Pairing-gap, pseudogap, and no-gap phases in the radio-frequency spectra of a trapped unitary 6Li gas

International Nuclear Information System (INIS)

Pieri, P.; Perali, A.; Strinati, G. C.; Riedl, S.; Altmeyer, A.; Grimm, R.; Wright, M. J.; Kohstall, C.; Sanchez Guajardo, E. R.; Hecker Denschlag, J.

2011-01-01

Radio frequency spectra of a trapped unitary 6 Li gas are reported and analyzed in terms of a theoretical approach that includes both final-state and trap effects. The different strength of the final-state interaction across the trap is crucial for evidencing two main peaks associated with two distinct phases residing in different trap regions. These are the pairing-gap and pseudo-gap phases below the critical temperature T c , which evolve into the pseudo-gap and no-gap phases above T c . In this way, a long standing puzzle about the interpretation of rf spectra for 6 Li in a trap is solved.

Sensing Characteristics of A Precision Aligner Using Moire Gratings for Precision Alignment System

Institute of Scientific and Technical Information of China (English)

ZHOU Lizhong; Hideo Furuhashi; Yoshiyuki Uchida

2001-01-01

Sensing characteristics of a precision aligner using moire gratings for precision alignment sysem has been investigated. A differential moire alignment system and a modified alignment system were used. The influence of the setting accuracy of the gap length and inclination of gratings on the alignment accuracy has been studied experimentally and theoretically. Setting accuracy of the gap length less than 2.5μm is required in modified moire alignment. There is no influence of the gap length on the alignment accuracy in the differential alignment system. The inclination affects alignment accuracies in both differential and modified moire alignment systems.

W-curve alignments for HIV-1 genomic comparisons.

Directory of Open Access Journals (Sweden)

Douglas J Cork

2010-06-01

Full Text Available The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly.We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison.The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE.Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison

W-curve alignments for HIV-1 genomic comparisons.

Science.gov (United States)

Cork, Douglas J; Lembark, Steven; Tovanabutra, Sodsai; Robb, Merlin L; Kim, Jerome H

2010-06-01

The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly. We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison. The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE. Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison technique of

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

Science.gov (United States)

Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

2012-01-01

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

AlignMe—a membrane protein sequence alignment web server

Science.gov (United States)

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Developing Secure Power Systems Professional Competence: Alignment and Gaps in Workforce Development Programs—Summary Report

Energy Technology Data Exchange (ETDEWEB)

O' Neil, Lori Ross; Assante, Michael; Tobey, D. H.; Conway, T. J.; Vanderhorst, Jr, T. J.; Januszewski, III, J.; Leo, R.; Perman, K.

2013-07-01

This document is a summarization of the report, Developing Secure Power Systems Professional Competence: Alignment and Gaps in Workforce Development Programs, the final report for phase 2 of the SPSP (DOE workforce study) project.

Bone-femoral component interface gap after sagittal mechanical axis alignment is filled with new bone after cementless total knee arthroplasty.

Science.gov (United States)

Kuriyama, Shinichi; Hyakuna, Katsufumi; Inoue, Satoshi; Kawai, Yasutsugu; Tamaki, Yasuyuki; Ito, Hiromu; Matsuda, Shuichi

2018-05-01

This study retrospectively evaluated the fate of mismatch between an uncemented femoral component and each femoral cut surface (i.e., wedge-shaped gap) relative to sagittal mechanical alignment in total knee arthroplasty (TKA). Primary TKA was performed on 99 consecutive knees. The femoral components were aligned to the sagittal mechanical axis with CT-based navigation. All patients were assessed with postoperative true lateral radiographs. Bone-side surfaces of the uncemented femoral component were divided into five zones: anterior flange, anterior chamfer, posterior chamfer, posterior part, and distal part, which were defined as zones 1 to 5, respectively. Bone filling of wedge-shaped gaps in each zone was evaluated after 1 year. Femoral anterior notching did not occur. However, wedge-shaped gaps were observed in at least one zone in 23 of 99 knees (23%), most frequently in zone 5 (18%). There were 9 and 7 gaps in zones 1 and 2, respectively. The femoral component showed malpositioning of approximately 3° of flexion in cases with wedge-shaped gaps in zones 2 and/or 5. After one year, 67% (6/9) of zone 1, 100% (7/7) of zone 2, and 94% (17/18) of zone 5 wedge-shaped gaps were filled in with new bone. Femoral alignment relative to sagittal mechanical axis caused wedge-shaped gaps due to unstable anterior bone cutting through hard bone, but the small gaps were not clinically significant and filled in within one year. Sagittal setting of the femoral component should aim for the anatomical axis rather than the mechanical axis. IV.

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

DEFF Research Database (Denmark)

Andreatta, Massimo; Nielsen, Morten

2016-01-01

. On this relatively simple system, we developed a sequence alignment method based on artificial neural networks that allows insertions and deletions in the alignment. Results: We show that prediction methods based on alignments that include insertions and deletions have significantly higher performance than methods...... trained on peptides of single lengths. Also, we illustrate how the location of deletions can aid the interpretation of the modes of binding of the peptide-MHC, as in the case of long peptides bulging out of the MHC groove or protruding at either terminus. Finally, we demonstrate that the method can learn...... the length profile of different MHC molecules, and quantified the reduction of the experimental effort required to identify potential epitopes using our prediction algorithm. Availability and implementation: The NetMHC-4.0 method for the prediction of peptide-MHC class I binding affinity using gapped...

Strategic Business-IT alignment of application software packages: Bridging the Information Technology gap

Directory of Open Access Journals (Sweden)

Wandi Kruger

2012-09-01

Full Text Available An application software package implementation is a complex endeavour, and as such it requires the proper understanding, evaluation and redefining of the current business processes to ensure that the implementation delivers on the objectives set at the start of the project. Numerous factors exist that may contribute to the unsuccessful implementation of application software packages. However, the most significant contributor to the failure of an application software package implementation lies in the misalignment of the organisation’s business processes with the functionality of the application software package. Misalignment is attributed to a gap that exists between the business processes of an organisation and what functionality the application software package has to offer to translate the business processes of an organisation into digital form when implementing and configuring an application software package. This gap is commonly referred to as the information technology (IT gap. This study proposes to define and discuss the IT gap. Furthermore this study will make recommendations for aligning the business processes with the functionality of the application software package (addressing the IT gap. The end result of adopting these recommendations will be more successful application software package implementations.

A generalized global alignment algorithm.

Science.gov (United States)

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Alignment of paired molecules of C60 within a hexagonal platform networked through hydrogen-bonds.

Science.gov (United States)

Hisaki, Ichiro; Nakagawa, Shoichi; Sato, Hiroyasu; Tohnai, Norimitsu

2016-07-28

We demonstrate, for the first time, that a hydrogen-bonded low-density organic framework can be applied as a platform to achieve periodic alignment of paired molecules of C60, which is the smallest example of a finite-numbered cluster of C60. The framework is a layered assembly of a hydrogen-bonded 2D hexagonal network (LA-H-HexNet) composed of dodecadehydrotribenzo[18]annulene derivatives.

Competition between Final-State and Pairing-Gap Effects in the Radio-Frequency Spectra of Ultracold Fermi Atoms

International Nuclear Information System (INIS)

Perali, A.; Pieri, P.; Strinati, G. C.

2008-01-01

The radio-frequency spectra of ultracold Fermi atoms are calculated by including final-state interactions affecting the excited level of the transition and compared with the experimental data. A competition is revealed between pairing-gap effects which tend to push the oscillator strength toward high frequencies away from threshold and final-state effects which tend instead to pull the oscillator strength toward threshold. As a result of this competition, the position of the peak of the spectra cannot be simply related to the value of the pairing gap, whose extraction thus requires support from theoretical calculations

AC dielectrophoresis alignment of single-walled carbon nano tubes (SWNTS) and palladium nano wires for hydrogen gas sensor

International Nuclear Information System (INIS)

Nur Ubaidah Saidin; Nur Ubaidah Saidin; Ying, K.K.; KKhuan, N.I.; Mohammad Hafizuddin Jumali

2013-01-01

Full-text: Using AC electric field, nano wires or nano tubes can be aligned, chained or accelerated in a direction parallel to the applied field, oriented or concentrated onto designated locations as well as dispersed in controlled manner under high efficiencies. In this work, systematic study on the alignment of nano wires/ nano tubes across the 3 μm-gaps between pairs of micro fabricated gold electrodes was carried out using AC dielectrophoresis technique. Densities and alignment of the nano wires/ nano tubes across the gaps of the electrodes were controlled by the applied AC field strengths and frequencies on the electrodes. Good alignments of SWNTs and Pd nano wires were achieved at an applied frequency of 5 MHz and a field strength as high as 25 V pp for Pd nano wires compared to only 2 V pp for SWNTs. The aligned nano wires/ nano tubes will be functioned as sensor elements for hydrogen gas sensing. (author)

Cooper pairs' magnetic moment in MCFL color superconductivity

International Nuclear Information System (INIS)

Feng Bo; Ferrer, Efrain J.; Incera, Vivian de la

2011-01-01

We investigate the effect of the alignment of the magnetic moments of Cooper pairs of charged quarks that form at high density in three-flavor quark matter. The high-density phase of this matter in the presence of a magnetic field is known to be the Magnetic Color-Flavor-Locked (MCFL) phase of color superconductivity. We derive the Fierz identities of the theory and show how the explicit breaking of the rotational symmetry by the uniform magnetic field opens new channels of interactions and allows the formation of a new diquark condensate. The new order parameter is a spin-1 condensate proportional to the component in the field direction of the average magnetic moment of the pairs of charged quarks. The magnitude of the spin-1 condensate becomes comparable to the larger of the two scalar gaps in the region of large fields. The existence of the spin-1 condensate is unavoidable, as in the presence of a magnetic field there is no solution of the gap equations with nonzero scalar gaps and zero magnetic moment condensate. This is consistent with the fact that the extra condensate does not break any symmetry that has not already been broken by the known MCFL gaps. The spin-1 condensate enhances the condensation energy of pairs formed by charged quarks and the magnetization of the system. We discuss the possible consequences of the new order parameter on the issue of the chromomagnetic instability that appears in color superconductivity at moderate density.

Fast global sequence alignment technique

KAUST Repository

Bonny, Mohamed Talal

2011-11-01

Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

Fast global sequence alignment technique

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

BinAligner: a heuristic method to align biological networks.

Science.gov (United States)

Yang, Jialiang; Li, Jun; Grünewald, Stefan; Wan, Xiu-Feng

2013-01-01

The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. However, such analyses are not trivial due to the complexity of network and high computational cost. Here we develop a mixture of global and local algorithm, BinAligner, for network alignments. Based on the hypotheses that the similarity between two vertices across networks would be context dependent and that the information from the edges and the structures of subnetworks can be more informative than vertices alone, two scoring schema, 1-neighborhood subnetwork and graphlet, were introduced to derive the scoring matrices between networks, besides the commonly used scoring scheme from vertices. Then the alignment problem is formulated as an assignment problem, which is solved by the combinatorial optimization algorithm, such as the Hungarian method. The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). Interestingly, we identified several putative functional orthologous proteins with similar functions but very low sequence similarity between the two viruses. For example, KSHV open reading frame 56 (ORF56) and VZV ORF55 are helicase-primase subunits with sequence identity 14.6%, and KSHV ORF75 and VZV ORF44 are tegument proteins with sequence identity 15.3%. These functional pairs can not be identified if one restricts the alignment into orthologous protein pairs. In addition, BinAligner identified a conserved pathway between two viruses, which consists of 7 orthologous protein pairs and these proteins are connected by conserved links. This pathway might be crucial for virus packing and

Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases lambda and mu for nonhomologous end joining in human whole-cell extracts.

