THERMIC: a 2-D finite-element tool to solve conductive and advective heat transfer problems in Earth Sciences

We present a C-language program, THERMIC, that solves the 2-dimensional (pseudo 3D for axi-symmetric cases) conductive and advective heat-transfer equation. THERMIC uses a finite-element method that takes into account realistic geometries, heterogeneous material properties and various boundary and initial conditions. As it also allows for latent heat (heat production due to crystallisation) and for thermal properties, such as thermal conductivity, to be dependent on temperature, it is particularly suited to heat transfer problems encountered in the Earth Sciences. We present sample applications from the various problems already treated by THERMIC (cooling of magma chambers and dykes, the study of a granitic magma ascent or of pore water flow in sedimentary basins).Successfully tested on SUN® and SGI® UNIX workstations and on Microsoft Windows 95®, 98® and NT® 4.0 system based PCs, the THERMIC package can be downloaded from the web (THERMIC home page: http://www.ipgp.jussieu.fr/UFP/thermic/html/Thermic_home.html) and contains source files, makefiles and environment files as well as executable files for both systems and an html directory with help and example files.     

QDENSITY—A Mathematica quantum computer simulation

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc.

New version program summary

Program title: QDENSITY 2.0Catalogue identifier: ADXH_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 26 055No. of bytes in distributed program, including test data, etc.: 227 540Distribution format: tar.gzProgramming language: Mathematica 6.0Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4Catalogue identifier of previous version: ADXH_v1_0Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914Classification: 4.15Does the new version supersede the previous version?: Offers an alternative, more up to date, implementationNature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters.Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed.Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.     

LevelScheme: A level scheme drawing and scientific figure preparation system for Mathematica

LevelScheme is a scientific figure preparation system for Mathematica. The main emphasis is upon the construction of level schemes, or level energy diagrams, as used in nuclear, atomic, molecular, and hadronic physics. LevelScheme also provides a general infrastructure for the preparation of publication-quality figures, including support for multipanel and inset plotting, customizable tick mark generation, and various drawing and labeling tasks. Coupled with Mathematica's plotting functions and powerful programming language, LevelScheme provides a flexible system for the creation of figures combining diagrams, mathematical plots, and data plots.

Program summary

Title of program:LevelSchemeCatalogue identifier:ADVZProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVZOperating systems:Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and LinuxProgramming language used:Mathematica 4Number of bytes in distributed program, including test and documentation:3 051 807Distribution format:tar.gzNature of problem:Creation of level scheme diagrams. Creation of publication-quality multipart figures incorporating diagrams and plots.Method of solution:A set of Mathematica packages has been developed, providing a library of level scheme drawing objects, tools for figure construction and labeling, and control code for producing the graphics.     

The Landsat Image Mosaic of Antarctica

The Landsat Image Mosaic of Antarctica (LIMA) is the first true-color, high-spatial-resolution image of the seventh continent. It is constructed from nearly 1100 individually selected Landsat-7 ETM⁺ scenes. Each image was orthorectified and adjusted for geometric, sensor and illumination variations to a standardized, almost seamless surface reflectance product. Mosaicing to avoid clouds produced a high quality, nearly cloud-free benchmark data set of Antarctica for the International Polar Year from images collected primarily during 1999–2003. Multiple color composites and enhancements were generated to illustrate additional characteristics of the multispectral data including: the true appearance of the surface; discrimination between snow and bare ice; reflectance variations within bright snow; recovered reflectance values in regions of sensor saturation; and subtle topographic variations associated with ice flow. LIMA is viewable and individual scenes or user defined portions of the mosaic are downloadable at http://lima.usgs.gov. Educational materials associated with LIMA are available at http://lima.nasa.gov.     

Pansharpening using data-centric optimization approach

Earth’s observation satellites provide simultaneously both multispectral (XS) and panchromatic (pan) images but XS image has a lower spatial resolution when compared to pan image. Pansharpening is a pixel-level fusion technique resulting in a high-resolution multispectral image in terms of both spatial and spectral resolution. The problem lies in maintaining the spectral characteristics of each channel of the XS image when pan image is used to estimate the high spatial XS image. Many techniques have been proposed to address the problem. A popular method involves a sensor-based approach where correlation among the XS channels and correlation between the pan and spectral channels are incorporated. In this paper, we take a wholesome approach based on the reflectance data irrespective of the sensor physics. A linear regression model is formulated between the XS channel and the panchromatic data. We formulate an optimization problem in terms of Lagrange multiplier to maximise the spectral consistency of the fused data with respect to the original XS data, and to minimise the error in variance between the reference data and the computed data. We validate and compare our method with IHS and Brovey methods based on evaluation metrics such as Chi-square test and the R² test. The implementation is done and presented using IKONOS satellite data.     

