An electronic structure-based polarization method, called the X-POL potential, has been described for the purpose of constructing an empirical force field for modeling polypeptides. In the X-POL potential, the internal, bonded interactions are fully represented by an electronic structure theory augmented with some empirical torsional terms. Non-bonded interactions are modeled by an iterative, c...

In this paper, we propose an analytical method for modeling a permanent magnets axial field magnetic coupling. The three-dimensional model takes into account the radial fringing effects of the coupler. The analytical solution requires resolving the Laplace equation in low permeability subdomains. The magnetic field calculation allows the determination of global quantities like axial force and t...

Geometries and resonance Raman (RR) spectra have been modeled for the type 1 Cu active sites of plastocyanin and azurin, as well as two azurin site-directed mutants, M121G and H46D. Using force constants for the Cu coordination group chosen to fit the RR spectra in conjunction with the AMBER force field, we calculated geometries and vibrational spectra. The fitting procedure utilized a chromoph...

We have performed 2.5-dimensional general relativistic magnetohydrodynamic (MHD) simulations of the gravitational collapse of a magnetized rotating massive star as a model of gamma ray bursts (GRBs). The current calculation focuses on general relativistic MHD with simplified microphysics (we ignore neutrino cooling, physical equation of state, and photodisintegration). Initially, we assume that...

In this article, we present a parallel implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The smooth particle mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the direct inversion in the iter...

Abstract: A hybrid snake algorithm is presented in this paper. The procedure is based on combining a dynamic balloon force, a GVF force and a traditional gradient force. The balloon force is modified in order to increase the capture range and convergence speed of active contour in a dynamic way. Our interest is to give the balloon force a bigger preponderance at the early of procedure and a sma...

N -body simulation is a time consuming task in which force calculation part is most dominant part. The simplest and most accurate algorithm for force calculation is direct summation which has time complexity O(N). It is not practically suitable for large-scale simulations on most general-purpose computers. To cut down cost of force calculation one applies fast algorithms or performs force calcu...