Substrate influence on the structure of thin films

A Mössbauer spectroscopic study of the influence of the substrate on the structure of FeTe thin films has indicated the possibility of controlling the film structure by suitably modifying the substrate.     

Second order elastic effects in a homogeneous isotropic compressible infinite medium with an elliptic hole and acted upon by a tensile force at infinity

Analytic expressions for the second order elasticity case of the problem of an isotropic, infinite medium of compressible material having an elliptic hole and acted upon by a tensile force at infinity are obtained. These results are improvements on the classical elasticity theory in which the elastic constants do not play any role for determination of the stresses. The expressions for the second order effects in the cases of a circular hole and a slit along the major axis have been obtained as particular cases.     

Mathematical analysis of coupled parallel simulations

A set of parallel replicas of a single simulation can be statistically coupled to closely approximate long trajectories. In many cases, this produces nearly linear speedup over a single simulation ( M times faster with M simulations), rendering previously intractable problems within reach of large computer clusters. Interestingly, by varying the coupling of the parallel simulations, it is possible in some systems to obtain greater than linear speedup. The methods are generalizable to any search algorithm with long residence times in intermediate states.     

Atomistic folding simulations of the five-helix bundle protein λ(6−85)

Protein folding is a classic grand challenge that is relevant to numerous human diseases, such as protein misfolding diseases like Alzheimer’s disease. Solving the folding problem will ultimately require a combination of theory, simulation, and experiment, with theory and simulation providing an atomically detailed picture of both the thermodynamics and kinetics of folding and experimental tests grounding these models in reality. However, theory and simulation generally fall orders of magnitude short of biologically relevant time scales. Here we report significant progress toward closing this gap: an atomistic model of the folding of an 80-residue fragment of the λ repressor protein with explicit solvent that captures dynamics on a 10 milliseconds time scale. In addition, we provide a number of predictions that warrant further experimental investigation. For example, our model’s native state is a kinetic hub, and biexponential kinetics arises from the presence of many free-energy basins separated by barriers of different heights rather than a single low barrier along one reaction coordinate (the previously proposed incipient downhill folding scenario).     

Solvent viscosity dependence of the protein folding dynamics

Solvent viscosity has been frequently adopted as an adjustable parameter in various computational studies (e.g., protein folding simulations) with implicit solvent models. A common approach is to use low viscosities to expedite simulations. While using viscosities lower than that of aqueous is unphysical, such treatment is based on observations that the viscosity affects the kinetics (rates) in a well-defined manner as described by Kramers' theory. Here, we investigate the effect of viscosity on the detailed dynamics (mechanism) of protein folding. On the basis of a simple mathematical model, we first show that viscosity may indeed affect the dynamics in a complex way. By applying the model to the folding of a small protein, we demonstrate that the detailed dynamics is affected rather pronouncedly especially at unphysically low viscosities, cautioning against using such viscosities. In this regard, our model may also serve as a diagnostic tool for validating low-viscosity simulations. It is also suggested that the viscosity dependence can be further exploited to gain information about the protein folding mechanism.     

Resin-immobilized CuO and Cu nanocomposites for alcohol oxidation

Resin immobilized stable, spherical CuO nanoparticles prepared in the presence of cyclodextrin (CD) act as catalysts for liquid phase alcohol oxidation in air. The catalytic activity of the CuO nanocomposites and its green chemistry approach make it superior to the related resin-bound Cu(0) nanocomposite. The effect of alcohol chain length and electron-donating or -withdrawing groups influence product yield. The nanocomposites exhibit good reusability, simple workup procedure, and a straightforward approach to aldehyde formation.     

Dye Degradation and Sulfur Oxidation of Methyl Orange and Thiophenol via Newly Designed Nanocomposite GQDs/NiSe-NiO Photocatalyst Under Homemade LED Light

Photocatalytic processes triggered by graphene-based photocatalysts under solar light have sparked interest as a new sort of instrument for solar chemical synthesis. Herein we investigated self-assembled graphene quantum dots (GQDs)/NiSe-NiO composite photocatalyst for organic transformation as well as dye degradation. The synthesized GQDs/NiSe-NiO composite photocatalyst has an excellent suitable band gap, high molar extinction coefficient, low toxicity and chemical/thermal stability. The GQDs/NiSe-NiO composite photocatalyst emerges as a new standard for sulfur oxidation and dye degradation reactions under homemade LED light with high yield.     

Interaction of DNA bases with silver nanoparticles: assembly quantified through SPRS and SERS

Colloidal silver nanoparticles were prepared by reducing silver nitrate with sodium borohydride. The synthesized silver particles show an intense surface plasmon band in the visible region. The work reported here describes the interaction between nanoscale silver particles and various DNA bases (adenine, guanine, cytosine, and thymine), which are used as molecular linkers because of their biological significance. In colloidal solutions, the color of silver nanoparticles may range from red to purple to orange to blue, depending on the degree of aggregation as well as the orientation of the individual particles within the aggregates. Transmission electron microscopy (TEM), X-ray diffraction (XRD), and absorption spectroscopy were used to characterize the assemblies. DNA base-induced differential silver nanoparticle aggregation was quantified from the peak separation (relates to color) of surface plasmon resonance spectroscopy (SPRS) and the signal intensity of surface-enhanced Raman scattering (SERS), which rationalize the extent of silver-nucleobase interactions.