Dynamics of bound dyes in a nonpolymeric aqueous gel derived from a tripodal bile salt

Rotational dynamics of polarity sensitive fluorescent dyes (ANS and DPH) in a nonpolymertic aqueous gel derived from tripodal cholamide I was studied using ultrafast time-resolved fluorescence technique. Results were compared with that of naturally occurring di- and trihydroxy bile salts. ANS in the gel showed two rotational correlation time (phi) components, 13.2 ns (bound to the hydrophobic region of the gel) and 1.0 ns (free aqueous ANS), whereas DPH showed only one component (4.8 ns). In the sol state, faster rotational motion was observed, both for ANS and DPH. Our data revealed that dyes get encapsulated more tightly in the gel network when compared to the micellar aggregates. ANS has more restrained rotation compared to DPH. This was attributed to the interaction of the sulfonate group of ANS with water molecules and hydrophilic parts of the gelator molecule. No restricted rotation was observed for DPH in the gel state unlike when it is in the gel phase of lipid bilayer.

Dynamics of pulsed flow in an elastic tube

Internal haemorrhage, often leading to cardio-vascular arrest happens to be one of the prime sources of high fatality rates in mammals. We propose a simplistic model of fluid flow in our attempt to specify the location of the haemorrhagic spot, which, if located accurately, could possibly be operated leading to an instant cure. The model we employ for the purpose is basically fluid mechanical in origin and consists of a viscous fluid, pumped by a periodic force and flowing through an elastic tube. The analogy is with that of blood, pumped from the heart and flowing through an artery or vein. Our results, aided by graphical illustrations, match reasonably well with experimental observations.

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

Theory of Gas Hydrates: Effect of the Approximation of Rigid Water Lattice

One of the assumptions of the van der Waals and Platteeuw theory for gas hydrates is that the host water lattice is rigid and not distorted by the presence of guest molecules. In this work, we study the effect of this approximation on the triple-point lines of the gas hydrates. We calculate the triple-point lines of methane and ethane hydrates via Monte Carlo molecular simulations and compare the simulation results with the predictions of van der Waals and Platteeuw theory. Our study shows that even if the exact intermolecular potential between the guest molecules and water is known, the dissociation temperatures predicted by the theory are significantly higher. This has serious implications to the modeling of gas hydrate thermodynamics, and in spite of the several impressive efforts made toward obtaining an accurate description of intermolecular interactions in gas hydrates, the theory will suffer from the problem of robustness if the issue of movement of water molecules is not adequately addressed.

String-like propagation of the 5-coordinated defect state in supercooled water: molecular origin of dynamic and thermodynamic anomalies

We find that at low temperature water, large amplitude (similar to 60 degrees) rotational jumps propagate like a string, with the length of propagation increasing with lowering temperature. The strings are formed by mobile 5-coordinated water molecules which move like a Glarum defect (J. Chem. Phys., 1960, 33, 1371), causing water molecules on the path to change from 4-coordinated to 5-coordinated and again back to 4-coordinated water, and in the process cause the tagged water molecule to jump, by following essentially the Laage-Hynes mechanism (Science, 2006, 311, 832-835). The effects on relaxation of the propagating defect causing large amplitude jumps are manifested most dramatically in the mean square displacement (MSD) and also in the rotational time correlation function of the O-H bond of the molecule that is visited by the defect (transient transition to the 5-coordinated state). The MSD and the decay of rotational time correlation function, both remain quenched in the absence of any visit by the defect, as postulated by Glarum long time ago. We establish a direct connection between these propagating events and the known thermodynamic and dynamic anomalies in supercooled water. These strings are found largely in the regions that surround the relatively rigid domains of 4-coordinated water molecules. The propagating strings give rise to a noticeable dynamical heterogeneity, quantified here by a sharp rise in the peak of the four-point density response function, chi(4)(t). This dynamics heterogeneity is also responsible for the breakdown of the Stokes-Einstein relation.

Fluid dynamics study of a new vacuum degassing process

Recently, the demand of the steel having superior chemical and physical properties has increased for which the content of carbon must be in ultra low range. There are many processes which can produce low carbon steel such as Tank degasser and RH (Rheinstahl-Heraeus) processes. It has been claimed that using a new process, called REDA (Revolutionary Degassing Activator), one can achieve the carbon content below 10ppm in less time. REDA process in terms of installment cost is in between tank degasser and RH processes. As such, REDA process has not been studied thoroughly. Fluid flow phenomena affect the decarburization rate the most besides the chemical reaction rate. Therefore, momentum balance equations along with k-ε turbulent model have been solved for gas and liquid phases in two-dimension (2D) for REDA process. The fluid flow phenomena have been studied in details for this process by varying gas flow rate, depth of immersed snorkel in the steel, diameter of the snorkel and change in vacuum pressure. It is found that design of snorkel affects the mixing process of the bath significantly.