Abstract: SIRT6 and COX-2 are oncogenes target that promote the expression of proinflammatory and pro-survival proteins through a signaling pathway, which leads to increased survival and proliferation of tumor cells. However, COX-2 also suppresses skin tumorigenesis and their relationship with SIRT6, making it an interesting target for the discovery of drugs with anti-inflammatory and anti-cancer properties. Herein, we studied the interaction of thieno[3,2-c] pyran analogs and RONS species with SIRT6 and COX-2 through the use of molecular docking and molecular dynamic simulations. Molecular docking studies revealed the importance of hydrophobic and hydrophilic amino acid residues for the stability. The molecular dynamics study examined conformational changes in the enzymes caused by the binding of the substrates and how those changes affected the stability of the protein-drug complex. The average RMSD values of the backbone atoms in compounds 6 and 10 were calculated from 1000 ps to 10000 ps and were found to be 0.13 nm for both compounds. Similarly, the radius of gyration values for compounds 6 and 10 were found to be 1.87 +/- 0.03 nm and 1.86 +/- 0.02 nm, respectively. The work presented here, will be of great help in lead identification and optimization for early drug discovery.

Abstract: Heterostructures of III-V materials under a mechanical strain are being actively researched to enhance the performance of the tunnel field-effect transistor (TFET). In scaled III-V device structures, however, the interplay between the effects of strain and quantum confinement on the semiconductor band structure and hence the performance is highly non-trivial. We have therefore developed a computationally efficient quantum mechanical simulator Pharos, which enables self-consistent full-zone k.p-based simulations of III-V TFETs under a general non-uniform strain. We present the self-consistent procedure and demonstrate it on confined staggered bandgap GaAs0.5Sb0.5/In0.53Ga0.47As TFETs. We find a large performance degradation due to size-induced quantum confinement compared to non-confined devices. We show that some performance can be regained either by applying a uniform biaxial tensile strain or through the non-uniform strain profile at a lattice-mismatched heterostructure.

Abstract: In this study, the healing of N-vacancy boron carbonitride nanosheet (NV-BC2NNS) and nanotube (NV-BC2NNT) by NO molecule is studied by means of density functional theory calculations. Two different N-vacancies are considered in each of these structures in which the vacancy site is surrounded by either three B-atoms (NB) or by two B- and one C-atom (NBC). By means of the healed BC2NNS and BC2NNT as a support, the removal of two toxic gas molecules (NO and CO) are applicable. It should be noted that the obtained energy barriers of both healing and oxidizing processes are significantly lower than those of graphene, carbon nanotubes or boron nitride nanostructures. Also, at the end of the oxidation process, the pure BC2NNS or BC2NNT is obtained without any additional defects. Therefore, by using this method, we can considerably purify the defective BC2NNS/BC2NNT. Moreover, according to the thermochemistry calculations we can further confirm that the healing process of the NV-BC2NNS and NV-BC2NNT by NO are feasible at room temperature. So, we can claim that this study could be very helpful in both purifying the defective BC2NNS/BC2NNT while in the same effort removing toxic NO and CO gases.

Abstract: Heterostructures of low-dimensional semiconducting materials, such as transition metal dichalcogenides (MX2), are promising building blocks for future electronic and optoelectronic devices. The patterning of one MX2 material on top of another one is challenging due to their structural similarity. This prevents an intrinsic etch stop when conventional anisotropic dry etching processes are used. An alternative approach consist in a two-step process, where a sacrificial silicon layer is pre-patterned with a low damage plasma process, stopping on the underlying MoS2 film. The pre-patterned layer is used as sacrificial template for the formation of the top WS2 film. This study describes the optimization of a cyclic Ar/Cl-2 atomic layer etch process applied to etch silicon on top of MoS2, with minimal damage, followed by a selective conversion of the patterned Si into WS2. The impact of the Si atomic layer etch towards the MoS2 is evaluated: in the ion energy range used for this study, MoS2 removal occurs in the over-etch step over 1-2 layers, leading to the appearance of MoOx but without significant lattice distortions to the remaining layers. The combination of Si atomic layer etch, on top of MoS2, and subsequent Si-to-WS2 selective conversion, allows to create a WS2/MoS2 heterostructure, with clear Raman signals and horizontal lattice alignment. These results demonstrate a scalable, transfer free method to achieve horizontally individually patterned heterostacks and open the route towards wafer-level processing of 2D materials.

