Hybrid-DFT Modeling of Lattice and Surface Vacancies in MnO

We have investigated the properties of defects in MnO bulk and at (100) surfaces, as used in catalytic applications, using hybrid-level density functional theory (i.e., inclusion of exact exchange within the exchange-correlation evaluation) in a hybrid QM/MM embedded-cluster approach. Initially, we calculate the formation energy for bulk Mn and O vacancies, comparing charged-defect compensation with charge carriers at the Fermi Level (ϵf) and through Schottky defect formation. Oxygen vacancies were also investigated at the (100) surface, where the vacancy formation energy is very similar to the bulk. Defect levels associated with the most stable vacancies are calculated using the ΔSCF method: all are positioned mid band gap, with surface environments failing to alter strongly the overall nature of the defect relative to bulk. Chemical activity of the (100) MnO surface was considered through the adsorption of a probe CO2 molecule, which is considered the initial step in the transformation of CO2 into hydrocarbons. CO2 adsorption was strongest over a neutral oxygen vacancy, where the associated trapped electrons of the defect transfer to the adsorbate and thus activate it. However, we have shown with our embedded-cluster approach that the neutral oxygen vacancy is not necessarily the dominant species, which has implications when interpreting results for future catalytic applications

An Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160,000 atoms

Determination of the nitrogen vacancy as a shallow compensating center in GaN doped with divalent metals

We report accurate energetics of defects introduced in GaN on doping with divalent metals, focussing on the technologically important case of Mg doping, using a model which takes into consideration both the effect of hole localisation and dipolar polarisation of the host material, and includes a well-defined reference level. Defect formation and ionisation energies show that divalent dopants are counterbalanced in GaN by nitrogen vacancies and not by holes, which explains both the difficulty in achieving p-type conductivity in GaN and the associated major spectroscopic features, including the ubiquitous 3.46 eV photoluminescence line, a characteristic of all lightly divalent metal-doped GaN materials that has also been shown to occur in pure GaN samples. Our results give a comprehensive explanation for the observed behaviour of GaN doped with low concentrations of divalent metals in good agreement with relevant experiment

Demonstration of the donor characteristics of Si and O defects in GaN using hybrid QM/MM

Using hybrid quantum mechanical/molecular mechanical (QM/MM) embedded cluster calculations, we investigate the stabilization of silicon and oxygen dopants in GaN. Formation energies of Si on a Ga site and O on an N site are calculated at two levels of theory using conventional thermochemical and kinetic exchange and correlation density functionals (B97-2 and BB1k). We confirm the shallow donor nature of these substitutional defects. We find that the 0/1+ transition levels for both Si and O species lie well above the bottom of the conduction band, in agreement with previous supercell-based simulations. The origin of this artifact is discussed in the context of relevant experimental results and we show how correct in-gap shallow levels can be ascertained in good agreement with experiment

Demonstration of the donor characteristics of Si and O defects in GaN using hybrid QM/MM

Using hybrid quantum mechanical/molecular mechanical (QM/MM) embedded cluster calculations, we investigate the stabilization of silicon and oxygen dopants in GaN. Formation energies of Si on a Ga site and O on an N site are calculated at two levels of theory using conventional thermochemical and kinetic exchange and correlation density functionals (B97-2 and BB1k). We confirm the shallow donor nature of these substitutional defects. We find that the 0/1+ transition levels for both Si and O species lie well above the bottom of the conduction band, in agreement with previous supercell-based simulations. The origin of this artifact is discussed in the context of relevant experimental results and we show how correct in-gap shallow levels can be ascertained in good agreement with experiment

Ab-Externo AAV-Mediated Gene Delivery to the Suprachoroidal Space Using a 250 Micron Flexible Microcatheter

The current method of delivering gene replacement to the posterior segment of the eye involves a three-port pars plana vitrectomy followed by injection of the agent through a 37-gauge cannula, which is potentially wrought with retinal complications. In this paper we investigate the safety and efficacy of delivering adeno-associated viral (AAV) vector to the suprachoroidal space using an ab externo approach that utilizes an illuminated microcatheter.6 New Zealand White rabbits and 2 Dutch Belted rabbits were used to evaluate the ab externo delivery method. sc-AAV5-smCBA-hGFP vector was delivered into the suprachoroidal space using an illuminated iTrackTM 250A microcatheter. Six weeks after surgery, the rabbits were sacrificed and their eyes evaluated for AAV transfection using immunofluorescent antibody staining of GFP.Immunostaining of sectioned and whole-mounted eyes demonstrated robust transfection in all treated eyes, with no fluorescence in untreated control eyes. Transfection occurred diffusely and involved both the choroid and the retina. No apparent adverse effects caused by either the viral vector or the procedure itself could be seen either clinically or histologically.The ab externo method of delivery using a microcatheter was successful in safely and effectively delivering a gene therapy agent to the suprachoroidal space. This method presents a less invasive alternative to the current method of virally vectored gene delivery

