Optimal allocation of replicas in parallel tempering simulations

We have studied the efficiency of parallel tempering simulations for a variety of systems including a coarse-grained protein, an atomistic model polypeptide, and the Lennard-Jones fluid. A scheme is proposed for the optimal allocation of temperatures in these simulations. The method is compared to the existing empirical approaches used for this purpose. Accuracy associated with the computed thermodynamic quantities such as specific heat is also computed and their dependence on the trial-exchange acceptance rate is reported.     

Surface correlations of hydrodynamic drag for transitionally rough engineering surfaces

Rough surfaces are usually characterised by a single equivalent sand-grain roughness height scale that typically needs to be determined from laboratory experiments. Recently, this method has been complemented by a direct numerical simulation approach, whereby representative surfaces can be scanned and the roughness effects computed over a range of Reynolds number. This development raises the prospect over the coming years of having enough data for different types of rough surfaces to be able to relate surface characteristics to roughness effects, such as the roughness function that quantifies the downward displacement of the logarithmic law of the wall. In the present contribution, we use simulation data for 17 irregular surfaces at the same friction Reynolds number, for which they are in the transitionally rough regime. All surfaces are scaled to the same physical roughness height. Mean streamwise velocity profiles show a wide range of roughness function values, while the velocity defect profiles show a good collapse. Profile peaks of the turbulent kinetic energy also vary depending on the surface. We then consider which surface properties are important and how new properties can be incorporated into an empirical model, the accuracy of which can then be tested. Optimised models with several roughness parameters are systematically developed for the roughness function and profile peak turbulent kinetic energy. In determining the roughness function, besides the known parameters of solidity (or frontal area ratio) and skewness, it is shown that the streamwise correlation length and the root-mean-square roughness height are also significant. The peak turbulent kinetic energy is determined by the skewness and root-mean-square roughness height, along with the mean forward-facing surface angle and spanwise effective slope. The results suggest feasibility of relating rough-wall flow properties (throughout the range from hydrodynamically smooth to fully rough) to surface parameters.     

Random matrix theory for transition strength densities in finite quantum systems: Results from embedded unitary ensembles

Embedded random matrix ensembles are generic models for describing statistical properties of finite isolated interacting quantum many-particle systems. For the simplest spinless fermion (or boson) systems, with say m$m$ fermions (or bosons) in N$N$ single particle states and interacting via k$k$-body interactions, we have EGUE(k$k$) [embedded GUE of k$k$-body interactions] with GUE embedding and the embedding algebra is U(N)$U\left(N\right)$. A finite quantum system, induced by a transition operator, makes transitions from its states to the states of the same system or to those of another system. Examples are electromagnetic transitions (then the initial and final systems are same), nuclear beta and double beta decay (then the initial and final systems are different), particle addition to or removal from a given system and so on. Towards developing a complete statistical theory for transition strength densities (transition strengths multiplied by the density of states at the initial and final energies), we have derived formulas for the lower order bivariate moments of the strength densities generated by a variety of transition operators. Firstly, for a spinless fermion system, using EGUE(k$k$) representation for a Hamiltonian that is k$k$-body and an independent EGUE(t$t$) representation for a transition operator that is t$t$-body and employing the embedding U(N)$U\left(N\right)$ algebra, finite-N$N$ formulas for moments up to order four are derived, for the first time, for the transition strength densities. Secondly, formulas for the moments up to order four are also derived for systems with two types of spinless fermions and a transition operator similar to beta decay and neutrinoless beta decay operators. In addition, moments formulas are also derived for a transition operator that removes k₀$k_0$ number of particles from a system of m$m$ spinless fermions. In the dilute limit, these formulas are shown to reduce to those for the EGOE version derived using the asymptotic limit theory of Mon and French (1975). Numerical results obtained using the exact formulas for two-body (k=2$k=2$) Hamiltonians (in some examples for k=3$k=3$ and 4$4$) and the asymptotic formulas clearly establish that in general the smoothed (with respect to energy) form of the bivariate transition strength densities take bivariate Gaussian form for isolated finite quantum systems. Extensions of these results to bosonic systems and EGUE ensembles with further symmetries are discussed.     

Trash GGBFS-based geopolymer as a novel sunlight-responsive photocatalyst for dye discolouration

In this study, we report a waste material-ground granulated blast furnace slag (GGBFS) as a low cost geopolymer, hybridised with ZnO to form a novel and efficient photocatalyst capable of discolouring textile wastewater. GGBFS is a waste material in an iron industry. Methylene blue was used as the probe dye and natural sunlight was used for activation of the photocatalyst. It was observed that under the experimental conditions, ZnGP-40 exhibited twice the discoloration efficiency than conventionally used ZnO or TiO₂. This enhanced performance is majorly attributed to increased surface area of ZnO when strewn in the GGBFS matrix. The photocatalysts were characterized by SEM, TEM, PSA, TGA, BET and UV–Vis/NIR. The effect of photocatalyst loading, speed of agitation and solar insolation has also been studied. Since this study has been performed in direct sunlight, it exhibits a realizable application of solar energy in the treatment of wastewater.     