Abstract: In this paper we employ first-principles calculations to investigate the effect of substitutional Si doping in the amorphous calcium-phosphate (a-HAP) structure on the work of adhesion, integral charge transfer, charge density difference and theoretical tensile strengths between an a-HAP coating and amorphous titanium dioxide (a-TiO2) substrate systemically. Our calculations demonstrate that substitution of a P atom by a Si atom in a-HAP (a-Si-HAP) with the creation of OH-vacancies as charge compensation results in a significant increase of the bonding strength of the coating to the substrate. The work of adhesion of the optimized Si-doped interfaces reaches a value of up to -2.52 J m(-2), which is significantly higher than for the stoichiometric a-HAP/a-TiO2. Charge density difference analysis indicates that the dominant interactions at the interface have significant covalent character, and in particular two Ti-O and three Ca-O bonds are formed for a-Si-HAP/a-TiO2 and one Ti-O and three Ca-O bonds for a-HAP/a-TiO2. From the stress-strain curve, the Young's modulus of a-Si-HAP/a-TiO2 is calculated to be about 25% higher than that of the a-HAP/a-TiO2, and the yielding stress is about 2 times greater than that of the undoped model. Our calculations therefore demonstrate that the presence of Si in the a-HAP structure strongly alters not only the bioactivity and resorption rates, but also the mechanical properties of the a-HAP/a-TiO2 interface. The results presented here provide an important theoretical insight into the nature of the chemical bonding at the a-HAP/a-TiO2 interface, and are particularly significant for the practical medical applications of HAP-based biomaterials.

Abstract: Molecular dynamics simulations are carried out for describing growth of Pd and PdO nanoclusters using the ReaxFF force field. The resulting nanocluster structures are successfully compared to those of nanoclusters experimentally grown in a gas aggregation source. The PdO structure is quasi-crystalline as revealed by high resolution transmission microscope analysis for experimental PdO nanoclusters. The role of the nanocluster temperature in the molecular dynamics simulated growth is highlighted.

Abstract: Almost 30 years after the detection of chronic interstitial nephritis in agricultural communities (CINAC) its etiology remains unknown. To help define this we examined 34 renal biopsies from Sri Lanka, El Salvador, India and France of patients with chronic kidney disease 2-3 and diagnosed with CINAC by light and electron microscopy. In addition to known histopathology, we identified a unique constellation of proximal tubular cell findings including large dysmorphic lysosomes with a light-medium electron-dense matrix containing dispersed dark electron-dense non-membrane bound “aggregates”. These aggregates associated with varying degrees of cellular/tubular atrophy, apparent cell fragment shedding and no-weak proximal tubular cell proliferative capacity. Identical lysosomal lesions, identifiable by electron microscopy, were observed in 9% of renal transplant implantation biopsies, but were more prevalent in six month (50%) and 12 month (67%) protocol biopsies and in indication biopsies (76%) of calcineurin inhibitor treated transplant patients. The phenotype was also found associated with nephrotoxic drugs (lomustine, clomiphene, lithium, cocaine) and in some patients with light chain tubulopathy, all conditions that can be directly or indirectly linked to calcineurin pathway inhibition or modulation. One hundred biopsies of normal kidneys, drug/toxin induced nephropathies, and overt proteinuric patients of different etiologies to some extent could demonstrate the light microscopic proximal tubular cell changes, but rarely the electron microscopic lysosomal features. Rats treated with the calcineurin inhibitor cyclosporine for four weeks developed similar proximal tubular cell lysosomal alterations, which were absent in a dehydration group. Overall, the finding of an identical proximal tubular cell (lysosomal) lesion in CINAC and calcineurin inhibitor nephrotoxicity in different geographic regions suggests a common paradigm where CINAC patients undergo a tubulotoxic mechanism similar to calcineurin inhibitor nephrotoxicity.

Abstract: On several paintings of James Ensor (1860−1949), a gradual fading of originally bright yellow areas, painted with the pigment cadmium yellow (CdS), is observed. Additionally, in some areas exposed to light, the formation of small white-colored globules on top of the original paint surface is observed. In this paper the chemical transformation leading to the color change and to the formation of the globules is elucidated. Microscopic X-ray absorption near-edge spectroscopy (ì-XANES) experiments show that sulfur, originally present in sulfidic form (S2−), is oxidized during the transformation to the sulfate form (S6+). Upon formation (at or immediately below the surface), the highly soluble cadmium sulfate is assumed to be transported to the surface in solution and reprecipitates there, forming the whitish globules. The presence of cadmium sulfate (CdSO4·2H2O) and ammonium cadmium sulfate [(NH4)2Cd(SO4)2] at the surface is confirmed by microscopic X-ray diffraction measurements, where the latter salt is suspected to result from a secondary reaction of cadmium sulfate with ammonia. Measurements performed on cross sections reveal that the oxidation front has penetrated into the yellow paint down to ca. 1−2 ìm. The morphology and elemental distribution of the paint and degradation product were examined by means of scanning electron microscopy equipped with an energy-dispersive spectrometer (SEM-EDS) and synchrotron radiation based micro-X-ray fluorescence spectrometry (SR ì-XRF). In addition, ultraviolet-induced visible fluorescence photography (UIVFP) revealed itself to be a straightforward technique for documenting the occurrence of this specific kind of degradation on a macroscale by painting conservators.