Science.gov (United States)

Akopiants, Konstantin; Zhou, Rui-Zhe; Mohapatra, Susovan; Valerie, Kristoffer; Lees-Miller, Susan P; Lee, Kyung-Jong; Chen, David J; Revy, Patrick; de Villartay, Jean-Pierre; Povirk, Lawrence F

2009-07-01

XLF/Cernunnos is a core protein of the nonhomologous end-joining pathway of DNA double-strand break repair. To better define the role of Cernunnos in end joining, whole-cell extracts were prepared from Cernunnos-deficient human cells. These extracts effected little joining of DNA ends with cohesive 5' or 3' overhangs, and no joining at all of partially complementary 3' overhangs that required gap filling prior to ligation. Assays in which gap-filled but unligated intermediates were trapped using dideoxynucleotides revealed that there was no gap filling on aligned DSB ends in the Cernunnos-deficient extracts. Recombinant Cernunnos protein restored gap filling and end joining of partially complementary overhangs, and stimulated joining of cohesive ends more than twentyfold. XLF-dependent gap filling was nearly eliminated by immunodepletion of DNA polymerase lambda, but was restored by addition of either polymerase lambda or polymerase mu. Thus, Cernunnos is essential for gap filling by either polymerase during nonhomologous end joining, suggesting that it plays a major role in aligning the two DNA ends in the repair complex.

Semiautomated improvement of RNA alignments

DEFF Research Database (Denmark)

Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne

2007-01-01

connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster......: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

libgapmis: extending short-read alignments.

Science.gov (United States)

Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

2013-01-01

A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. We present libgapmis, a library for extending pairwise short-read alignments. We

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

Science.gov (United States)

Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

2016-03-28

Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

In situ observation of thermal relaxation of interstitial-vacancy pair defects in a graphite gap.

Science.gov (United States)

Urita, Koki; Suenaga, Kazu; Sugai, Toshiki; Shinohara, Hisanori; Iijima, Sumio

2005-04-22

Direct observation of individual defects during formation and annihilation in the interlayer gap of double-wall carbon nanotubes (DWNT) is demonstrated by high-resolution transmission electron microscopy. The interlayer defects that bridge two adjacent graphen layers in DWNT are stable for a macroscopic time at the temperature below 450 K. These defects are assigned to a cluster of one or two interstitial-vacancy pairs (I-V pairs) and often disappear just after their formation at higher temperatures due to an instantaneous recombination of the interstitial atom with vacancy. Systematic observations performed at the elevated temperatures find a threshold for the defect annihilation at 450-500 K, which, indeed, corresponds to the known temperature for the Wigner energy release.

In situ observation of thermal relaxation of interstitial-vacancy pair defects in a graphite gap

International Nuclear Information System (INIS)

Urita, Koki; Suenaga, Kazu; Iijima, Sumio; Sugai, Toshiki; Shinohara, Hisanori

2005-01-01

Direct observation of individual defects during formation and annihilation in the interlayer gap of double-wall carbon nanotubes (DWNT) is demonstrated by high-resolution transmission electron microscopy. The interlayer defects that bridge two adjacent graphen layers in DWNT are stable for a macroscopic time at the temperature below 450 K. These defects are assigned to a cluster of one or two interstitial-vacancy pairs (I-V pairs) and often disappear just after their formation at higher temperatures due to an instantaneous recombination of the interstitial atom with vacancy. Systematic observations performed at the elevated temperatures find a threshold for the defect annihilation at 450-500 K, which, indeed, corresponds to the known temperature for the Wigner energy release

Properties of entangled photon pairs generated in one-dimensional nonlinear photonic-band-gap structures

International Nuclear Information System (INIS)

Perina, Jan Jr.; Centini, Marco; Sibilia, Concita; Bertolotti, Mario; Scalora, Michael

2006-01-01

We have developed a rigorous quantum model of spontaneous parametric down-conversion in a nonlinear 1D photonic-band-gap structure based upon expansion of the field into monochromatic plane waves. The model provides a two-photon amplitude of a created photon pair. The spectra of the signal and idler fields, their intensity profiles in the time domain, as well as the coincidence-count interference pattern in a Hong-Ou-Mandel interferometer are determined both for cw and pulsed pumping regimes in terms of the two-photon amplitude. A broad range of parameters characterizing the emitted down-converted fields can be used. As an example, a structure composed of 49 layers of GaN/AlN is analyzed as a suitable source of photon pairs having high efficiency

Superconducting gap anisotropy and d-wave pairing in YBa2Cu3O7-δ

Science.gov (United States)

Verma, Sanjeev K.; Gupta, Anushri; Kumari, Anita; Indu, B. D.

2018-02-01

Considering Born-Mayer-Huggins potential as a most suitable potential to study the dynamical properties of high-temperature superconductors (HTS), the many-body quantum dynamics to obtain phonon Green’s functions has been developed via a Hamiltonian that incorporates the contributions of harmonic electron and phonon fields, phonon field anharmonicities, defects and electron-phonon interactions without considering BCS structure. This enables one to develop the quasiparticle renormalized frequency dispersion in the representative high-temperature cuprate superconductor YBa2Cu3O7-δ. The superconducting gap shows substantial changes with increased doping. The in-plane gap study revealed a v-shape gap with a nodal point along kx = ±ky direction for optimum doping (δ = 0.16) and the nodal point vanished in underdoped and overdoped regimes. The dx2-y2 pairing symmetry is observed at optimum doping with the presence of s or dxy components ( < 3%) in underdoped and overdoped regimes.

GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

Directory of Open Access Journals (Sweden)

Pablo H C G de Sá

Full Text Available The advent of NGS (Next Generation Sequencing technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.

Possibility of Cooper-pair formation controlled by multi-terminal spin injection

Science.gov (United States)

Ohnishi, K.; Sakamoto, M.; Ishitaki, M.; Kimura, T.

2018-03-01

A multi-terminal lateral spin valve consisting of three ferromagnetic nanopillars on a Cu/Nb bilayer has been fabricated. We investigated the influence of the spin injection on the superconducting properties at the Cu/Nb interface. The non-local spin valve signal exhibits a clear spin insulation signature due to the superconducting gap of the Nb. The magnitude of the spin signal is found to show the probe configuration dependence. From the careful analysis of the bias current dependence, we found the suppression of the superconductivity due to the exchange interaction between the Cooper pair and accumulated spin plays an important role in the multi-terminal spin injections. We also discuss about the possibility of the Cooper-pair formation due to the spin injection from the two injectors with the anti-parallel alignment.

Geodetic alignment of laser power installations

International Nuclear Information System (INIS)

Shtorm, V.V.; Gostev, A.M.; Drobikov, A.V.

1989-01-01

Main problems occuring in applied geodesy under initial alignment of laser power installation optical channel are considered. Attention is paid to alignment of lens beamguide telescopic pairs and alignment quality control. Methods and means of geodetic measurements under alignment are indicated. Conclusions are made about the degree of working through certain aspects of the problem

Pareto optimal pairwise sequence alignment.

Science.gov (United States)

DeRonne, Kevin W; Karypis, George

2013-01-01

Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

Topological Nodal Cooper Pairing in Doped Weyl Metals

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Li, Yi; Haldane, F. D. M.

2018-02-01

We generalize the concept of Berry connection of the single-electron band structure to that of a two-particle Cooper pairing state between two Fermi surfaces with opposite Chern numbers. Because of underlying Fermi surface topology, the pairing Berry phase acquires nontrivial monopole structure. Consequently, pairing gap functions have topologically protected nodal structure as vortices in the momentum space with the total vorticity solely determined by the pair monopole charge qp. The nodes of gap function behave as the Weyl-Majorana points of the Bogoliubov-de Gennes pairing Hamiltonian. Their relation with the connection patterns of the surface modes from the Weyl band structure and the Majorana surface modes inside the pairing gap is also discussed. Under the approximation of spherical Fermi surfaces, the pairing symmetry are represented by monopole harmonic functions. The lowest possible pairing channel carries angular momentum number j =|qp|, and the corresponding gap functions are holomorphic or antiholomorphic functions on Fermi surfaces. After projected on the Fermi surfaces with nontrivial topology, all the partial-wave channels of pairing interactions acquire the monopole charge qp independent of concrete pairing mechanism.

Probabilistic biological network alignment.

Science.gov (United States)

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Directory of Open Access Journals (Sweden)

Genki Terashi

Full Text Available Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align, which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1 agreement with the gold standard alignment, (2 alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3 consistency of the multiple alignments, and (4 classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Science.gov (United States)

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

MANGO: a new approach to multiple sequence alignment.

Science.gov (United States)

Zhang, Zefeng; Lin, Hao; Li, Ming

2007-01-01

Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

Creation of paired electron states in the gap of semiconducting carbon nanotubes by correlated hydrogen adsorption

International Nuclear Information System (INIS)

Buchs, Gilles; Krasheninnikov, Arkady V; Ruffieux, Pascal; Groening, Pierangelo; Foster, Adam S; Nieminen, Risto M; Groening, Oliver

2007-01-01

The specific, local modification of the electronic structure of carbon nanomaterials is as important for novel electronic device fabrication as the doping in the case of silicon-based electronics. Here, we report low temperature scanning tunneling microscopy and spectroscopy study of semiconducting carbon nanotubes subjected to hydrogen-plasma treatment. We show that plasma treatment mostly results in the creation of paired electronic states in the nanotube band gap. Combined with extensive first-principle simulations, our results provide direct evidence that these states originate from correlated chemisorption of hydrogen adatoms on the tube surface. The energy splitting of the paired states is governed by the adatom-adatom interaction, so that controlled hydrogenation can be used for engineering the local electronic structure of nanotubes and other sp 2 -bonded nanocarbon systems

BFAST: an alignment tool for large scale genome resequencing.

Directory of Open Access Journals (Sweden)

Nils Homer

2009-11-01

Full Text Available The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

Science.gov (United States)

Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

2013-09-01

Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

Esaki Diodes in van der Waals Heterojunctions with Broken-Gap Energy Band Alignment.

Science.gov (United States)

Yan, Rusen; Fathipour, Sara; Han, Yimo; Song, Bo; Xiao, Shudong; Li, Mingda; Ma, Nan; Protasenko, Vladimir; Muller, David A; Jena, Debdeep; Xing, Huili Grace

2015-09-09

van der Waals (vdW) heterojunctions composed of two-dimensional (2D) layered materials are emerging as a solid-state materials family that exhibits novel physics phenomena that can power a range of electronic and photonic applications. Here, we present the first demonstration of an important building block in vdW solids: room temperature Esaki tunnel diodes. The Esaki diodes were realized in vdW heterostructures made of black phosphorus (BP) and tin diselenide (SnSe2), two layered semiconductors that possess a broken-gap energy band offset. The presence of a thin insulating barrier between BP and SnSe2 enabled the observation of a prominent negative differential resistance (NDR) region in the forward-bias current-voltage characteristics, with a peak to valley ratio of 1.8 at 300 K and 2.8 at 80 K. A weak temperature dependence of the NDR indicates electron tunneling being the dominant transport mechanism, and a theoretical model shows excellent agreement with the experimental results. Furthermore, the broken-gap band alignment is confirmed by the junction photoresponse, and the phosphorus double planes in a single layer of BP are resolved in transmission electron microscopy (TEM) for the first time. Our results represent a significant advance in the fundamental understanding of vdW heterojunctions and broaden the potential applications of 2D layered materials.

