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cctbx news

Description: The 'Computational Crystallography Toolbox' (cctbx, http://cctbx.sourceforge.net/) is the open-source component of the Phenix project (http://www.phenix-online.org/). Most recent cctbx developments are geared towards supporting new features of the phenix.refine application. Thus, the open-source mmtbx (macromolecular toolbox) module is currently being most rapidly developed. In this article we give an overview of some of the recent developments. However, the main theme of this article is the presentation of a light-weight example command-line application that was specifically developed for this newsletter: sequence alignment and superposition of two molecules read from files in PDB format. This involves parameter input based on the Phil module presented in Newsletter No. 5, fast reading of the PDB files with the new iotbx.pdb.input class, simple sequence alignment using the new mmtbx.alignment module, and use of the Kearsley (1989) superposition algorithm to find the least-squares solution for superposing C-alpha positions. The major steps are introduced individually, followed by a presentation of the complete application. The example application is deliberately limited in functionality to make it concise enough for this article. The main goal is to show how the open-source components are typically combined into an application. Even though the example is quite specific to macromolecular crystallography, we believe it will also be useful for a small-molecule audience interested in utilizing the large open-source library of general crystallographic algorithms (see our previous articles in this newsletter series) to build an application. We describe recent developments of the Computational Crystallography Toolbox.
Date: November 22, 2006
Creator: Grosse-Kunstleve, Ralf W.; Zwart, Peter H.; Afonine, Pavel V.; Ioerger, Thomas R. & Adams, Paul D.
Partner: UNT Libraries Government Documents Department

The optical wing aligning device of the Langley Field tunnel

Description: Described here is a convenient and accurate method of aligning the wing chord with the airflow. The device was developed to permit rapid and accurate alignment of airfoils and models with the airstream passing through the tunnel. It consists of three main parts: a projector, a reflector, and a target. The arrangement, which is shown in a figure, has proven satisfactory in operation. It is far better than the old method of sighting across a long batten, as the operator of a balance may see the target and correctly judge the accuracy of his alignment. Whereas the old method required two operators and several minutes time to align to within 1/10 degree, this method enables one operator to align a wing to within 1/100 of a degree in a few seconds. This method also has the advantage of being able to measure the angle of the wing while the tunnel is running. Thus, the true angle of incidence is shown.
Date: January 1921
Creator: Norton, F. H. & Bacon, D. L.
Partner: UNT Libraries Government Documents Department

Using aberration test patterns to optimize the performance of EUV aerial imaging microscopes

Description: The SEMATECH Berkeley Actinic Inspection Tool (AIT) is a prototype EUV-wavelength zoneplate microscope that provides high quality aerial image measurements of EUV reticles. To simplify and improve the alignment procedure we have created and tested arrays of aberration-sensitive patterns on EUV reticles and we have compared their images collected with the AIT to the expected shapes obtained by simulating the theoretical wavefront of the system. We obtained a consistent measure of coma and astigmatism in the center of the field of view using two different patterns, revealing a misalignment condition in the optics.
Date: June 16, 2009
Creator: Mochi, Iacopo; Goldberg, Kenneth A.; Miyakawa, Ryan; Naulleau, Patrick; Han, Hak-Seung & Huh, Sungmin
Partner: UNT Libraries Government Documents Department

Business/it Alignment: the Impact of Incentive Plans on the Development of Shared Vision

Description: This study, utilizing Preston and Karahanna’s framework for shared vision development and Agency Theory, explores the impact of vision development factors and factors associated with incentive plans on shared vision and alignment. Results of the study confirm the strong relationship between shared vision and alignment, and indicate that having an effective management team is important with respect to developing and maintaining shared vision and alignment within the organization. Several vision development factors such as using the language of the business, participation on the top management team (TMT), and having knowledge of the business impact shared vision through their influence on teamwork. Also, results of this study suggest that participation on the TMT by the CIO/IT leader is more important than the individual’s position in the organizational hierarchy. In addition, attributes associated with incentive plans such as achievable and clear measures, measures linked to organizational goals, measures that align the interests of the individual with those of the organization, regular plan reviews, and using a balanced scorecard approach with respect to incentive plan design positively impact teamwork and shared vision. For practitioners, this highlights the importance of incentive plans as powerful tools that can be used to reinforce shared vision, effective teamwork, and alignment within the organization. Also, the CIO/IT leader needs to be knowledgeable of the business and must fill the role of both a technologist as well as an enterprise leader. This person must be an evangelist communicating the value and benefits of IT to the rest of the organization.
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Date: December 2014
Creator: Johnson, Vess L.
Partner: UNT Libraries