Securing the Operating System: Does lesser-known mean less at risk? Is the OS an example of security though obscurity?

It is no secret that Microsoft Windows NT is the hacker’s favourite Operating System (OS). According to defacement-tracking site Attrition.org, (www.Attrition.org) Windows NT received 54.41% of all recorded OS attacks between August 1999 and April 2001. In stark contrast, some of the lesser-known Operating Systems made up for as little as 0.1% of all OS attacks. However, despite the huge difference in the quantity of attacks, companies that employ the lesser-known systems may be at greater risk…     

Design and implementation of software for assembly and browsing of 3D brain atlases

Visualization software for three dimensional digital brain atlases present many challenges in design and implementation. These challenges include the design of an effective human interface, management of large data sets, display speed when slicing the data set for viewing/browsing, and the display of delineated volumes of interest (VOI). We present a software design, implementation and storage architecture that addresses these issues, allowing the user to navigate through a reconstructed volume quickly and smoothly, with an easy-to-use human interface. The software (macostat, for use with Macintosh OS) allows the user to rapidly display slices of the digital atlas at any arbitrary slicing angle, complete with delineated VOIs. The VOIs can be assigned colors of the user's choosing. The entire atlas, or selected portions, may be resliced with slices stored as individual image files, complete with delineations. These delineations may be transferred to corresponding sections of experimental materials using our analysis program (brain). The software may be obtained from the laboratory's web site: http://www.neuroterrain.org     

The development of a spectral-spatial classifier for earth observational data

Over the last several years a classifier for earth observational image data has been under development which is intended to achieve improved performance by utilizing spatial characteristics of the data as an adjunct to multispectral ones. This paper provides an overview of the conception, development, evaluation and documentation of this spectral-spatial classifier. The research program leading to this classifier is described, the algorithms of the current implementation called ECHO are outlined, and results on its performance are summarized. These results show it to have improved accuracy, with greater computation efficiency, and only slightly increased operator complexity.     

ISICSoo: A class for the calculation of ionization cross sections from ECPSSR and PWBA theory

ISICS, originally a C language program for calculating K-, L- and M-shell ionization and X-ray production cross sections from ECPSSR and PWBA theory, has been reengineered into a C++ language class, named ISICSoo. The new software design enables the use of ISICS functionality in other software systems. The code, originally developed for Microsoft Windows operating systems, has been ported to Linux and Mac OS platforms to facilitate its use in a wider scientific environment. The reengineered software also includes some fixes to the original implementation, which ensure more robust computational results and a review of some physics parameters used in the computation. The paper describes the software design and the modifications to the implementation with respect to the previous version; it also documents the test process and provides some indications about the software performance.Program summaryProgram title: ISICSooCatalogue identifier: AEKN_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKN_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 26 420No. of bytes in distributed program, including test data, etc.: 459 548Distribution format: tar.gzProgramming language: C++Computer: 80486 or higher-level PC or MacOperating system: Any OS with gcc compiler version 4.1 (or newer); tested on Scientific Linux 5 (gcc 4.1.2), Mac OS X 10.6.5 (gcc 4.2.1) and Windows XP (MS Visual C++ 2010 Express)Classification: 16.7Nature of problem: Ionization and X-ray production cross section calculations for ion–atom collisions.Solution method: Numerical integration of form factor using a logarithmic transform and Gaussian quadrature, plus exact integration limits.Additional comments: This program is a portable version of the program ADDS_v4_0.Reasons for the new version: Capability of using ISICS physics functionality in other software systems; porting the software to other platforms than Microsoft Windows; improved computational robustness and performance.Summary of revisions: Reengineering into a C++ class; several internal modifications to improve correctness and robustness; updated binding energies tabulations; performance improvements.Running time: The running time depends on the selected atomic shell and the number of polynomials used in the Gaussian quadrature integration. The examples provided only take seconds to run.     

Imitation happens [micro economics]

Imitation happens. Sometimes it is obvious when it happens, such as the resemblance of Internet Explorer 1.0 to Netscape Navigator 1.0. Sometimes it is vaguely in the details, such as the resemblance of the trash can in Windows to the same symbol in the Macintosh OS. A common perception is that there is more competitive imitation today than in the past. Is there truth to this perception? To understand the broader point, consider dividing the world into fast and slow imitation. We explain how each of these imitation work.     

