Dynamics of water at the interface of a small protein, enterotoxin

Fully atomistic molecular dynamics simulations have been carried out to investigate the correlation of biological activity with dynamics of water molecules in an aqueous protein solution of the toxic domain of enterotoxin (PDB ID: 1ETN). This is a small protein of 13 amino acid residues. Our study of this water soluble protein clearly reveals that water dynamics slows down in the hydration layer. Despite this general slowing down, water molecules in the vicinity of the second beta turn of this protein exhibit faster dynamics than those near other regions of the protein. Since this beta turn is believed to play a critical role in the receptor binding of this protein, the faster dynamics of water near the beta turn m ay have biological significance. The collective orientational dynamics of the water molecules in the protein solution exhibits a characteristic long time component of 27 ps, which agrees well with dielectric relaxation experiments.

Identity, energetics, dynamics and environment of interfacial water molecules in a micellar solution

The structure and energetics of interfacial water molecules in the aqueous micelle of cesium perfluorooctanoate have been investigated, using large-scale atomistic molecular dynamics simulations, with the primary objective of classifying them. The simulations show that the water molecules at the interface fall into two broad classes: bound and free, present in a ratio of 9:1. The bound water molecules can be further categorized on the basis of the number of hydrogen bonds (one or two) that they form with the surfactant headgroups. The hydrogen bonds of the doubly hydrogen-bonded species are found to be, on the average, slightly weaker than those in the singly bonded species. The environment around interfacial water molecules is more ordered than that in the bulk. The surface water molecules have substantially lower potential energy, because of interaction with the micelle. In particular, both forms of bound water have energies that are lower by �2.5-4.0 kcal/ mol. Entropy is found to play an important role in determining the relative concentration of the species.

Study of the dynamics of protein folding through minimalistic models

Starting with the Levinthal paradox, a brief introduction to the protein folding problem is presented. The existing theories of protein folding, including the folding funnel scenario, are discussed. After briefly discussing different simulation studies of model proteins, we discuss our recent work on the dynamics of folding of the model HP-36 (the chicken villin headpiece) protein by using a simplified hydropathy scale. Special attention has been paid to the statics and dynamics of contact formation among the hydrophobic residues. The results obtained from this simple model appear to be surprisingly similar to several features observed in the folding of real proteins. The account concludes with a discussion of future problems.

Vortex dynamics and upper critical fields in ultrathin Bi films

Current-voltage (I-V) characteristics of quench condensed, superconducting, ultrathin Bi films in a magnetic field are reported. These I-V's show hysteresis for all films, grown both with and without thin Ge underlayers. Films on Ge underlayers, close to superconductor-insulator transition, show a peak in the critical current, indicating a structural transformation of the vortex solid. These underlayers, used to make the films more homogeneous, are found to be more effective in pinning the vortices. The upper critical fields (B-c2) of these films are determined from the resistive transitions in perpendicular magnetic field. The temperature dependence of the upper critical field is found to differ significantly from Ginzburg-Landau theory, after modifications for disorder.

Dynamics of pulled desorption with effects of excluded-volume interaction: The p-Laplacian diffusion equation and its exact solution

We analyze the dynamics of desorption of a polymer molecule which is pulled at one of its ends with force f, trying to desorb it. We assume a monomer to desorb when the pulling force on it exceeds a critical value f(c). We formulate an equation for the average position of the n-th monomer, which takes into account excluded-volume interaction through the blob-picture of a polymer under external constraints. The approach leads to a diffusion equation with a p-Laplacian for the propagation of the stretching along the chain. This has to be solved subject to a moving boundary condition. Interestingly, within this approach, the problem can be solved exactly in the trumpet, stem-flower and stem regimes. In the trumpet regime, we get tau = tau(0)n(d)(2), where n(d) is the number of monomers that have desorbed at the time tau. tau(0) is known only numerically, but for f close to f(c), it is found to be tau(0) similar to f(c)/(f(2/3) - f(c)(2/3)) If one used simple Rouse dynamics, this result would change to tau similar to f(c)n(d)(2)/(f - f(c)). In the other regimes too, one can find exact solution, and interestingly, in all regimes tau similar to n(d)(2). Copyright (C) EPLA, 2011

Procedural aspects of modeling the dynamics of a three wheeled vehicle using ADAMS-CAR

We describe in some detail the process of development of a dynamic model of a three wheeled vehicle using ADAMS-CAR. We first describe the rigid body model, and then the modeling of structural flexibilities. The aim of this report is to document procedural details of such modeling, with a view to presenting more research and development oriented investigations in the future. The contents of this report may also be of interest to practicing engineers engaged in multi-body dynamics modeling of wheeled vehicles.

An Adaptive Feature Based Low Power Motion Estimation Algorithm

Motion Estimation is one of the most power hungry operations in video coding. While optimal search (eg. full search)methods give best quality, non optimal methods are often used in order to reduce cost and power. Various algorithms have been used in practice that trade off quality vs. complexity. Global elimination is an algorithm based on pixel averaging to reduce complexity of motion search while keeping performance close to that of full search. We propose an adaptive version of the global elimination algorithm that extracts individual macro-block features using Hadamard transform to optimize the search. Performance achieved is close to the full search method and global elimination. Operational complexity and hence power is reduced by 30% to 45% compared to global elimination method.