Effects of interlayer Sn-Sn lone pair interaction on the band gap of bulk and nanosheet SnO

Science.gov (United States)

Umezawa, Naoto; Zhou, Wei

2015-03-01

Effects of interlayer lone-pair interactions on the electronic structure of SnO are firstly explored by the density-functional theory. Our comprehensive study reveals that the band gap of SnO opens as increase in the interlayer Sn-Sn distance. The effect is rationalized by the character of band edges which consists of bonding and anti-bonding states from interlayer lone pair interactions. The band edges for several nanosheets and strained double-layer SnO are estimated. We conclude that the double-layer SnO is a promising material for visible-light driven photocatalyst for hydrogen evolution. This work is supported by the Japan Science and Technology Agency (JST) Precursory Research for Embryonic Science and Technology (PRESTO) program.

Nanoscratch technique for aligning multiwalled carbon nanotubes ...

Indian Academy of Sciences (India)

Carbon nanotube; arc discharge; characterization; alignment; nanoscratch. 1. Introduction ... During arc discharge, when the gap between the electrodes is ∼ 1 mm, ..... increase in the D band intensity in the aligned region may not be possibly ...

Alignment of CEBAF cryomodules

International Nuclear Information System (INIS)

Schneider, W.J.; Bisognano, J.J.; Fischer, J.

1993-06-01

CEBAF, the Continuous Electron Beam Accelerator Facility, when completed, will house a 4 GeV recirculating accelerator. Each of the accelerator's two linacs contains 160 superconducting radio frequency (SRF) 1497 MHz niobium cavities in 20 cryomodules. Alignments of the cavities within the cryomodule with respect to beam axis is critical to achieving the optimum accelerator performance. This paper discusses the rationale for the current specification on cavity mechanical alignment: 2 mrad (rms) applied to the 0.5 m active length cavities. We describe the tooling that was developed to achieve the tolerance at the time of cavity pair assembly, to preserve and integrate alignment during cryomodule assembly, and to translate alignment to appropriate installation in the beam line

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.

Science.gov (United States)

Ibarra, Ignacio L; Melo, Francisco

2010-07-01

Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening/extension penalties. We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications. The software is freely available at: http:/melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX. All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl.

PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

Science.gov (United States)

Kuznetsov, Igor B; McDuffie, Michael

2015-05-07

Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities. PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach. PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Directory of Open Access Journals (Sweden)

Kierzynka Michal

2011-05-01

Full Text Available Abstract Background Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. Results In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. Conclusions The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

DEFF Research Database (Denmark)

Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

2013-01-01

Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general...... comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22495 3D modules in all PDB files results in 977 internal loop...

Genomic multiple sequence alignments: refinement using a genetic algorithm

Directory of Open Access Journals (Sweden)

Lefkowitz Elliot J

2005-08-01

slightly; but significantly, this occurred at the same time that the overall alignment length decreased – through the removal of gaps – by approximately 200 gapped regions representing roughly 1,300 gaps. Conclusion We have implemented a genetic algorithm in parallel mode to optimize multiple genomic sequence alignments initially generated by various alignment tools. Benchmarking experiments showed that the refinement algorithm improved genomic sequence alignments within a reasonable period of time.

Considerations in the identification of functional RNA structural elements in genomic alignments

Directory of Open Access Journals (Sweden)

Blencowe Benjamin J

2007-01-01

Full Text Available Abstract Background Accurate identification of novel, functional noncoding (nc RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score potential RNA secondary structures on the basis of thermodynamic stability, conservation, and/or covariance in sequence alignments. Neither the algorithms nor the information gained from the individual inputs have been independently assessed. Furthermore, due to issues in modelling background signal, it has been difficult to gauge the precision of these algorithms on a genomic scale, in which even a seemingly small false-positive rate can result in a vast excess of false discoveries. Results We developed a shuffling algorithm, shuffle-pair.pl, that simultaneously preserves dinucleotide frequency, gaps, and local conservation in pairwise sequence alignments. We used shuffle-pair.pl to assess precision and recall of six ncRNA search tools (MSARI, QRNA, ddbRNA, RNAz, Evofold, and several variants of simple thermodynamic stability on a test set of 3046 alignments of known ncRNAs. Relative to mononucleotide shuffling, preservation of dinucleotide content in shuffling the alignments resulted in a drastic increase in estimated false-positive detection rates for ncRNA elements, precluding evaluation of higher order alignments, which cannot not be adequately shuffled maintaining both dinucleotides and alignment structure. On pairwise alignments, none of the covariance-based tools performed markedly better than thermodynamic scoring alone. Although the high false-positive rates call into question the veracity of any individual predicted secondary structural element in our analysis, we nevertheless identified intriguing global trends in human genome alignments. The distribution of ncRNA prediction scores in 75-base windows overlapping UTRs, introns, and intergenic regions analyzed using both thermodynamic stability and EvoFold (which has no thermodynamic component was

Geometric phase and entanglement of Raman photon pairs in the presence of photonic band gap

International Nuclear Information System (INIS)

Berrada, K.; Ooi, C. H. Raymond; Abdel-Khalek, S.

2015-01-01

Robustness of the geometric phase (GP) with respect to different noise effects is a basic condition for an effective quantum computation. Here, we propose a useful quantum system with real physical parameters by studying the GP of a pair of Stokes and anti-Stokes photons, involving Raman emission processes with and without photonic band gap (PBG) effect. We show that the properties of GP are very sensitive to the change of the Rabi frequency and time, exhibiting collapse phenomenon as the time becomes significantly large. The system allows us to obtain a state which remains with zero GP for longer times. This result plays a significant role to enhance the stabilization and control of the system dynamics. Finally, we investigate the nonlocal correlation (entanglement) between the pair photons by taking into account the effect of different parameters. An interesting correlation between the GP and entanglement is observed showing that the PBG stabilizes the fluctuations in the system and makes the entanglement more robust against the change of time and frequency

Unsupervised image matching based on manifold alignment.

Science.gov (United States)

Pei, Yuru; Huang, Fengchun; Shi, Fuhao; Zha, Hongbin

2012-08-01

This paper challenges the issue of automatic matching between two image sets with similar intrinsic structures and different appearances, especially when there is no prior correspondence. An unsupervised manifold alignment framework is proposed to establish correspondence between data sets by a mapping function in the mutual embedding space. We introduce a local similarity metric based on parameterized distance curves to represent the connection of one point with the rest of the manifold. A small set of valid feature pairs can be found without manual interactions by matching the distance curve of one manifold with the curve cluster of the other manifold. To avoid potential confusions in image matching, we propose an extended affine transformation to solve the nonrigid alignment in the embedding space. The comparatively tight alignments and the structure preservation can be obtained simultaneously. The point pairs with the minimum distance after alignment are viewed as the matchings. We apply manifold alignment to image set matching problems. The correspondence between image sets of different poses, illuminations, and identities can be established effectively by our approach.

Deep donor-acceptor pair recombination in bulk GaP studied by ODMR and DLTS techniques

International Nuclear Information System (INIS)

Awadelkarim, O.O.; Godlewski, M.; Monemar, B.

1989-01-01

Deep level transient spectroscopy (DLTS) and optically detected magnetic resonance (ODMR) are applied to study deep defect levels with photoluminescence bands observed in the near infrared region in S- and Te-doped bulk GaP crystals grown by the liquid encapsulated Czochralski method. The ODMR data suggest that the emission bands with maxima observed at 8000-8200 A (∼ 1.5 eV), common to both materials, and at 7750 A (1.6 eV), present only in GaP:Te, are due to donor-acceptor pair recombinations. The latter band, reported here for the first time, is tentatively associated with deep states observed by DLTS. (author) 19 refs., 5 figs

Nuclear pairing reduction due to rotation and blocking

International Nuclear Information System (INIS)

Wu Xi; Zhang Zhenhua; Lei Yi'an; Zeng Jinyan

2010-01-01

Nuclear pairing gaps of well-deformed and superdeformed nuclei are investigated using the particle-number conserving (PNC) formalism for the cranked shell model, in which the blocking effects are treated exactly and no spurious states appear. Both the rotational frequency ω-dependence and seniority ν-dependence of the pairing gap Δ-bar are addressed. For the ground-state bands of even-even nuclei, PNC calculations show that in general Δ-bar decreases with increasing ω, but the ω-dependence is much weaker than that calculated by the number-projected Hartree-Fock-Bogolyubov (NHFB) approach. For the multi quasiparticle bands (seniority ν > 2), the pairing gaps keep almost ω-independent. As a function of the seniority ν, the bandhead pairing gaps Δ-bar (ν, ω = 0) decrease slowly with increasing ν. Even for the highest seniority ν bands identified so far, Δ-bar (ν, ω = 0) keep 70% larger than Δ-bar (ν = 0, ω = 0). (authors)

Nuclear pairing reduction due to rotation and blocking

International Nuclear Information System (INIS)

Wu, X.; Zhang, Z. H.; Zeng, J. Y.; Lei, Y. A.

2011-01-01

Nuclear pairing gaps of normally deformed and superdeformed nuclei are investigated using the particle-number-conserving (PNC) formalism for the cranked shell model, in which the blocking effects are treated exactly. Both rotational frequency ω dependence and seniority (number of unpaired particles) ν dependence of the pairing gap Δ-tilde are investigated. For the ground-state bands of even-even nuclei, PNC calculations show that, in general, Δ-tilde decreases with increasing ω, but the ω dependence is much weaker than that calculated by the number-projected Hartree-Fock-Bogolyubov approach. For the multiquasiparticle bands (seniority ν>2), the pairing gaps stay almost ω independent. As a function of the seniority ν, the bandhead pairing gaps Δ-tilde(ν,ω=0) decrease slowly with increasing ν. Even for the highest seniority ν bands identified so far, Δ-tilde(ν,ω=0) remains greater than 70% of Δ-tilde(ν=0,ω=0).