Neuroprotective Potential of Biphalin, Multireceptor Opioid Peptide, Against Excitotoxic Injury in Hippocampal Organotypic Culture

Biphalin is a dimeric opioid peptide that exhibits affinity for three types of opioid receptors (MOP, DOP and KOP). Biphalin is undergoing intensive preclinical study. It was recognized that activation of δ-opioid receptor elicits neuroprotection against brain hypoxia and ischemia. We compare the effect of biphalin and morphine and the inhibition of opioid receptors by naltrexone on survival of neurons in rat organotypic hippocampal cultures challenged with NMDA. Findings: (1) 0.025–0.1 μM biphalin reduces NMDA-induced neuronal damage; (2) biphalin neuroprotection is abolished by naltrexone; (3) reduced number of dead cells is shown even if biphalin is applied with delay after NMDA challenge

Microarray Analysis Reveals Distinct Gene Expression Profiles Among Different Tumor Histology, Stage and Disease Outcomes in Endometrial Adenocarcinoma

Endometrial cancer is the most common gynecologic malignancy in developed countries and little is known about the underlying mechanism of stage and disease outcomes. The goal of this study was to identify differentially expressed genes (DEG) between late vs. early stage endometrioid adenocarcinoma (EAC) and uterine serous carcinoma (USC), as well as between disease outcomes in each of the two histological subtypes.Gene expression profiles of 20 cancer samples were analyzed (EAC = 10, USC = 10) using the human genome wide illumina bead microarrays. There was little overlap in the DEG sets between late vs. early stages in EAC and USC, and there was an insignificant overlap in DEG sets between good and poor prognosis in EAC and USC. Remarkably, there was no overlap between the stage-derived DEGs and the prognosis-derived DEGs for each of the two histological subtypes. Further functional annotation of differentially expressed genes showed that the composition of enriched function terms were different among different DEG sets. Gene expression differences for selected genes of various stages and outcomes were confirmed by qRT-PCR with a high validation rate.This data, although preliminary, suggests that there might be involvement of distinct groups of genes in tumor progression (late vs. early stage) in each of the EAC and USC. It also suggests that these genes are different from those involved in tumor outcome (good vs. poor prognosis). These involved genes, once clinically verified, may be important for predicting tumor progression and tumor outcome

Molecular basis of structure and function of the microvillus membrane of intestinal epithelial cells

Correlation of molecular structure with biochemical functions of the plasma membrane of the microvilli of intestinal epithelial cells has been investigated by biochemical and electron microscopic procedures. Repeating particles, measuring approximately 60 &#197;in diameter, were found on the surface of the microvilli membrane which had been isolated or purified from rabbit intestinal epithelial cells and negatively stained with phosphotungstic acid. These particles were proved to be inherent components of the microvillus membrane, attached to the outer surface of its trilaminar structure, and were designated as the elementary particles of the microvilli of intestinal epithelial cells. Biochemical and electron microscopic identification of these elementary particles has been carried out by isolation of the elementary particles with papain from the isolated microvillus membrane, followed by purification of the particles by chromatographies on DEAE-cellulose and Sephadex columns. The partially purified particles containing invertase and leucine aminopeptidase are similar in size and structure to those of the elementary particles in the microvillus membrane. Evidence indicates that each of the elementary particles coincide with or include an enzyme molecule such as disaccharidase or peptidase, which carry out the terminal hydrolytic digestion of carbohydrates and proteins, respectively, on the surface of the microvillus membrane. Magnesium ionactivated adenosine triphosphatase and alkaline phosphatase cannot be solubilized with papain but remains in the smooth-surface membrane after the elementary particles have been removed. Cytochemical electron microscopic observation revealed that the active site of magnesium ion-activated adenosine triphosphatase is localized predominantly in the inner surface of the trilaminar structure of the microvillus membrane.</p

Ocean and land forcing of the record-breaking Dust Bowl heat waves across central United States

International audienceThe severe drought of the 1930s Dust Bowl decade coincided with record-breaking summer heatwaves that contributed to the socioeconomic and ecological disaster over North America's Great Plains. It remains unresolved to what extent these exceptional heatwaves, hotter than in historically forced coupled climate model simulations, were forced by sea surface temperatures (SSTs) and exacerbated through human-induced deterioration of land cover. Here we show, using an atmospheric-only model, that anomalously warm North Atlantic SSTs enhance heatwave activity through an association with drier spring conditions resulting from weaker moisture transport. Model devegetation simulations, that represent the widespread exposure of bare soil in the 1930s, suggest human activity fueled stronger and more frequent heatwaves through greater evaporative drying in the warmer months. This study highlights the potential for the amplification of naturally occurring extreme events like droughts by vegetation feedbacks to create more extreme heatwaves in a warmer world