Lithographic characterization of low-order aberrations in a 0.3-NAEUV microfield exposure tool

Description: Although tremendous progress has been made in the crucial area of fabrication of extreme ultraviolet (EUV) projection optics, the realization diffraction-limited high numerical aperture (NA) optics (above 0.2 NA) remains a concern. The highest NA EUV optics available to date are the 0.3-NA Microfield Exposure Tool (MET) optics used in an experimental exposure station at Lawrence Berkeley National Laboratory [1] and commercial METs [2] at Intel and SEMATECH-North. Even though these optics have been interferometrically demonstrated to achieve diffraction-limited wavefront quality, the question remains as to whether or not such performance levels can be maintained after installation of the optics into the exposure tool. Printing-based quantitative aberration measurements provide a convenient mechanism for the characterization of the optic wavefront error in the actual lithography tool. We present the lithographic measurement of low-order aberrations in the Berkeley MET tool, including a quantitative measurement of astigmatism and spherical error and a qualitative measurement of coma. The lithographic results are directly compared to interferometry results obtained from the same optic. Measurements of the Berkeley MET indicate either an alignment drift or errors in the interferometry on the order of 0.5 to 1 nm.
Date: March 1, 2006
Creator: Naulleau, Patrick; Cain, Jason; Dean, Kim & Goldberg, Kenneth A.
Partner: UNT Libraries Government Documents Department

DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

Description: A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmer hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.
Date: March 21, 2011
Creator: Li, Mingkun; Copeland, Alex & Han, James
Partner: UNT Libraries Government Documents Department

Flow-Based Detection of Bar Coded Particles

Description: We have developed methods for flow control, electric field alignment, and readout of colloidal Nanobarcodes{copyright}. Our flow-based detection scheme leverages microfluidics and alternate current (AC) electric fields to align and image particles in a well-defined image plane. Using analytical models of the particle rotation in electric fields we can optimize the field strength and frequency necessary to align the particles. This detection platform alleviates loss of information in solution-based assays due to particle clumping during detection.
Date: June 24, 2005
Creator: Rose, K A; Dougherty, G M & Santiago, J G
Partner: UNT Libraries Government Documents Department

A magnetorheological study of single-walled and multi-walled carbon nanotube dispersions in mineral oil and epoxy resin.

Description: Single wall carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs) were dispersed in mineral oil and epoxy resin. The magnetorheological properties of these dispersions were studied using a parallel plate rheometer. Strain sweeps, frequency sweeps, magneto sweeps and steady shear tests were conducted in various magnetic fields. G', G", h* and ty increased with increasing magnetic field, which was partially attributed to the increasing degree of the alignment of nanotubes in a stronger magnetic field. The SWNT/mo dispersions exhibited more pronounced magnetic field dependence than SWNT/ep and MWNT/mo counterparts due to their much lower viscosity. The alignment of SWNTs in mineral oil increased with rising nanotube concentration up to 2.5vol% but were significantly restricted at 6.41vol% due to nanotube flocculation.
Date: May 2005
Creator: Yang, Zhengtao
Partner: UNT Libraries

Anisotropic fiber alignment in composite structures

Description: High strength material composite structures are formed with oriented fibers to provide controlled anisotropic fibers. Fibers suspended in non-dilute concentrations (e.g., up to 20 volume percent for fibers having an aspect ratio of 20) in a selected medium are oriented by moving an axially spaced array of elements in the direction of desired fiber alignment. The array elements are generally perpendicular to the desired orientation. The suspension medium may also include sphere-like particles where the resulting material is a ceramic.
Date: December 31, 1992
Creator: Graham, A.L.; Mondy, L.A. & Guell, D.C.
Partner: UNT Libraries Government Documents Department

Closed orbit response to quadrupole strength variation

Description: We derive two formulae relating the variation in closed orbit in a storage ring to variations in quadrupole strength, neglecting nonlinear and dispersive effects. These formulae correct results previously reported [1,2,3]. We compare the results of the formulae applied to the ATF with simulations using MAD, and consider their application to beam-based alignment.
Date: January 20, 2004
Creator: Wolski, Andrzej & Zimmermann, Frank
Partner: UNT Libraries Government Documents Department