ΛΛ pairing in NΛ composite matter

International Nuclear Information System (INIS)

Tanigawa, Tomonori; Matsuzaki, Masayuki; Chiba, Satoshi

2003-01-01

ΛΛ pairing correlation in binary mixed matter of nucleons and lambdas is studied within the relativistic Hartree-Bogoliubov model. Λ hyperons to be paired up are immersed in background nucleons in normal state. A phenomenological ΛΛ interaction, which is derived relativistically from the Lagrangian of the system, is adopted to the gap equation. It is found that increasing the nucleon density makes the ΛΛ pairing gap suppressed. This result suggests a mechanism, specific to relativistic models, of its dependence on the nucleon density. (author)

ΛΛ pairing in NΛ composite matter

International Nuclear Information System (INIS)

Tanigawa, Tomonori; Matsuzaki, Masayuki; Chiba, Satoshi

2002-01-01

ΛΛ pairing correlation in binary mixed matter of nucleons and lambdas is studied within the relativistic Hartree-Bogoliubov model. Λ hyperons to be paired up are immersed in background nucleons in normal state. A phenomenological ΛΛ interaction, which is derived relativistically from the Lagrangian of the system, is adopted to the gap equation. It is found that increasing the nucleon density makes the ΛΛ pairing gap suppressed. This result suggests a mechanism, specific to relativistic models, of its dependence on the nucleon density. (author)

Thermodynamics of pairing phase transition in nuclei

International Nuclear Information System (INIS)

Karim, Afaque; Ahmad, Shakeb

2014-01-01

The pairing gaps, pairing energy, heat capacity and entropy are calculated within BCS (Bardeen- Cooper-Schrieffer) based quasi particle approach, including thermal fluctuations on pairing field within pairing model for all nuclei (light, medium, heavy and super heavy nuclei). Quasi particles approach in BCS theory was introduced and reformulated to study various properties. For thermodynamic behavior of nuclei at finite temperatures, the anomalous averages of creation and annihilation operators are introduced. It is solved self consistently at finite temperatures to obtain BCS Hamiltonian. After doing unitary transformation, we obtained the Hamiltonian in the diagonal form. Thus, one gets temperature dependence gap parameter and pairing energy for nuclei. Moreover, the energy at finite temperatures is the sum of the condensation energy and the thermal energy of fermionic quasi particles. With the help of BCS Hamiltonian, specific heat, entropy and free energy are calculated for different nuclei. In this paper the gap parameter occupation number and pairing energy as a function of temperature which is important for all the light, medium, heavy and super heavy nuclei is calculated. Moreover, the various thermo dynamical quantities like specific heat, entropy and free energy is also obtained for different nuclei. Thus, the thermodynamics of pairing phase transition in nuclei is studied

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez and Y. Pakhotin

2012-01-01

  A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

Information Technology (IT) Strategic Alignment: A Correlational Study between the Impact of IT Governance Structures and IT Strategic Alignment

Science.gov (United States)

Asante, Keith K.

2010-01-01

This dissertation explored the extent to which Information Technology (IT) strategic alignment are impacted by IT governance structures. The study discusses several strategic alignment and IT governance literature that presents a gap in the literature domain. Subsequent studies researched issues surrounding why organizations are not able to align…

Pairing phase transition and thermodynamical quantities in 148,149Sm

International Nuclear Information System (INIS)

Razavi, R.; Behkami, A.N.; Dehghani, V.

2014-01-01

The nuclear level densities and entropies in 148,149 Sm have been calculated in the framework of the superconducting theory that includes modified nuclear pairing gap. For modified pairing gap parameter the smooth transition from the BCS to the Fermi type distributions is used. By applying modified pairing gap, the extracted S-shaped heat capacity as a function of nuclear temperature exhibits a physical and smoother behavior instead of the singular behavior predicted by the BCS equations at critical temperature

Junctionless Cooper pair transistor

Energy Technology Data Exchange (ETDEWEB)

Arutyunov, K. Yu., E-mail: konstantin.yu.arutyunov@jyu.fi [National Research University Higher School of Economics , Moscow Institute of Electronics and Mathematics, 101000 Moscow (Russian Federation); P.L. Kapitza Institute for Physical Problems RAS , Moscow 119334 (Russian Federation); Lehtinen, J.S. [VTT Technical Research Centre of Finland Ltd., Centre for Metrology MIKES, P.O. Box 1000, FI-02044 VTT (Finland)

2017-02-15

Highlights: • Junctionless Cooper pair box. • Quantum phase slips. • Coulomb blockade and gate modulation of the Coulomb gap. - Abstract: Quantum phase slip (QPS) is the topological singularity of the complex order parameter of a quasi-one-dimensional superconductor: momentary zeroing of the modulus and simultaneous 'slip' of the phase by ±2π. The QPS event(s) are the dynamic equivalent of tunneling through a conventional Josephson junction containing static in space and time weak link(s). Here we demonstrate the operation of a superconducting single electron transistor (Cooper pair transistor) without any tunnel junctions. Instead a pair of thin superconducting titanium wires in QPS regime was used. The current–voltage characteristics demonstrate the clear Coulomb blockade with magnitude of the Coulomb gap modulated by the gate potential. The Coulomb blockade disappears above the critical temperature, and at low temperatures can be suppressed by strong magnetic field.

Anisotropic hypersonic phonon propagation in films of aligned ellipsoids.

Science.gov (United States)

Beltramo, Peter J; Schneider, Dirk; Fytas, George; Furst, Eric M

2014-11-14

A material with anisotropic elastic mechanical properties and a direction-dependent hypersonic band gap is fabricated using ac electric field-directed convective self-assembly of colloidal ellipsoids. The frequency of the gap, which is detected in the direction perpendicular to particle alignment and entirely absent parallel to alignment, and the effective sound velocities can be tuned by the particle aspect ratio. We hypothesize that the band gap originates from the primary eigenmode peak, the m-splitted (s,1,2) mode, of the particle resonating with the effective medium. These results reveal the potential for powerful control of the hypersonic phononic band diagram by combining anisotropic particles and self-assembly.

Modeling Phase-Aligned Gamma-Ray and Radio Millisecond Pulsar Light Curves

Science.gov (United States)

Venter, C.; Johnson, T.; Harding, A.

2012-01-01

Since the discovery of the first eight gamma-ray millisecond pulsars (MSPs) by the Fermi Large Area Telescope, this population has been steadily expanding. Four of the more recent detections, PSR J00340534, PSR J1939+2134 (B1937+21; the first MSP ever discovered), PSR J1959+2048 (B1957+20; the first discovery of a black widow system), and PSR J2214+3000, exhibit a phenomenon not present in the original discoveries: nearly phase-aligned radio and gamma-ray light curves (LCs). To account for the phase alignment, we explore models where both the radio and gamma-ray emission originate either in the outer magnetosphere near the light cylinder or near the polar caps. Using a Markov Chain Monte Carlo technique to search for best-fit model parameters, we obtain reasonable LC fits for the first three of these MSPs in the context of altitude-limited outer gap (alOG) and two-pole caustic (alTPC) geometries (for both gamma-ray and radio emission). These models differ from the standard outer gap (OG)/two-pole caustic (TPC) models in two respects: the radio emission originates in caustics at relatively high altitudes compared to the usual conal radio beams, and we allow both the minimum and maximum altitudes of the gamma-ray and radio emission regions to vary within a limited range (excluding the minimum gamma-ray altitude of the alTPC model, which is kept constant at the stellar radius, and that of the alOG model, which is set to the position-dependent null charge surface altitude). Alternatively, phase-aligned solutions also exist for emission originating near the stellar surface in a slot gap scenario (low-altitude slot gap (laSG) models). We find that the alTPC models provide slightly better LC fits than the alOG models, and both of these give better fits than the laSG models (for the limited range of parameters considered in the case of the laSG models). Thus, our fits imply that the phase-aligned LCs are likely of caustic origin, produced in the outer magnetosphere, and

Gap Resolution

Energy Technology Data Exchange (ETDEWEB)

2017-04-25

Gap Resolution is a software package that was developed to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA. This is done by performing the follow steps:1) Identify and distribute the data for each gap in sub-projects. 2) Assemble the data associated with each sub-project using a secondary assembler, such as Newbler or PGA. 3) Determine if any gaps are closed after reassembly, and either design fakes (consensus of closed gap) for those that closed or lab experiments for those that require additional data. The software requires as input a genome assembly produce by the Newbler assembler provided by Roche and 454 data containing paired-end reads.

{lambda}{lambda} pairing in N{lambda} composite matter

Energy Technology Data Exchange (ETDEWEB)

Tanigawa, Tomonori [Japan Society for the Promotion of Science, Tokyo (Japan); Matsuzaki, Masayuki [Japan Atomic Energy Research Inst., Tokyo (Japan); Chiba, Satoshi [Fukuoka Univ. of Education, Dept. of Physics, Munakata, Fukuoka (Japan)

2002-09-01

{lambda}{lambda} pairing correlation in binary mixed matter of nucleons and lambdas is studied within the relativistic Hartree-Bogoliubov model. {lambda} hyperons to be paired up are immersed in background nucleons in normal state. A phenomenological {lambda}{lambda} interaction, which is derived relativistically from the Lagrangian of the system, is adopted to the gap equation. It is found that increasing the nucleon density makes the {lambda}{lambda} pairing gap suppressed. This result suggests a mechanism, specific to relativistic models, of its dependence on the nucleon density. (author)

Aligning with New Digital Strategy

DEFF Research Database (Denmark)

Yeow, Adrian; Soh, Christina; Hansen, Rina

2018-01-01

Prior IS research has not fully addressed the aligning process in the highly dynamic context of digital strategy. To address this gap, we conduct a longitudinal analysis of a B2B company's journey to enact its B2C digital strategy, using the dynamic capabilities approach. We found...... that as an organization shifts towards a digital strategy, misalignments between the emergent strategy and resources give rise to tension. Our study resulted in the development of an aligning process model that is comprised of three phases (exploratory, building, and extending) and generalizable organizational aligning...... actions that form the organization's sensing, seizing, and transforming capacities. These aligning actions iteratively reconfigured organizational resources and refined strategy in order to respond to both changes in the environment and internal tensions. We also recognized that there are challenges...

MICA: Multiple interval-based curve alignment

Science.gov (United States)

Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

2018-01-01

MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

The composite N1 component to gaps in noise.

Science.gov (United States)

Pratt, Hillel; Bleich, Naomi; Mittelman, Nomi

2005-11-01

To indicate whether the double peaked N(1) to gaps in continuous white noise is a composite of onset and offset responses to transients or whether it reflects higher processing such as change or mismatch detection and to assess the role of attention in this process. Evoked potentials were recorded to two binaural stimulus types: (1) gaps of different durations randomly distributed in continuous white noise; and (2) click pairs at intervals identical to those between gap onsets and offsets in the continuous noise stimulus. Potentials to these stimuli were recorded while subjects read a text and while detecting gaps in noise or click pairs. Potentials were detected to all click pairs and to gaps of 5 ms or longer, corresponding to the subjects' psychoacoustic gap detection threshold. With long gap durations of 200-800 ms, distinct potentials to gap onset and gap offset were observed. The waveforms to all click pairs and to offsets of long gaps were similar and single-peaked, while potentials to gaps of 10 ms and longer, and potentials to onsets of long gaps were double-peaked, consisting of two N(1) negativities, 60 ms apart, irrespective of gap duration. The first (N(1a)), was more frontal in its distribution and similar to that of clicks. The second (N(1b)) peak's distribution was more central/temporal and its source locations and time course of activity were distinct. No effects of attention on any of the varieties and constituents of N(1) were observed. Comparing potentials to gap onsets, to click pairs and to gap offsets, suggests that potentials to gap onsets involve not only sound onset/offset responses (N(1), N(1a)) but also the subsequent pre-attentive perception of the cessation of an ongoing sound (N(1b)). We propose that N(1b) is distinct from change or mismatch detection and is associated with termination of an ongoing continuous stimulus. We propose to call it the N(egation)-process. A constituent of the N(1) complex is shown to be associated with the

Model for pairing phase transition in atomic nuclei

International Nuclear Information System (INIS)

Schiller, A.; Guttormsen, M.; Hjorth-Jensen, M.; Rekstad, J.; Siem, S.