Quantitative small molecule bioanalysis using chip-based nanoESI-MS/MS

A fully automated chip-based nanoelectrospray (nanoESI) system, NanoMate^® 100 (Advion BioSciences, Inc., Ithaca, NY), was evaluated for its application on quantitative bioanalysis of small molecules in support of exploratory pharmacokinetic (PK) studies. The NanoMate^® 100 was compared with the conventional autosampler coupled with liquid chromatography-electrospray (LC-ESI) interface. An API^® 3000 triple quadrupole mass spectrometer (Applied Biosystems, Inc., Foster City, CA) was used for the evaluation. The results show that the NanoMate^® 100 performs comparably to LC-ESI in terms of standard curve fitting, low limit of quantitation (LLOQ), dynamic range, accuracy, and precision. Parallel analyses of exploratory PK study samples show high correlation (R² = 0.971) between the NanoMate^® 100 and the LC-ESI. The NanoMate^® 100 exhibits advantages in carryover, sample consumption, sample cycle time, and the ability to be full automated. Despite these advantages, the necessarily rigorous sample preparation process limits the application of the NanoMate^® 100 for quantitative analysis in areas such as exploratory PK studies, which often involve multiple compounds in one study and require rapid turnaround. However, the NanoMate^® 100 has great potential in qualitative work (e.g., metabolite identification) as well as in high-throughput quantitative analysis of compound in the development stage (i.e., a single analyte with a well-established sample extraction method).     

Visualization of A-Train vertical profiles using Google Earth

Online tools, such as those pioneered by Google Earth (GE), are changing the way in which scientists and the general public interact with three-dimensional geospatial data in a virtual environment. However, while GE provides a number of features to facilitate geospatial data visualization, there is currently no readily available method for rendering vertical geospatial data derived from Earth—viewing remote sensing satellites as an orbit curtain seen from above. Here, a solution (one of many possible) is demonstrated to render vertical profiles of atmospheric data from the A-Train satellite formation in GE, using as a proof-of-concept data from one of the instruments—the NASA CloudSat satellite. CloudSat carries a nadir-viewing Cloud Profiling Radar that produces data revealing the vertical distribution of cloud characteristics along the satellite track. These data are first rendered into a long vertical image for a user-selected spatial range through the NASA Goddard Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) system (http://giovanni.gsfc.nasa.gov/). The vertical image is then chopped into small slices representing 15 s of satellite time (～103 km long ground distance). Each small piece, as a texture, is fed into a generalized COLLAborative Design Activity (COLLADA) three-dimensional (3-D) model. Using the satellite orbit coordinates, the repeated 15 s “3-D model slices” are spliced together to form a vertical “curtain” image in Keyhole Markup Language (KML) format. Each model slice is geolocated along the CloudSat orbit path based on its size, scale and angle with the longitude line that are precisely calculated on the fly. The resulting vertical cloud data can be viewed in GE, either transparently or opaquely, superimposed above the Earth's surface with an exaggerated vertical scale. Since CloudSat is just a part of the A-Train formation, the full utility of this tool can be explored within the context of the A-Train Data Depot (ATDD, http://disc.gsfc.nasa.gov/atdd/) and the corresponding Giovanni instance (http://disc1.sci.gsfc.nasa.gov/daac-bin/G3/gui.cgi?instance_id=atrain). The latter portal allows scientists and the general public to access and visualize complex A-Train datasets without having to delve into data formats specific to a given mission.     

QDENSITY—A Mathematica Quantum Computer simulation

This Mathematica 5.2 package¹ is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. Selected examples of the basic commands are presented here and a tutorial notebook, Tutorial.nb is provided with the package (available on our website) that serves as a full guide to the package. Finally, application is made to a variety of relevant cases, including Teleportation, Quantum Fourier transform, Grover's search and Shor's algorithm, in separate notebooks: QFT.nb, Teleportation.nb, Grover.nb and Shor.nb where each algorithm is explained in detail. Finally, two examples of the construction and manipulation of cluster states, which are part of “one way computing” ideas, are included as an additional tool in the notebook Cluster.nb. A Mathematica palette containing most commands in QDENSITY is also included: QDENSpalette.nb.

Program summary

Title of program: QDENSITYCatalogue identifier: ADXH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v1_0Program available from: CPC Program Library, Queen's University of Belfast, N. IrelandOperating systems: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4Programming language used: Mathematica 5.2No. of bytes in distributed program, including test data, etc.: 180 581No. of lines in distributed program, including test data, etc.: 19 382Distribution format: tar.gzMethod of solution: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed.     