Targeting tribbles homolog 3 (TRIB3) protein against type 2 diabetes for the identification of potential inhibitors by in silico screening

Tribbles homolog 3 (TRIB3) protein is inhibiting the insulin signaling by directly binding to the Akt/PKB leading to insulin resistance in the pancreas causing type 2 diabetes mellitus. Hence, TRIB3 protein is considered as a possible drug target for the new lead identification against type 2 diabetes. In the present study, the homology model of TRIB3 protein was generated to explore its biochemical function and molecular interactions in the new lead identification. The energy minimization of TRIB3 protein was carried out and evaluated by validation protocols for structure reliability. The druggable binding site of TRIB3 protein was identified for the virtual screening and molecular docking studies. The Asinex-fragments library of 22634 small molecules was docked at TRIB3 active site using the Glide module to identify new chemical entities. A total of 9 molecules were identified as final hits from virtual screening and their potency was ranked using Glide score, Glide energies, and residues interactions. The 6 prioritized lead molecules were further optimized using AutoDock, Prime MM/GBSA, and percentage of human oral absorption for the identification of potential leads. The molecules L2, L5, and L6 are identified as lead inhibitors and are showing consistent interactions with key residues Glu194 and Lys196 of TRIB3 protein. The identified potential leads were analyzed by ADME properties for their drug likeness and HergIC50 values are predicted for the prevention of preclinical failures. The present work sheds light on the identification of the best lead molecules against TRIB3 protein and offers a route to design as novel potential drug candidates for T2DM.     

Phase-incoherent superconducting pairs in the normal state of Ba(Fe(1-x)Co(x))₂As₂

The normal state properties of the recently discovered ferropnictide superconductors might hold the key to understanding their exotic superconductivity. Using point-contact spectroscopy we show that Andreev reflection between an epitaxial thin film of Ba(Fe(0.92)Co(0.08))?As? and a silver tip can be seen in the normal state of the film up to temperature T～1.3T(c), where T(c) is the critical temperature of the superconductor. Andreev reflection far above T(c) can be understood only when superconducting pairs arising from strong fluctuation of the phase of the complex superconducting order parameter exist in the normal state. Our results provide spectroscopic evidence of phase-incoherent superconducting pairs in the normal state of the ferropnictide superconductors.     

新开花粉蛋白的盐酸胍去折叠过程

本文利用荧光光谱和园二色光谱了新开花粉蛋白的盐酸胍去折叠过程。结果显示：新开花粉蛋白的盐酸胍去折叠是一个只包含天然蛋白和变性终态的二态过程,与已经报道的天花粉蛋白的盐酸胍去折叠的过程不同。     

A technique for evaluating the oil/heavy-oil viscosity changes under ultrasound in a simulated porous medium

Theoretically, Ultrasound method is an economical and environmentally friendly or “green” technology, which has been of interest for more than six decades for the purpose of enhancement of oil/heavy-oil production. However, in spite of many studies, questions about the effective mechanisms causing increase in oil recovery still existed. In addition, the majority of the mechanisms mentioned in the previous studies are theoretical or speculative. One of the changes that could be recognized in the fluid properties is viscosity reduction due to radiation of ultrasound waves. In this study, a technique was developed to investigate directly the effect of ultrasonic waves (different frequencies of 25, 40, 68 kHz and powers of 100, 250, 500 W) on viscosity changes of three types of oil (Paraffin oil, Synthetic oil, and Kerosene) and a Brine sample. The viscosity calculations in the smooth capillary tube were based on the mathematical models developed from the Poiseuille’s equation. The experiments were carried out for uncontrolled and controlled temperature conditions. It was observed that the viscosity of all the liquids was decreased under ultrasound in all the experiments. This reduction was more significant for uncontrolled temperature condition cases. However, the reduction in viscosity under ultrasound was higher for lighter liquids compare to heavier ones. Pressure difference was diminished by decreasing in the fluid viscosity in all the cases which increases fluid flow ability, which in turn aids to higher oil recovery in enhanced oil recovery (EOR) operations. Higher ultrasound power showed higher liquid viscosity reduction in all the cases. Higher ultrasound frequency revealed higher and lower viscosity reduction for uncontrolled and controlled temperature condition experiments, respectively. In other words, the reduction in viscosity was inversely proportional to increasing the frequency in temperature controlled experiments. It was concluded that cavitation, heat generation, and viscosity reduction are three of the promising mechanisms causing increase in oil recovery under ultrasound.