2002-01-01

A model is developed which allows the investigation and classification of the pairing phase transition in atomic nuclei. The regions of the parameter space are discussed for which a pairing phase transition can be observed. The model parameters include number of particles, attenuation of pairing correlations with increasing seniority, single-particle level spacing, and pairing gap parameter

Vacuum Outer-Gap Structure in Pulsar Outer Magnetospheres

International Nuclear Information System (INIS)

Gui-Fang, Lin; Li, Zhang

2009-01-01

We study the vacuum outer-gap structure in the outer magnetosphere of rotation-powered pulsars by considering the limit of trans-field height through a pair production process. In this case, the trans-field height is limited by the photon-photon pair production process and the outer boundary of the outer gap can be extended outside the light cylinder. By solving self-consistently the Poisson equation for electrical potential and the Boltzmann equations of electrons/positrons and γ-rays in a vacuum outer gap for the parameters of Vela pulsar, we obtain an approximate geometry of the outer gap, i.e. the trans-field height is limited by the pair-production process and increases with the radial distance to the star and the width of the outer gap starts at the inner boundary (near the null charge surface) and ends at the outer boundary which locates inside or outside the light cylinder depending on the inclination angle. (geophysics, astronomy, and astrophysics)

Strong pairing approximation in comparison with the exact solutions to the pairing Hamiltonian

Directory of Open Access Journals (Sweden)

Lunyov A.V.

2016-01-01

Full Text Available Results of the Strong Pairing Approximation (SPA as a method with the exact particle number conservation are compared with those of the quasiparticle method (QM. It is shown that SPA comes to the same equations as QM for the gap parameter, chemical potential and one- and two-quasiparticle states. Calculations are performed for 14864Gd84 as an example, and compared with the exact solutions to the pairing Hamiltonian.

Influence of quadrupole pairing on backbending

International Nuclear Information System (INIS)

Faessler, A.; Wakai, M.

1978-01-01

The backbending phenomenon is attributed to the Coriolis antipairing and the rotational alignment effects. We can consider both effects simultaneously by applying the cranked Hartree-Fock-Bogoliubov theory to the description of the rotational motion of nuclei. In usual treatments of the backbending, however, only the monopole pairing force is considered and pairing forces of other types are neglected. This may be the main reason for starting of the backbending at too small total angular momentum in theoretical results. (orig.) [de

Creating a medical dictionary using word alignment: The influence of sources and resources

Directory of Open Access Journals (Sweden)

Åhlfeldt Hans

2007-11-01

Full Text Available Abstract Background Automatic word alignment of parallel texts with the same content in different languages is among other things used to generate dictionaries for new translations. The quality of the generated word alignment depends on the quality of the input resources. In this paper we report on automatic word alignment of the English and Swedish versions of the medical terminology systems ICD-10, ICF, NCSP, KSH97-P and parts of MeSH and how the terminology systems and type of resources influence the quality. Methods We automatically word aligned the terminology systems using static resources, like dictionaries, statistical resources, like statistically derived dictionaries, and training resources, which were generated from manual word alignment. We varied which part of the terminology systems that we used to generate the resources, which parts that we word aligned and which types of resources we used in the alignment process to explore the influence the different terminology systems and resources have on the recall and precision. After the analysis, we used the best configuration of the automatic word alignment for generation of candidate term pairs. We then manually verified the candidate term pairs and included the correct pairs in an English-Swedish dictionary. Results The results indicate that more resources and resource types give better results but the size of the parts used to generate the resources only partly affects the quality. The most generally useful resources were generated from ICD-10 and resources generated from MeSH were not as general as other resources. Systematic inter-language differences in the structure of the terminology system rubrics make the rubrics harder to align. Manually created training resources give nearly as good results as a union of static resources, statistical resources and training resources and noticeably better results than a union of static resources and statistical resources. The verified English

Creating a medical dictionary using word alignment: the influence of sources and resources.

Science.gov (United States)

Nyström, Mikael; Merkel, Magnus; Petersson, Håkan; Ahlfeldt, Hans

2007-11-23

Automatic word alignment of parallel texts with the same content in different languages is among other things used to generate dictionaries for new translations. The quality of the generated word alignment depends on the quality of the input resources. In this paper we report on automatic word alignment of the English and Swedish versions of the medical terminology systems ICD-10, ICF, NCSP, KSH97-P and parts of MeSH and how the terminology systems and type of resources influence the quality. We automatically word aligned the terminology systems using static resources, like dictionaries, statistical resources, like statistically derived dictionaries, and training resources, which were generated from manual word alignment. We varied which part of the terminology systems that we used to generate the resources, which parts that we word aligned and which types of resources we used in the alignment process to explore the influence the different terminology systems and resources have on the recall and precision. After the analysis, we used the best configuration of the automatic word alignment for generation of candidate term pairs. We then manually verified the candidate term pairs and included the correct pairs in an English-Swedish dictionary. The results indicate that more resources and resource types give better results but the size of the parts used to generate the resources only partly affects the quality. The most generally useful resources were generated from ICD-10 and resources generated from MeSH were not as general as other resources. Systematic inter-language differences in the structure of the terminology system rubrics make the rubrics harder to align. Manually created training resources give nearly as good results as a union of static resources, statistical resources and training resources and noticeably better results than a union of static resources and statistical resources. The verified English-Swedish dictionary contains 24,000 term pairs in base

Orientation- and position-controlled alignment of asymmetric silicon microrod on a substrate with asymmetric electrodes

Science.gov (United States)

Shibata, Akihide; Watanabe, Keiji; Sato, Takuya; Kotaki, Hiroshi; Schuele, Paul J.; Crowder, Mark A.; Zhan, Changqing; Hartzell, John W.; Nakatani, Ryoichi

2014-03-01

In this paper, we demonstrate the orientation-controlled alignment of asymmetric Si microrods on a glass substrate with an asymmetric pair of electrodes. The Si microrods have the shape of a paddle with a blade and a shaft part, and the pair of electrodes consists of a narrow electrode and a wide electrode. By applying AC bias to the electrodes, the Si microrods suspended in a fluid align in such a way to settle across the electrode pair, and over 80% of the aligned Si microrods have an orientation with the blade and the shaft of the paddle on the wide and the narrow electrodes, respectively. When Si microrods have a shell of dielectric film and its thickness on the top face is thicker than that on the bottom face, 97.8% of the Si microrods are aligned with the top face facing upwards. This technique is useful for orientation-controlled alignment of nano- and microsized devices that have polarity or a distinction between the top and bottom faces.

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

Directory of Open Access Journals (Sweden)

Toh Hiroyuki

2008-04-01

Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy

Directory of Open Access Journals (Sweden)

Searle Stephen MJ

2003-10-01

Full Text Available Abstract Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. Results The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with http://www.compbio.dundee.ac.uk. Conclusions The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94

Bridging the Gap: Development of the Entrepreneurial Philanthropy Alignment Model

NARCIS (Netherlands)

Rath, Jos; Schuyt, T.N.M.

2017-01-01

Partnerships are increasingly considered to have the potential to address societal problems that one single actor cannot solve. This paper rationalises the development of partnerships between entrepreneurs and non-profit organisations by the effects of its alignment. In organisations, the process of

Structure based alignment and clustering of proteins (STRALCP)

Science.gov (United States)

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Incorporating evolution of transcription factor binding sites into ...

Indian Academy of Sciences (India)

PRAKASH KUMAR

Identifying transcription factor binding sites (TFBSs) is essential to elucidate ... alignments with parts annotated as gap lessly aligned TFBSs (pair-profile hits) are generated. Moreover, the pair- profile related parameters are derived in a sound statistical framework. ... Much research has gone into the study of the evolution of.

BCS @ 50: derivation of gap equations in different lattice geometries

International Nuclear Information System (INIS)

Saurabh Basu

2007-07-01

We rigorously derive BCS gap equations for a square, triangular and a honeycomb lattice using a two-dimensional t-J model. The gap equations in all the three lattice geometries look usual, with band indices appearing and a minor modification in the separable pair potential for the (two band) honeycomb lattice. In each case, the gap equation is solved (self consistently with the number equation) at low densities assuming singlet pairing. (author)

Automated Registration of Multimodal Optic Disc Images: Clinical Assessment of Alignment Accuracy.

Science.gov (United States)

Ng, Wai Siene; Legg, Phil; Avadhanam, Venkat; Aye, Kyaw; Evans, Steffan H P; North, Rachel V; Marshall, Andrew D; Rosin, Paul; Morgan, James E

2016-04-01

To determine the accuracy of automated alignment algorithms for the registration of optic disc images obtained by 2 different modalities: fundus photography and scanning laser tomography. Images obtained with the Heidelberg Retina Tomograph II and paired photographic optic disc images of 135 eyes were analyzed. Three state-of-the-art automated registration techniques Regional Mutual Information, rigid Feature Neighbourhood Mutual Information (FNMI), and nonrigid FNMI (NRFNMI) were used to align these image pairs. Alignment of each composite picture was assessed on a 5-point grading scale: "Fail" (no alignment of vessels with no vessel contact), "Weak" (vessels have slight contact), "Good" (vessels with 50% contact), and "Excellent" (complete alignment). Custom software generated an image mosaic in which the modalities were interleaved as a series of alternate 5×5-pixel blocks. These were graded independently by 3 clinically experienced observers. A total of 810 image pairs were assessed. All 3 registration techniques achieved a score of "Good" or better in >95% of the image sets. NRFNMI had the highest percentage of "Excellent" (mean: 99.6%; range, 95.2% to 99.6%), followed by Regional Mutual Information (mean: 81.6%; range, 86.3% to 78.5%) and FNMI (mean: 73.1%; range, 85.2% to 54.4%). Automated registration of optic disc images by different modalities is a feasible option for clinical application. All 3 methods provided useful levels of alignment, but the NRFNMI technique consistently outperformed the others and is recommended as a practical approach to the automated registration of multimodal disc images.

Determination of the pairing-strength constants in the isovector plus isoscalar pairing case

Science.gov (United States)

Mokhtari, D.; Fellah, M.; Allal, N. H.

2016-05-01

A method for the determination of the pairing-strength constants, in the neutron-proton (n-p) isovector plus isoscalar pairing case, is proposed in the framework of the BCS theory. It is based on the fitting of these constants to reproduce the experimentally known pairing gap parameters as well as the root-mean-squared (r.m.s) charge radii values. The method is applied to some proton-rich even-even nuclei. The single-particle energies used are those of a deformed Woods-Saxon mean field. It is shown that the obtained value of the ratio GnpT=0/G npT=1 is of the same order as the ones, arbitrary chosen, of some previous works. The effect of the inclusion of the isoscalar n-p pairing in the r.m.s matter radii is then numerically studied for the same nuclei.

Pairing properties of realistic effective interactions

Directory of Open Access Journals (Sweden)

Gargano A.

2016-01-01

Full Text Available We investigate the pairing properties of an effective shell-model interaction defined within a model space outside 132Sn and derived by means of perturbation theory from the CD-Bonn free nucleon-nucleon potential. It turns out that the neutron pairing component of the effective interaction is significantly weaker than the proton one, which accounts for the large pairing gap difference observed in the two-valence identical particle nuclei 134Sn and 134Te. The role of the contribution arising from one particle-one hole excitations in determining the pairing force is discussed and its microscopic structure is also analyzed in terms of the multipole decomposition.

