Computer simulation of heteroepitaxial oxide/oxide and metal/oxide interfaces

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Amorphisation and recrystallisation study of lithium intercalation into TiO 2 nano-architecture.

Titanium dioxide is playing an increasingly significant role in easing environmental and energy concerns. Its rich variety of polymorphic crystal structures has facilitated a wide range of applications such as photo-catalysis, photo-splitting of water, photoelectrochromic devices, insulators in metal oxide, semiconductors devices, dye sensitized solar cells (DSSCs) (energy conversions), rechargeable lithium batteries (electrochemical storage). The complex structural aspects in nano TiO 2 , are elucidated by microscopic visualization and quantification of the microstructure for electrode materials, since cell performance and various aging mechanisms depend strongly on the appearance and changes in the microstructure. Recent studies on MnO 2 have demonstrated that amorphisation and recrystallisation simulation method can adequately generate various nanostructures, for Li-ion battery compounds. The method was also previously employed to produce nano-TiO 2 . In the current study, the approach is used to study lithiated nanoporous structure for TiO 2 which have been extensively studied experimentally, as mentioned above. Molecular graphic images showing microstructural features, including voids and channels have accommodated lithium’s during lithiation and delithiation. Preliminary lithiation of TiO 2 will be considered

Ga+, In+ and Tl+ Impurities in Alkali Halide Crystals: Distortion Trends

A computational study of the doping of alkali halide crystals (AX: A = Na, K; X = Cl, Br) by ns2 cations (Ga+, In+ and Tl+) is presented. Active clusters of increasing size (from 33 to 177 ions) are considered in order to deal with the large scale distortions induced by the substitutional impurities. Those clusters are embedded in accurate quantum environments representing the surrounding crystalline lattice. The convergence of the distortion results with the size of the active cluster is analyced for some selected impurity systems. The most important conclusion from this study is that distortions along the (100) and (110) crystallographic directions are not independent. Once a reliable cluster model is found, distortion trends as a function of impurity, alkali cation and halide anion are identified and discussed. These trends may be useful when analycing other cation impurities in similar host lattices.Comment: LaTeX file. 7 pages and 2 pictures. Accepted for publication in J. Chem. Phy

Ein Beitrag zur klinischen Diagnostik des ektopischen ACTH-Syndroms

Es wird über einen Fall von ektopischem ACTH-Syndrom mit Hypercortizismus und hypokaliämischer Alkalose bei einem metastasierten Pankreas-Carcinom berichtet. Das Fehlen einer Differenz zwischen den ACTH-Spiegeln im Plasma aus dem Bulbus cranialis venae jugularis und aus der Vena femoralis unterstützte die Annahme einer nicht hypophysären Herkunft der erhöhten ACTH-Spiegel.A case of ectopic ACTH syndrome is reported presenting with hypercorticism and pronounced hypokalemic alkalosis in a woman aged 55 y. with metastatic cancer of the pancreas. The failure to show a significant difference of plasma ACTH-levels from bulbus superior venae jugularis resp. femoral vein supported the clinical assumption of non pituitary origin of elevated plasma ACTH

Lattice Distortions Around a Tl+ Impurity in NaI:Tl+ and CsI:Tl+ Scintillators. An Ab Initio Study Involving Large Active Clusters

Ab initio Perturbed Ion cluster-in-the-lattice calculations of the impurity centers NaI:Tl+ and CsI:Tl+ are pressented. We study several active clusters of increasing complexity and show that the lattice relaxation around the Tl+ impurity implies the concerted movement of several shells of neighbors. The results also reveal the importance of considering a set of ions that can respond to the geometrical displacements of the inner shells by adapting selfconsistently their wave functions. Comparison with other calculations involving comparatively small active clusters serves to assert the significance of our conclusions. Contact with experiment is made by calculating absorption energies. These are in excellent agreement with the experimental data for the most realistic active clusters considered.Comment: 7 pages plus 6 postscript figures, LaTeX. Submmited to Phys, Rev.

MMDB: 3D structures and macromolecular interactions

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure

Annotated chemical patent corpus: A gold standard for text mining

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, t

Remediation of the protein data bank archive

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented

Three Pseudomonas putida FNR Family Proteins with Different Sensitivities to O-2

The Escherichia coli fumarate-nitrate reduction regulator (FNR) protein is the paradigm for bacterial O2-sensing transcription factors. However, unlike E. coli, some bacterial species possess multiple FNR proteins that presumably have evolved to fulfill distinct roles. Here, three FNR proteins (ANR, PP_3233, and PP_3287) from a single bacterial species, Pseudomonas putida KT2440, have been analyzed. Under anaerobic conditions, all three proteins had spectral properties resembling those of [4Fe-4S] proteins. The reactivity of the ANR [4Fe-4S] cluster with O2 was similar to that of E. coli FNR, and during conversion to the apo-protein, via a [2Fe-2S] intermediate, cluster sulfur was retained. Like ANR, reconstituted PP_3233 and PP_3287 were converted to [2Fe-2S] forms when exposed to O2, but their [4Fe-4S] clusters reacted more slowly. Transcription from an FNR-dependent promoter with a consensus FNR-binding site in P. putida and E. coli strains expressing only one FNR protein was consistent with the in vitro responses to O2. Taken together, the experimental results suggest that the local environments of the iron-sulfur clusters in the different P. putida FNR proteins influence their reactivity with O2, such that ANR resembles E. coli FNR and is highly responsive to low concentrations of O2, whereas PP_3233 and PP_3287 have evolved to be less sensitive to O2