Liquid–solid equilibria in quinary system Na,Mg/Cl,SO4,NO3–H2O at 298.15 K

In order to develop the nitrate deposits found close to Lop Nur in the Xinjiang region in China, the solubilities of the system Na⁺,Mg²⁺/Cl⁻,SO₄²⁻, NO₃⁻–H₂O and its subsystems, the quaternary systems Na⁺,Mg²⁺/SO₄²⁻,NO₃⁻–H₂O and Mg²⁺/Cl⁻,SO₄²⁻,NO₃⁻–H₂O, were studied at 298.15 K. The phase diagrams were plotted according to the solubilities achieved. In the equilibrium phase diagram of Mg²⁺/Cl⁻,SO₄²⁻,NO₃⁻–H₂O, there are two invariant points, five univariant curves and four regions of crystallization: Mg(NO₃)₂6H₂O,MgCl₂6H₂O,MgSO₄7H₂O and MgSO₄(1–6)H₂O. In the equilibrium phase diagram of Na⁺,Mg²⁺/SO₄²⁻, NO₃⁻–H₂O, there are five invariant points, eleven univariant curves and seven regions of crystallization: Na₂SO₄,Na₂SO₄10H₂O,NaNO₃,MgSO₄Na₂SO₄4H₂O,NaNO₃Na₂SO₄2H₂O,Mg(NO₃)₂6H₂O and MgSO₄7H₂O. In the equilibrium phase diagram of the Na⁺, Mg²⁺/Cl⁻,SO₄²⁻,NO₃⁻–H₂O system, there are six invariant points, and ten regions of crystallization: NaCl, NaNO₃,Na₂SO₄,Na₂SO₄10H₂O,MgSO₄Na₂SO₄4H₂O, NaNO₃Na₂SO₄2H₂O,MgCl₂6H₂O,Mg(NO₃)₂6H₂O, MgSO₄(1–6)H₂O and MgSO₄7H₂O.     

FeynEdit—a tool for drawing Feynman diagrams

We describe the FeynEdit tool for drawing Feynman diagrams. Input and output is done using the macros of FeynArts, which also implies that diagrams drawn by FeynArts can be edited with FeynEdit. The code can be conveniently transferred using copy-and-paste.

Program summary

Program title: FeynEditCatalogue identifier: AEBX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 31 729No. of bytes in distributed program, including test data, etc.: 500 240Distribution format: tar.gzProgramming language: JavaComputer: All Java-capable platformsOperating system: Linux, Mac OS, WindowsRAM: 1-2 MBytesClassification: 4.4Nature of problem: Graphical editing of Feynman diagrams.Solution method: The user copy-and-pastes the LaTeX code of the Feynman diagram into the editor, clicks a button to visualize the diagram, modifies it using the mouse, and finally copy-and-pastes it back into the text.Restrictions: Propagators are presently drawn only as straight lines. This is largely for performance reasons and may be added in a future version. It is not a serious deficit because that information can easily be added in the LaTeX code.Unusual features: Uses FeynArts' LaTeX representation for input and outputRunning time: User-dependent     

IQ technology: an automated, high-throughput screening assay for kinase, phosphatase, and protease targets

IQ^® Technology, a homogeneous, universal-detection platform, originally designed for high-throughput screening (HTS) of kinases and phosphatases, has now been applied to protease screening. Representative enzymes from the major classes of proteases have been assayed in the IQ^® format. Enzyme activity and compound inhibition data are presented for such enzymes as Trypsin, Matrix Metalloproteinase 3 (MMP-3) and Calpain 1. The technology has been tested in 96- to 384- to 1536-well microplate formats and is universally suited for automated screening. IQ^® Technology is a direct, noncompetitive assay that does not require antibodies or radioisotopes. Fluorophore-labeled peptides are used as enzyme substrates. Kinase or phosphatase activity is quantified by direct measurement of the phosphorylation state of the substrate. For protease activity, cleavage is quantified with a peptide substrate containing a phospho-residue distal to the fluorphore. Cleavage of the substrate liberates the fluorphore-labeled terminus from the terminus containing the phospho-residue. Protease activity is measured by the change in fluorescence intensity that occurs when a proprietary compound binds specifically to phosphoryl groups on peptides and quenches the fluorescence. IQ^® Technology can be used with any peptide sequence and is insensitive to high concentrations of ATP and substrate. The IQ^® Technology has been validated against a large number of detergents, organics, and other reagents found in reaction mixtures and has been optimized for HTS applications exhibiting representative Z' values of 0.7.