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

Science.gov (United States)

Yang, Rendong; Nelson, Andrew C; Henzler, Christine; Thyagarajan, Bharat; Silverstein, Kevin A T

2015-12-07

Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel.

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

Science.gov (United States)

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were

Comparison of muon-pair production to the quark-antiquark annihilation model

International Nuclear Information System (INIS)

Hogan, G.E.; Anderson, K.J.; Coleman, R.N.; Karhi, K.P.; McDonald, K.T.; Newman, C.B.; Pilcher, J.E.; Rosenberg, E.I.; Sanders, G.H.; Smith, A.J.S.; Thaler, J.J.

1979-01-01

New data on muon-pair production at 225 GeV/c by π - , π + , and proton beams are analyzed with regard to the production mechanism. The observed spin alignment of the pair and the dependence of the cross section on beam-particle type are strong indications that the production is through electromagnetic quark-antiquark annihilation

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

Science.gov (United States)

Lu, Yang Young; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

2017-03-15

The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L 1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT. The software is available at https://github.com/younglululu/COCACOLA . fsun@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

Science.gov (United States)

Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

2010-01-01

SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

Coherent Bremsstrahlung, Coherent Pair Production, Birefringence and Polarimetry in the 20-170 GeV energy range using aligned crystals

CERN Document Server

Apyan, A; Badelek, B; Ballestrero, S; Biino, C; Birol, I; Cenci, P; Connell, S H; Eichblatt, S; Fonseca, T; Freund, A; Gorini, B; Groess, R; Ispirian, K; Ketel, T; Kononets, Y V; López, A; Mangiarotti, A; Sellschop, J P Friedel; Shieh, M; Sona, P; Strakhovenko, V M; Uggerhøj, U; Uggerhøj, Erik; Van Rens, B; Velasco, M; Vilakazi, Z Z; Wessely, O; Ünel, G; Kononets, Yu V

2008-01-01

The processes of coherent bremsstrahlung (CB) and coherent pair production (CPP) based on aligned crystal targets have been studied in the energy range 20-170 GeV. The experimental arrangement allowed these phenomena as well as their polarization dependence to be evaluated under conditions where single-photon cross-sections could be measured. This proved very important as the theoretical description of CB and CPP is an area of active theoretical debate and development. The theoretical approach used in this paper predicts both the cross sections and polarization observables very well for the experimental conditions investigated, indicating that the understanding of CB and CPP is reliable up to energies of 170 GeV. A birefringence effect in CPP was studied and it was demonstrated this enabled new technologies for high energy photon beam optics, such as polarimeters (for both linear and circular polarization) and phase plates. We also present new results regarding the features of coherent high energy photon emis...

Competition between the pairing and aligned coupling schemes

International Nuclear Information System (INIS)

Rowe, D.J.

2003-01-01

We have only give a solution to the pairing plus quadrupole problem in an unrealistic situation. And we have certainly not given a solution to the general problem of a Hamiltonian with components of incompatible symmetry. However, we have valuable insights into the nature of the problem. In particular, we have identified the concept of a quasidynamical symmetry, both of the rigid rotor and SU(3) types, as a characteristic of a soft rotor whose quadrupole shape fluctuations are caused either by centrifugal forces or residual pairing interactions. In this brief review, I have outlined the appearance of highly coherent mixing of rigid rotor and SU(3) irreps in two models. In fact, the idea of a quasi-dynamical symmetry was conceived on purely physical grounds, and phrased mathematically in terms of an embedded representation, before the model examples to illustrate its occurrence were constructed. The underlying idea is that rotational states are seen in nuclei only when the rotational motions are adiabatic relative to other internal degrees of freedom. In such a situation, a rotating intrinsic frame of reference is close to being an inertial frame in as much as the Coriolis and centrifugal forces are negligible. Moreover, in the adiabatic limit, any residual interactions which are rotationally invariant and not functions of the angular momentum, can have strong effects on the intrinsic structure of a rotational nucleus. Moreover, whatever structure emerges should be the same for all states of a rotational band for which the angular momentum and, hence, the inertial forces are sufficiently small. These ideas lead naturally to the concept of quasi-dynamical symmetry. (author)

Aligning Biomolecular Networks Using Modular Graph Kernels

Science.gov (United States)

Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

Superconducting gap anomaly in heavy fermion systems

International Nuclear Information System (INIS)

Rout, G.C.; Ojha, M.S.; Behera, S.N.

2008-01-01

The heavy fermion system (HFS) is described by the periodic Anderson model (PAM), treating the Coulomb correlation between the f-electrons in the mean-field Hartree-Fock approximation. Superconductivity is introduced by a BCS-type pairing term among the conduction electrons. Within this approximation the equation for the superconducting gap is derived, which depends on the effective position of the energy level of the f-electrons relative to the Fermi level. The latter in turn depends on the occupation probability n f of the f-electrons. The gap equation is solved self-consistently with the equation for n f ; and their temperature dependences are studied for different positions of the bare f-electron energy level, with respect to the Fermi level. The dependence of the superconducting gap on the hybridization leads to a re-entrant behaviour with increasing strength. The induced pairing between the f-electrons and the pairing of mixed conduction and f-electrons due to hybridization are also determined. The temperature dependence of the hybridization parameter, which characterizes the number of electrons with mixed character and represents the number of heavy electrons is studied. This number is shown to be small. The quasi-particle density of states (DOS) shows the existence of a pseudo-gap due to superconductivity and the signature of a hybridization gap at the Fermi level. For the choice of the model parameters, the DOS shows that the HFS is a metal and undergoes a transition to the gap-less superconducting state. (author)

A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing

Directory of Open Access Journals (Sweden)

Pan-Gyu Kim

2008-01-01

Full Text Available We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.

Beam based alignment of the SLC final focus sextupoles

International Nuclear Information System (INIS)

Emma, P.; Irwin, J.; Phinney, N.; Raimondi, P.; Toge, N.; Walker, N.J.; Ziemann, V.

1993-05-01

The strong demagnification inherent in final focus systems requires local cancellation of the resulting chromaticty. Strong sextupole pair separated by a -I transform are positioned π/2 in the betatron phase away from the Interaction Point (IP) in order to cancel chromatic aberrations primarily due to the final quadrupoles. Sextupole alignment is critical in order to provide orthogonal tuning of the chromaticty and, in the case of the SLC, to limit the third and higher order optical aberrations generated from misaligned and 'nested' horizontal and vertical sextupole pairs. Reported here is a novel technique for aligning the beam centroid to the sextupole centers, which uses measurements of the criticality dependent parameter - the beam size at the IP. Results for the SLC final focus sextupoles are presented, where a resolution of <50 μm is achieved

Accelerated convergence and robust asymptotic regression of the Gumbel scale parameter for gapped sequence alignment

International Nuclear Information System (INIS)

Park, Yonil; Sheetlin, Sergey; Spouge, John L

2005-01-01

Searches through biological databases provide the primary motivation for studying sequence alignment statistics. Other motivations include physical models of annealing processes or mathematical similarities to, e.g., first-passage percolation and interacting particle systems. Here, we investigate sequence alignment statistics, partly to explore two general mathematical methods. First, we model the global alignment of random sequences heuristically with Markov additive processes. In sequence alignment, the heuristic suggests a numerical acceleration scheme for simulating an important asymptotic parameter (the Gumbel scale parameter λ). The heuristic might apply to similar mathematical theories. Second, we extract the asymptotic parameter λ from simulation data with the statistical technique of robust regression. Robust regression is admirably suited to 'asymptotic regression' and deserves to be better known for it

Image correlation method for DNA sequence alignment.

Science.gov (United States)

Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

2012-01-01

The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

Sequence and expression analysis of gaps in human chromosome 20

DEFF Research Database (Denmark)

Minocherhomji, Sheroy; Seemann, Stefan; Mang, Yuan

2012-01-01

/or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing......The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and...... and chromatin, methylation and expression analyses. We found histone 3 trimethylated at Lysine 27 to be distributed across all three gaps in immortalized B-lymphocytes. In one gap, five novel CpG islands were predominantly hypermethylated in genomic DNA from peripheral blood lymphocytes and human cerebellum...

Pair-breaking effects by parallel magnetic field in electric-field-induced surface superconductivity

International Nuclear Information System (INIS)

Nabeta, Masahiro; Tanaka, Kenta K.; Onari, Seiichiro; Ichioka, Masanori

2016-01-01

Highlights: • Zeeman effect shifts superconducting gaps of sub-band system, towards pair-breaking. • Higher-level sub-bands become normal-state-like electronic states by magnetic fields. • Magnetic field dependence of zero-energy DOS reflects multi-gap superconductivity. - Abstract: We study paramagnetic pair-breaking in electric-field-induced surface superconductivity, when magnetic field is applied parallel to the surface. The calculation is performed by Bogoliubov-de Gennes theory with s-wave pairing, including the screening effect of electric fields by the induced carriers near the surface. Due to the Zeeman shift by applied fields, electronic states at higher-level sub-bands become normal-state-like. Therefore, the magnetic field dependence of Fermi-energy density of states reflects the multi-gap structure in the surface superconductivity.

Attitude sensor alignment calibration for the solar maximum mission

Science.gov (United States)

Pitone, Daniel S.; Shuster, Malcolm D.

1990-01-01

An earlier heuristic study of the fine attitude sensors for the Solar Maximum Mission (SMM) revealed a temperature dependence of the alignment about the yaw axis of the pair of fixed-head star trackers relative to the fine pointing Sun sensor. Here, new sensor alignment algorithms which better quantify the dependence of the alignments on the temperature are developed and applied to the SMM data. Comparison with the results from the previous study reveals the limitations of the heuristic approach. In addition, some of the basic assumptions made in the prelaunch analysis of the alignments of the SMM are examined. The results of this work have important consequences for future missions with stringent attitude requirements and where misalignment variations due to variations in the temperature will be significant.

Stochastic sampling of the RNA structural alignment space.

Science.gov (United States)

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

2009-07-01

A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

Nuclear Storage Overpack Door Actuator and Alignment Apparatus

International Nuclear Information System (INIS)

Andreyko, Gregory M.

2005-01-01

The invention is a door actuator and alignment apparatus for opening and closing the 15,000-pound horizontally sliding door of a storage overpack. The door actuator includes a ball screw mounted horizontally on a rigid frame including a pair of door panel support rails. An electrically powered ball nut moves along the ball screw. The ball nut rotating device is attached to a carriage. The carriage attachment to the sliding door is horizontally pivoting. Additional alignment features include precision cam followers attached to the rails and rail guides attached to the carriage

A Unifying Perspective on Oxygen Vacancies in Wide Band Gap Oxides.

Science.gov (United States)

Linderälv, Christopher; Lindman, Anders; Erhart, Paul

2018-01-04

Wide band gap oxides are versatile materials with numerous applications in research and technology. Many properties of these materials are intimately related to defects, with the most important defect being the oxygen vacancy. Here, using electronic structure calculations, we show that the charge transition level (CTL) and eigenstates associated with oxygen vacancies, which to a large extent determine their electronic properties, are confined to a rather narrow energy range, even while band gap and the electronic structure of the conduction band vary substantially. Vacancies are classified according to their character (deep versus shallow), which shows that the alignment of electronic eigenenergies and CTL can be understood in terms of the transition between cavity-like localized levels in the large band gap limit and strong coupling between conduction band and vacancy states for small to medium band gaps. We consider both conventional and hybrid functionals and demonstrate that the former yields results in very good agreement with the latter provided that band edge alignment is taken into account.