An Integrated Support and Alignment System for Large ILC Lattice Elements

Description: The manipulators used to support and position lattice elements are critical components of all particle accelerators. The increased use of large superconducting magnets and accelerator modules places even greater demands on these manipulators. However, the performance of these support systems has not kept pace with the advances made in other areas of accelerator technology. This results in accelerators that are difficult to align and may not be capable of achieving target luminosities. An innovative new type of positioning mechanism tailored to the requirements of the International Linear Collider is proposed. The Tri-Sphere System provides secure support for large lattice elements and precision adjustment in six degrees of freedom. Integrated target sockets allow the support system to be rapidly pre-aligned. The system’s kinematic design passively guides lattice elements into their correct location during installation. A complimentary Portable Actuation Unit provides the advantages of automated adjustment and allows these adjustments to be completely decoupled from surveying.
Date: May 15, 2013
Creator: Viola, Robert
Partner: UNT Libraries Government Documents Department

Transverse centroid oscillations in solenoidially focused beam transport lattices

Description: Linear equations of motion are derived that describe small-amplitude centroid oscillations induced by displacement and rotational misalignments of the focusing solenoids in the transport lattice, dipole steering elements, and initial centroid offset errors. These equations are analyzed in a local rotating Larmor frame to derive complex-variable"alignment functions" and"bending functions" that efficiently describe the characteristics of the centroid oscillations induced by mechanical misalignments of the solenoids and dipole steering elements. The alignment and bending functions depend only on properties of the ideal lattice in the absence of errors and steering and have associated expansion amplitudes set by the misalignments and steering fields. Applications of this formulation are presented for statistical analysis of centroid deviations, calculation of actual lattice misalignments from centroid measurements, and optimal beam steering.
Date: August 1, 2008
Creator: Lund, Steven M.; Wootton, Christopher J. & Lee, Edward P.
Partner: UNT Libraries Government Documents Department

Multiple Whole Genome Alignments Without a Reference Organism

Description: Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.
Date: January 16, 2009
Creator: Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey & Brudno, Michael
Partner: UNT Libraries Government Documents Department


Description: A powder metallurgical approach is utilized to prepare grain oriented Laves phase compounds of Tb{sub x}Dy{sub 1-x}Fe{sub 2}. The magnetostrains observed in the oriented compounds, though containing {approx}20% porosity as presently prepared, are far superior to those of arc cast and highly dense liquid phase sintered materials. Also, it is shown that the alignment achieved is strongly dependent on the Tb/Dy ratio.
Date: October 1, 1977
Creator: Malekzadeh, M. & Pickus, M.R.
Partner: UNT Libraries Government Documents Department

Toward a simple molecular understanding of sum frequency generation at air-water interfaces

Description: Second-order vibrational spectroscopies successfully isolate signals from interfaces, but they report on intermolecular structure in a complicated and indirect way. Here we adapt a perspective on vibrational response developed for bulk spectroscopies to explore the microscopic fluctuations to which sum frequency generation (SFG), a popular surface-specific measurement, is most sensitive. We focus exclusively on inhomogeneous broadening of spectral susceptibilities for OH stretching of HOD as a dilute solute in D{sub 2}O. Exploiting a simple connection between vibrational frequency shifts and an electric field variable, we identify several functions of molecular orientation whose averages govern SFG. The frequency-dependence of these quantities is well captured by a pair of averages, involving alignment of OH and OD bonds with the surface normal at corresponding values of the electric field. The approximate form we obtain for SFG susceptibility highlights a dramatic sensitivity to the way a simulated liquid slab is partitioned for calculating second-order response.
Date: January 13, 2009
Creator: Noah-Vanhoucke, Joyce; Smith, Jared D. & Geissler, Phillip L.
Partner: UNT Libraries Government Documents Department

Alignment of the Pixel and SCT Modules for the 2004 ATLAS Combined Test Beam

Description: A small set of final prototypes of the ATLAS Inner Detector silicon tracking system(Pixel Detector and SemiConductor Tracker), were used to take data during the 2004 Combined Test Beam. Data were collected from runs with beams of different flavour (electrons, pions, muons and photons) with a momentum range of 2 to 180 GeV/c. Four independent methods were used to align the silicon modules. The corrections obtained were validated using the known momenta of the beam particles and were shown to yield consistent results among the different alignment approaches. From the residual distributions, it is concluded that the precision attained in the alignmentof the silicon modules is of the order of 5 mm in their most precise coordinate.
Date: June 2, 2008
Creator: Collaboration, ATLAS; Ahmad, A.; Andreazza, A.; Atkinson, T.; Baines, J.; Barr, A.J. et al.
Partner: UNT Libraries Government Documents Department

