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

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.

Ab Initio Calculation of the Lattice Distortions induced by Substitutional Ag- and Cu- Impurities in Alkali Halide Crystals

An ab initio study of the doping of alkali halide crystals (AX: A = Li, Na, K, Rb; X = F, Cl, Br, I) by ns2 anions (Ag- and Cu-) is presented. Large active clusters with 179 ions embedded in the surrounding crystalline lattice are considered in order to describe properly the lattice relaxation induced by the introduction of substitutional impurities. In all the cases considered, the lattice distortions imply the concerted movement of several shells of neighbors. The shell displacements are smaller for the smaller anion Cu-, as expected. The study of the family of rock-salt alkali halides (excepting CsF) allows us to extract trends that might be useful at a predictive level in the study of other impurity systems. Those trends are presented and discussed in terms of simple geometric arguments.Comment: LaTeX file. 8 pages, 3 EPS pictures. New version contains calculations of the energy of formation of the defects with model clusters of different size

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

Islands of change vs. islands of disaster: Managing pigs and birds in the Anthropocene of the North Atlantic

The offshore islands of the North Atlantic were among some of the last settled places on earth, with humans reaching the Faroes and Iceland in the late Iron Age and Viking period. While older accounts emphasizing deforestation and soil erosion have presented this story of island colonization as yet another social–ecological disaster, recent archaeological and paleoenvironmental research combined with environmental history, environmental humanities, and bioscience is providing a more complex understanding of long-term human ecodynamics in these northern islands. An ongoing interdisciplinary investigation of the management of domestic pigs and wild bird populations in Faroes and Iceland is presented as an example of sustained resource management using local and traditional knowledge to create structures for successful wild fowl management on the millennial scale

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

Real-Time PyMOL Visualization for Rosetta and PyRosetta

Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for the sole purpose of visualizing biomolecules; one of the most popular tools, PyMOL (Schrödinger), is a powerful, highly extensible, user friendly, and attractive package. Integrating Rosetta and PyMOL directly has many technical and logistical obstacles inhibiting usage. To circumvent these issues, we developed a novel solution based on transmitting biomolecular structure and energy information via UDP sockets. Rosetta and PyMOL run as separate processes, thereby avoiding many technical obstacles while visualizing information on-demand in real-time. When Rosetta detects changes in the structure of a protein, new coordinates are sent over a UDP network socket to a PyMOL instance running a UDP socket listener. PyMOL then interprets and displays the molecule. This implementation also allows remote execution of Rosetta. When combined with PyRosetta, this visualization solution provides an interactive environment for protein structure prediction and design

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Principal manifolds are defined as lines or surfaces passing through ``the middle'' of data distribution. Linear principal manifolds (Principal Components Analysis) are routinely used for dimension reduction, noise filtering and data visualization. Recently, methods for constructing non-linear principal manifolds were proposed, including our elastic maps approach which is based on a physical analogy with elastic membranes. We have developed a general geometric framework for constructing ``principal objects'' of various dimensions and topologies with the simplest quadratic form of the smoothness penalty which allows very effective parallel implementations. Our approach is implemented in three programming languages (C++, Java and Delphi) with two graphical user interfaces (VidaExpert http://bioinfo.curie.fr/projects/vidaexpert and ViMiDa http://bioinfo-out.curie.fr/projects/vimida applications). In this paper we overview the method of elastic maps and present in detail one of its major applications: the visualization of microarray data in bioinformatics. We show that the method of elastic maps outperforms linear PCA in terms of data approximation, representation of between-point distance structure, preservation of local point neighborhood and representing point classes in low-dimensional spaces.Comment: 35 pages 10 figure