367 research outputs found
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
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