At room temperature, proteins undergo dynamic excursions away from their average three-dimensional structure, which plays an essential role for function.1 Molecular dynamics (MD) computer simulations can provide detailed insights into the nature of these motions by representing the state of a protein as a conformational ensemble that follows the laws of statistical thermodynamics.2 While the co...

A model has been considered to describe the development of a surface discharge over conductor electrically exploding in strong magnetic field. simulation performed using this shown that initial stage explosion, plasma layer several tens micrometers thick with an electron temperature electronvolts is formed on metal surface. Based theory small perturbations, thermal filamentation instabilities f...

Neuroimmune factors contribute on the pathogenesis of sickness behaviors. Nigella sativa (NS) has anti-inflammatory, anti-anxiety and anti-depressive effects. In the present study, the effect of NS hydro-alcoholic extract on sickness behavior induced by lipopolysaccharide (LPS) was investigated. The rats were divided into five groups (n=10 in each): (1) control (saline), (2) LPS (1 mg/kg, admin...

Antimicrobial peptides (AMPs) that disrupt bacterial membranes are promising therapeutics against the growing number of antibiotic-resistant bacteria. The mechanism of membrane disruption by the AMP piscidin 1 was examined with multimicrosecond all-atom molecular dynamics simulations and solid-state NMR spectroscopy. The primary simulation was initialized with 20 peptides in four barrel-stave p...

We propose a method for obtaining the intrinsic, long-time mean square displacement (MSD) of atoms and molecules in proteins from finite-time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns, and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD...

Multicasting can improve the efficiency of the wireless link when sending multiple copies of messages by exploiting the inherent broadcast property of wireless transmission. Although multicast routing algorithms in MANETs could be efficient in many situations, but the devices in MANETs are more vulnerable to attacks. In the areas where secured information is primary requirement then developers ...

By using the hybrid formalism, superstrings in four-dimensional NS-NS plane waves are studied in a manifest supersymmetric manner. This description of the superstring is obtained by a field redefinition of the RNS worldsheet fields and defined as a topological N = 4 string theory. The Hilbert space consists of two types of representations describing short and long strings. We study the physical...

A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtain...

A model of postphotodissociative monomolecular (geminate) recombination of heme proteins with small ligands (NO, O2 or CO) is represented. The non-exponential decay with time for the probability to find a heme in unbound state is interpreted in terms of diffusion-like migration of ligand between protein cavities. The temporal behavior for the probability is obtained from numerical simulation an...