshold energy marks the border between saddle-dominated and minima-dominated regions of the energy landscape. The temperature where the potential energy of the Stillinger-Weber minima becomes equal to the threshold energy turns out to be very close to the mode-coupling transition temperature.Comment: Invited talk presented by A.C. at the Conference: Disordered and Complex Systems, King's College London, July 200

Light bending in the galactic halo by Rindler-Ishak method

After the work of Rindler and Ishak, it is now well established that the bending of light is influenced by the cosmological constant {\Lambda} appearing in the Schwarzschild-de Sitter spacetime. We show that their method, when applied to the galactic halo gravity parametrized by a constant {\gamma}, yields exactly the same {\gamma}- correction to Schwarzschild bending as obtained by standard methods. Different cases are analyzed, which include some corrections to the special cases considered in the original paper by Rindler and Ishak.Comment: 15 page

Fatigue Fracture of Functionally Graded Materials Under Elastic-Plastic Loading Conditions Using Extended Finite Element Method

In this chapter, extended finite element method (XFEM) has been used to simulate the fatigue crack growth problems in functionally graded material (FGM) in the presence of hole, inclusion and minor crack under elastic and plastic conditions. The fatigue crack growth analysis of alloy/ceramic FGMs, alloy and equivalent composite is done by XFEM in the presence of multiple discontinuities under mode-I mechanical load. The validity of linear elastic fracture mechanics (LEFM) theory is limited to the brittle materials. Therefore, the elastic plastic fracture mechanics (EPFM) theory needs to be utilized to characterize the plastic behavior of the material. A generalized Ramberg-Osgood material model has been used to model the stress-strain behavior of the material. Plasticity has been checked by Von Mises Yield criteria. J-integral has been used to calculate the SIF. Crack growth direction is determined by maximum principal stress criteria

Identification of insertion hot spots for non-LTR retrotransposons: computational and biochemical application to entamoeba histolytica

The genome of the human pathogen Entamoeba histolytica contains non-long terminal repeat (LTR) retrotransposons, the EhLINEs and EhSINEs, which lack targeted insertion. We investigated the importance of local DNA structure, and sequence preference of the element-encoded endonuclease (EN) in selecting target sites for retrotransposon insertion. Pre-insertion loci were tested computationally to detect unique features based on DNA structure, thermodynamic considerations and protein interaction measures. Target sites could readily be distinguished from other genomic sites based on these criteria. The contribution of the EhLINE1-encoded EN in target site selection was investigated biochemically. The sequence-specificity of the EN was tested in vitro with a variety of mutated substrates. It was possible to assign a consensus sequence, 5'-GCATT-3', which was efficiently nicked between A-T and T-T. The upstream G residue enhanced EN activity, possibly serving to limit retrotransposition in the A+T-rich E.histolytica genome. Mutated substrates with poor EN activity showed structural differences compared with normal substrates. Analysis of retrotransposon insertion sites from a variety of organisms showed that, in general, regions of favorable DNA structure were recognized for retrotransposition. A combination of favorable DNA structure and preferred EN nicking sequence in the vicinity of this structure may determine the genomic hotspots for retrotransposition

Perturbations of spiky strings in AdS3

Perturbations of a class of semiclassical spiky strings in three dimensional Anti-de Sitter (AdS) spacetime, are investigated using the well-known Jacobi equations for small, normal deformations of an embedded timelike surface. We show that the equation for the perturbation scalar which governs the behaviour of such small deformations, is a special case of the well-known Darboux-Treibich-Verdier (DTV) equation. The eigenvalues and eigensolutions of the DTV equation for our case are obtained by solving certain continued fractions numerically. These solutions are thereafter utilised to further demonstrate that there do exist finite perturbations of the AdS spiky strings. Our results therefore establish that the spiky string configurations in AdS3 are indeed stable against small fluctuations. Comments on future possibilities of work are included in conclusion.Comment: 22 pages, 18 figures, minor changes, to appear in JHE