Alignment strategy for the ATLAS tracker

Description: The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider. For the reconstruction of charged particles, and their production and their decay vertices, ATLAS is equipped with a sophisticated tracking system, unprecedented in size and complexity. Full exploitation of both the Inner Detector and the muon spectrometer requires an accurate alignment. The challenge of aligning the ATLAS tracking devices is discussed, and the ATLAS alignment strategy is presented and illustrated with both data and Monte Carlo results.
Date: September 23, 2007
Creator: ATLAS & Golling, T.
Partner: UNT Libraries Government Documents Department


Description: Both the magnitude and alignment of the transferred angular momentum in the reaction {sup 165}Ho + {sup 165}Ho have been measured as a function of Q value via continuum {gamma}-ray multiplicity and anisotropy techniques. Two regimes are observed: A low-Q-value regime where the aligned angular momentum component dominates over the random components, and a large-Q-value regime where the random components dominate and decrease the spin alignment.
Date: July 1, 1980
Creator: Wozniak, G.J.; McDonald, R.J.; Pacheco, A.J.; Hsu, C.C.; Morrissey, D.J.; Sobotka, L.G. et al.
Partner: UNT Libraries Government Documents Department

Emittance Growth in TESLA

Description: The results of collective simulation of a typical TeV Energy Superconducting Linear Accelerator (TESLA) are reported. Because of accelerating gradient is low and the accelerator is long compared to other TeV colliders, betatron phase mixing must be suppressed along with the usual sources of emittance growth. Including single bunch effects, alignment tolerances consistent with reasonable emittance growth are given. When such tolerances are achieved, multibunch effects do not cause excessive effective emittance growth. In addition, longitudinal multibunch effects are discussed.
Date: May 1, 1991
Creator: Krafft, Geoffrey & Bisognano, Joseph
Partner: UNT Libraries Government Documents Department

Using Gradients, Alignment and Proximity to Extract Curves and Connect Roads in Overhead Images

Description: A robust approach for automatically extracting roads from overhead images is developed in this paper. The first step involves extracting a very dense set of edge pixels using a technique based on the magnitude and direction of pixel gradients. In step two, the edges are separated into successive channels of edge orientation that each contain edge pixels whose gradient directions lie within a different angular range. A de-cluttered map of edge curve segments is extracted from each channel, and the results are merged into a single composite map of broken edge curves. The final step divides broken curves into segments that are nearly linear and classifies each segment as connected at both ends or disconnected. A measure of connectability between two disconnected line segments based on proximity and relative alignment is defined mathematically. Each disconnected segment is paired with the disconnected segment that it is most connectable to. Pairs of segments are merged if their separation and misalignment are below thresholds (manually specified at present) and the connectability of the pair is two-way optimal. Extended curve and road extraction examples are provided using commercial overhead images.
Date: January 13, 2006
Creator: Chen, B Y & Paglieroni, D W
Partner: UNT Libraries Government Documents Department

Chemical strategies for die/wafer submicron alignment and bonding.

Description: This late-start LDRD explores chemical strategies that will enable sub-micron alignment accuracy of dies and wafers by exploiting the interfacial energies of chemical ligands. We have micropatterned commensurate features, such as 2-d arrays of micron-sized gold lines on the die to be bonded. Each gold line is functionalized with alkanethiol ligands before the die are brought into contact. The ligand interfacial energy is minimized when the lines on the die are brought into registration, due to favorable interactions between the complementary ligand tails. After registration is achieved, standard bonding techniques are used to create precision permanent bonds. We have computed the alignment forces and torque between two surfaces patterned with arrays of lines or square pads to illustrate how best to maximize the tendency to align. We also discuss complex, aperiodic patterns such as rectilinear pad assemblies, concentric circles, and spirals that point the way towards extremely precise alignment.
Date: September 1, 2010
Creator: Martin, James Ellis; Baca, Alicia I.; Chu, Dahwey & Rohwer, Lauren Elizabeth Shea
Partner: UNT Libraries Government Documents Department