Atomic-scale Visualization of Electronic Nematicity and Cooper Pairing in Iron-based Superconductors

Science.gov (United States)

Allan, Milan P.

2013-03-01

The mechanism of high-temperature superconductivity in the relatively novel iron-based high-Tc superconductors is unresolved, both in terms of how the phases evolve with doping, and in terms of the actual Cooper pairing process. To explore these issues, we used spectroscopic-imaging scanning tunneling microscopy to study the electronic structure of CaFe2As2 in the antiferromagnetic-orthorhombic `parent' state from which the superconductivity emerges. We discovered and visualized the now widely studied electronic `nematicity' of this phase, whose suppression is associated with the emergence of superconductivity (Science 327, 181, 2010). As subsequent transport experiments discovered a related anisotropic conductance which increases with dopant concentration, the interplay between the electronic structure surrounding each dopant atom, quasiparticle scattering therefrom, and the transport nematicity has become a pivotal focus of research. We find that substituting Co for Fe atoms in underdoped Ca(Fe1-xCox)2As2 generates a dense population of identical and strongly anisotropic impurity states that are distributed randomly but aligned with the antiferromagnetic a-axis. We also demonstrate, by imaging their surrounding interference patterns, that these impurity states scatter quasiparticles and thus influence transport in a highly anisotropic manner (M.P. Allan et al., 2013). Next, we studied the momentum dependence of the energy gaps of iron-based superconductivity, now focusing on LiFeAs. If strong electron-electron interactions mediate the Cooper pairing, then momentum-space anisotropic superconducting energy gaps Δi (k) were predicted by multiple techniques to appear on the different electronic bands i. We introduced intraband Bogoliubov quasiparticle scattering interference (QPI) techniques for the determination of anisotropic energy gaps to test these hypotheses and discovered the anisotropy, magnitude, and relative orientations of the energy gaps on multiple

MSuPDA: A Memory Efficient Algorithm for Sequence Alignment.

Science.gov (United States)

Khan, Mohammad Ibrahim; Kamal, Md Sarwar; Chowdhury, Linkon

2016-03-01

Space complexity is a million dollar question in DNA sequence alignments. In this regard, memory saving under pushdown automata can help to reduce the occupied spaces in computer memory. Our proposed process is that anchor seed (AS) will be selected from given data set of nucleotide base pairs for local sequence alignment. Quick splitting techniques will separate the AS from all the DNA genome segments. Selected AS will be placed to pushdown automata's (PDA) input unit. Whole DNA genome segments will be placed into PDA's stack. AS from input unit will be matched with the DNA genome segments from stack of PDA. Match, mismatch and indel of nucleotides will be popped from the stack under the control unit of pushdown automata. During the POP operation on stack, it will free the memory cell occupied by the nucleotide base pair.

Fermi level alignment in molecular nanojunctions and its relation to charge transfer

DEFF Research Database (Denmark)

Stadler, Robert; Jacobsen, Karsten Wedel

2006-01-01

The alignment of the Fermi level of a metal electrode within the gap of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of a molecule is a key quantity in molecular electronics, which can vary the electron transparency of a single-molecule junction...... by orders of magnitude. We present a quantitative analysis of the relation between this level alignment (which can be estimated from charging free molecules) and charge transfer for bipyridine and biphenyl dithiolate (BPDT) molecules attached to gold leads based on density functional theory calculations...... end of the gap in the transmission function for bipyridine and at its lower end for BPDT....

COMPARISON OF 2D AND 3D APPROACHES FOR THE ALIGNMENT OF UAV AND LIDAR POINT CLOUDS

Directory of Open Access Journals (Sweden)

R. A. Persad

2017-08-01

Full Text Available The automatic alignment of 3D point clouds acquired or generated from different sensors is a challenging problem. The objective of the alignment is to estimate the 3D similarity transformation parameters, including a global scale factor, 3 rotations and 3 translations. To do so, corresponding anchor features are required in both data sets. There are two main types of alignment: i Coarse alignment and ii Refined Alignment. Coarse alignment issues include lack of any prior knowledge of the respective coordinate systems for a source and target point cloud pair and the difficulty to extract and match corresponding control features (e.g., points, lines or planes co-located on both point cloud pairs to be aligned. With the increasing use of UAVs, there is a need to automatically co-register their generated point cloud-based digital surface models with those from other data acquisition systems such as terrestrial or airborne lidar point clouds. This works presents a comparative study of two independent feature matching techniques for addressing 3D conformal point cloud alignment of UAV and lidar data in different 3D coordinate systems without any prior knowledge of the seven transformation parameters.

Comparability of results from pair and classical model formulations for different sexually transmitted infections.

Directory of Open Access Journals (Sweden)

Jimmy Boon Som Ong

Full Text Available The "classical model" for sexually transmitted infections treats partnerships as instantaneous events summarized by partner change rates, while individual-based and pair models explicitly account for time within partnerships and gaps between partnerships. We compared predictions from the classical and pair models over a range of partnership and gap combinations. While the former predicted similar or marginally higher prevalence at the shortest partnership lengths, the latter predicted self-sustaining transmission for gonorrhoea (GC and Chlamydia (CT over much broader partnership and gap combinations. Predictions on the critical level of condom use (C(c required to prevent transmission also differed substantially when using the same parameters. When calibrated to give the same disease prevalence as the pair model by adjusting the infectious duration for GC and CT, and by adjusting transmission probabilities for HIV, the classical model then predicted much higher C(c values for GC and CT, while C(c predictions for HIV were fairly close. In conclusion, the two approaches give different predictions over potentially important combinations of partnership and gap lengths. Assuming that it is more correct to explicitly model partnerships and gaps, then pair or individual-based models may be needed for GC and CT since model calibration does not resolve the differences.

Coexistence of pairing gaps in three-component Fermi gases

International Nuclear Information System (INIS)

Nummi, O H T; Kinnunen, J J; Toermae, P

2011-01-01

We study a three-component superfluid Fermi gas in a spherically symmetric harmonic trap using the Bogoliubov-deGennes method. We predict a coexistence phase in which two pairing field order parameters are simultaneously non-zero, in stark contrast to studies performed for trapped gases using local density approximation. We also discuss the role of atom number conservation in the context of a homogeneous system.

TMRG studies on spin alignment in molecule-based ferrimagnetics [rapid communication

Science.gov (United States)

Liu, Q. M.; Yao, K. L.; Liu, Z. L.

2005-05-01

A physical picture of spin alignment in organic molecule-based ferrimagnets is presented from studying the thermal effective magnetic moment of the sublattice by use of the transfer matrix renormalization group. We conclude that the classical antiparallel spin alignment is not the most stable state. The three-spin system tends to parallel alignment when the exchange interaction between the biradical and the monoradical molecules is much weaker than that within the biradical, which can result in the decrease of the effective magnetic moment upon lowering the temperature. More importantly, we give the theoretical evidence that even the antiparallel spin alignment in the biradical monoradical alternating chain does not necessarily lead to ferrimagnetic spin ordering due to the formation of the spin singlet pairs, which suppresses the ferrimagnetic spin alignment.

Comment on "Astronomical alignments as the cause of ~M6+ seismicity"

OpenAIRE

Zanette, Damian H.

2011-01-01

It is shown that, according to the criteria used by M. Omerbashich (arXiv:1104.2036v4 [physics.gen-ph]), during 2010 the Earth was aligned with at least one pair of planets some 98.6% of the time. This firmly supports Omerbashich's claim that 2010 strongest earthquakes occurred during such astronomical alignments. On this basis, we argue that seismicity is, generally, a phenomenon of astrological origin.

Field Emission of ITO-Coated Vertically Aligned Nanowire Array.

KAUST Repository

Lee, Changhwa

2010-04-29

An indium tin oxide (ITO)-coated vertically aligned nanowire array is fabricated, and the field emission characteristics of the nanowire array are investigated. An array of vertically aligned nanowires is considered an ideal structure for a field emitter because of its parallel orientation to the applied electric field. In this letter, a vertically aligned nanowire array is fabricated by modified conventional UV lithography and coated with 0.1-μm-thick ITO. The turn-on electric field intensity is about 2.0 V/μm, and the field enhancement factor, β, is approximately 3,078 when the gap for field emission is 0.6 μm, as measured with a nanomanipulator in a scanning electron microscope.

Field Emission of ITO-Coated Vertically Aligned Nanowire Array.

KAUST Repository

Lee, Changhwa; Lee, Seokwoo; Lee, Seung S

2010-01-01

An indium tin oxide (ITO)-coated vertically aligned nanowire array is fabricated, and the field emission characteristics of the nanowire array are investigated. An array of vertically aligned nanowires is considered an ideal structure for a field emitter because of its parallel orientation to the applied electric field. In this letter, a vertically aligned nanowire array is fabricated by modified conventional UV lithography and coated with 0.1-μm-thick ITO. The turn-on electric field intensity is about 2.0 V/μm, and the field enhancement factor, β, is approximately 3,078 when the gap for field emission is 0.6 μm, as measured with a nanomanipulator in a scanning electron microscope.

Precise Alignment and Permanent Mounting of Thin and Lightweight X-ray Segments

Science.gov (United States)

Biskach, Michael P.; Chan, Kai-Wing; Hong, Melinda N.; Mazzarella, James R.; McClelland, Ryan S.; Norman, Michael J.; Saha, Timo T.; Zhang, William W.

2012-01-01

To provide observations to support current research efforts in high energy astrophysics. future X-ray telescope designs must provide matching or better angular resolution while significantly increasing the total collecting area. In such a design the permanent mounting of thin and lightweight segments is critical to the overall performance of the complete X-ray optic assembly. The thin and lightweight segments used in the assemhly of the modules are desigued to maintain and/or exceed the resolution of existing X-ray telescopes while providing a substantial increase in collecting area. Such thin and delicate X-ray segments are easily distorted and yet must be aligned to the arcsecond level and retain accurate alignment for many years. The Next Generation X-ray Optic (NGXO) group at NASA Goddard Space Flight Center has designed, assembled. and implemented new hardware and procedures mth the short term goal of aligning three pairs of X-ray segments in a technology demonstration module while maintaining 10 arcsec alignment through environmental testing as part of the eventual design and construction of a full sized module capable of housing hundreds of X-ray segments. The recent attempts at multiple segment pair alignment and permanent mounting is described along with an overview of the procedure used. A look into what the next year mll bring for the alignment and permanent segment mounting effort illustrates some of the challenges left to overcome before an attempt to populate a full sized module can begin.

Enhanced Andreev reflection in gapped graphene

Science.gov (United States)

Majidi, Leyla; Zareyan, Malek

2012-08-01

We theoretically demonstrate unusual features of superconducting proximity effect in gapped graphene that presents a pseudospin symmetry-broken ferromagnet with a net pseudomagnetization. We find that the presence of a band gap makes the Andreev conductance of graphene superconductor/pseudoferromagnet (S/PF) junction to behave similar to that of a graphene ferromagnet-superconductor junction. The energy gap ΔN can enhance the pseudospin inverted Andreev conductance of S/PF junction to reach a limiting maximum value for ΔN≫μ, which depending on the bias voltage can be larger than the value for the corresponding junction with no energy gap. We further demonstrate a damped-oscillatory behavior for the local density of states of the PF region of S/PF junction and a long-range crossed Andreev reflection process in PF/S/PF structure with antiparallel alignment of pseudomagnetizations of PFs, which confirm that, in this respect, the gapped normal graphene behaves like a ferromagnetic graphene.

Development of a group work assessment pedagogy using constructive alignment theory.

Science.gov (United States)

Croy, Suzanne R

2018-02-01

The purpose of this paper is to explore group work assessment underpinned by constructive alignment theory to develop a new assessment pedagogy. A review was undertaken of an existing module 'Mental Health Nursing 1', with student nurses participating in the BSc (Hons) Nursing Programme. Constructive alignment theory requires teachers to adopt a deep approach to learning where module learning outcomes are aligned with the teaching environment and modes of assessment. As the module progressed, reviewing the Mental Health Nursing 1 module became an excellent opportunity to begin to understand how constructive alignment theory can inform a group work assessment pedagogy. Working using a constructively aligned assessment process became a valuable learning experience for the module leader whilst at the same time revealed a gap in the research around the impact of constructively aligned teaching and group work assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

SOAP2: an improved ultrafast tool for short read alignment

DEFF Research Database (Denmark)

Li, Ruiqiang; Yu, Chang; Li, Yingrui

2009-01-01

SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy...... for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports...... multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn....

ASH structure alignment package: Sensitivity and selectivity in domain classification

Directory of Open Access Journals (Sweden)

Toh Hiroyuki

2007-04-01

Full Text Available Abstract Background Structure alignment methods offer the possibility of measuring distant evolutionary relationships between proteins that are not visible by sequence-based analysis. However, the question of how structural differences and similarities ought to be quantified in this regard remains open. In this study we construct a training set of sequence-unique CATH and SCOP domains, from which we develop a scoring function that can reliably identify domains with the same CATH topology and SCOP fold classification. The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website http://www.pdbj.org/ASH/. Results The new ASH score shows increased selectivity and sensitivity compared with values reported for several popular programs using the same test set of 4,298,905 structure pairs, yielding an area of .96 under the receiver operating characteristic (ROC curve. In addition, weak sequence homologies between similar domains are revealed that could not be detected by BLAST sequence alignment. Also, a subset of domain pairs is identified that exhibit high similarity, even though their CATH and SCOP classification differs. Finally, we show that the ranking of alignment programs based solely on geometric measures depends on the choice of the quality measure. Conclusion ASH shows high selectivity and sensitivity with regard to domain classification, an important step in defining distantly related protein sequence families. Moreover, the CPU cost per alignment is competitive with the fastest programs, making ASH a practical option for large-scale structure classification studies.

Possibility of ΛΛ pairing and its dependence on background density in a relativistic Hartree-Bogoliubov model

International Nuclear Information System (INIS)

Tanigawa, Tomonori; Matsuzaki, Masayuki; Chiba, Satoshi

2003-01-01

We calculate a ΛΛ pairing gap in binary mixed matter of nucleons and Λ hyperons within the relativistic Hartree-Bogoliubov model. Λ hyperons to be paired up are immersed in background nucleons in a normal state. The gap is calculated with a one-boson-exchange interaction obtained from a relativistic Lagrangian. It is found that at background density ρ N =2.5ρ 0 the ΛΛ pairing gap is very small, and that a denser background makes it rapidly suppressed. This result suggests a mechanism, specific to mixed matter dealt with relativistic models, of its dependence on the nucleon density. An effect of weaker ΛΛ attraction on the gap is also examined in connection with the revised information of the ΛΛ interaction

Exotic Paired States with Anisotropic Spin-Dependent Fermi Surfaces

International Nuclear Information System (INIS)

Feiguin, Adrian E.; Fisher, Matthew P. A.

2009-01-01

We propose a model for realizing exotic paired states in cold Fermi gases by using a spin-dependent optical lattice to engineer mismatched Fermi surfaces for each hyperfine species. The BCS phase diagram shows a stable paired superfluid state with coexisting pockets of momentum space with gapless unpaired carriers, similar to the Sarma state in polarized mixtures, but in our case the system is unpolarized. We propose the possible existence of an exotic 'Cooper-pair Bose-metal' phase, which has a gap for single fermion excitations but gapless and uncondensed 'Cooper-pair' excitations residing on a 'Bose surface' in momentum space.

The power of change: interpersonal attraction as a function of attitude similarity and attitude alignment.

Science.gov (United States)

Reid, Chelsea A; Davis, Jody L; Green, Jeffrey D

2013-01-01

Does attitude alignment predict attraction? Would you like a stranger more who shifts her/his attitudes to more closely align with yours? In pairs, participants (N = 77) discussed social issues about which they disagreed and received false feedback on whether the partner engaged in attitude alignment (shifted her/his attitudes toward the participant's attitude) following discussion. Participants also received false feedback about the proportion of similarity to the partner on a set of issues (i.e., 25%, 50%, or 75%). Participants reported greater attraction to partners who engaged in attitude alignment and who were more similar. Moreover, similarity and attitude alignment interacted. Similarity predicted attraction when attitude alignment did not occur, but did not predict attraction when attitude alignment did occur. Finally, partner attitude alignment led to participant attitude alignment, and perceived reasoning ability mediated the attitude alignment-attraction relationship.

Treatment management between orthodontists and general practitioners performing clear aligner therapy.

Science.gov (United States)

Best, Alexandra D; Shroff, Bhavna; Carrico, Caroline K; Lindauer, Steven J

2017-05-01

To investigate differences in case selection, treatment management, and aligner treatment expertise between orthodontists and general practitioners. A parallel pair of original surveys with three sections (case selection, treatment management, and demographics) was sent to orthodontists (N = 1000) and general dentists (N = 1000) who were providers of aligner treatment. Orthodontists had treated significantly more patients with aligners, had treated more patients with aligners in the previous 12 months, and had received more aligner training than general dentists (P aligner case confidence between orthodontists and general dentists for several malocclusions. General dentists were more confident than orthodontists in treating deep bite, severe crowding, and Class II malocclusions with aligners (P ≤ .0001). Significant differences were also found for all treatment management techniques except interproximal reduction. There was a significant difference in case selection, treatment management, and aligner expertise between orthodontists and general dentists, although the differences in case selection were small. Overall, it was shown that orthodontists and general dentists elected to treat a variety of moderate to severe malocclusions with aligners but with different utilization of recommended auxiliaries, perhaps demonstrating a difference in treatment goals.

Self-alignment of RFID dies on four-pad patterns with water droplet for sparse self-assembly

International Nuclear Information System (INIS)

Chang, Bo; Routa, Iiris; Sariola, Veikko; Zhou, Quan

2011-01-01

This paper reports an in-depth study of a water-droplet-assisted self-alignment technique that self-aligns radio frequency identification (RFID) dies on four-pad patterns. The segmented structure of four hydrophilic pads on a hydrophobic substrate brings freedom to the design of the electrical functionality and the surface functionality. The paper investigates the influence of the key parameters that may affect the self-alignment in theory and experiment. The theoretical model justifies that RFID dies can be reliably aligned on the segmented four-pad pattern even when the initial placement error is as large as 50% of the size of the die and the gap between the four pads is about 10% of the size of the die. A method has been introduced to estimate the sufficient droplet volume for self-alignment. A series of experiments have been carried out to verify the results of the model. The experiments indicate that the self-alignment between the 730 × 730 µm RFID dies and the pattern occurs reliably when the releasing bias between the RFID die and antenna is less than 400 µm for patterns with 50 and 100 µm gaps, and successful self-alignment is possible even with greater bias of 500 µm

Universal spectral signatures in pnictides and cuprates: the role of quasiparticle-pair coupling.

Science.gov (United States)

Sacks, William; Mauger, Alain; Noat, Yves

2017-11-08

Understanding the physical properties of a large variety of high-T c superconductors (SC), the cuprate family as well as the more recent iron-based superconductors, is still a major challenge. In particular, these materials exhibit the 'peak-dip-hump' structure in the quasiparticle density of states (DOS). The origin of this structure is explained within our pair-pair interaction (PPI) model: The non-superconducting state consists of incoherent pairs, a 'Cooper-pair glass' which, due to the PPI, undergoes a Bose-like condensation below T c to the coherent SC state. We derive the equations of motion for the quasiparticle operators showing that the DOS 'peak-dip-hump' is caused by the coupling between quasiparticles and excited pair states, or 'super-quasiparticles'. The renormalized SC gap function becomes energy-dependent and non retarded, reproducing accurately the experimental spectra of both pnictides and cuprates, despite the large difference in gap value.

Pair Fermi contour and high-temperature superconductivity

CERN Document Server

Belyavsky, V I

2002-01-01

The holes superconducting coupling with the pair high summarized pulse and the relative motion low pulses is considered with an account of the quasi-two-dimensional electron structure of the HTSC-cuprates with the clearly-pronounced nesting of the Fermi contour. The superconducting energy gap and the condensation energy are determined and their dependences on the doping level are qualitatively studied. It is shown that the energy gap takes place in some holes concentration area, limited on both sides. The superconducting state, whereby the condensation energy is positive, originates in the more narrower doping interval inside this area. The hole pair redistribution in the pulse space constitutes the cause of the superconducting state origination by the holes repulsive screened Coulomb interaction. The coupling mechanism discussed hereby, males it possible to explain qualitatively not only the phase diagram basic peculiarities but also the key experimental facts, related to the cuprate HTSC-materials

Nucleon-pair approximation to the nuclear shell model

Energy Technology Data Exchange (ETDEWEB)

Zhao, Y.M., E-mail: ymzhao@sjtu.edu.cn [Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240 (China); Arima, A. [Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240 (China); Musashi Gakuen, 1-26-1 Toyotamakami Nerima-ku, Tokyo 176-8533 (Japan)

2014-12-01

Atomic nuclei are complex systems of nucleons–protons and neutrons. Nucleons interact with each other via an attractive and short-range force. This feature of the interaction leads to a pattern of dominantly monopole and quadrupole correlations between like particles (i.e., proton–proton and neutron–neutron correlations) in low-lying states of atomic nuclei. As a consequence, among dozens or even hundreds of possible types of nucleon pairs, very few nucleon pairs such as proton and neutron pairs with spin zero, two (in some cases spin four), and occasionally isoscalar spin-aligned proton–neutron pairs, play important roles in low-energy nuclear structure. The nucleon-pair approximation therefore provides us with an efficient truncation scheme of the full shell model configurations which are otherwise too large to handle for medium and heavy nuclei in foreseeable future. Furthermore, the nucleon-pair approximation leads to simple pictures in physics, as the dimension of nucleon-pair subspace is always small. The present paper aims at a sound review of its history, formulation, validity, applications, as well as its link to previous approaches, with the focus on the new developments in the last two decades. The applicability of the nucleon-pair approximation and numerical calculations of low-lying states for realistic atomic nuclei are demonstrated with examples. Applications of pair approximations to other problems are also discussed.

Real-space description of semiconducting band gaps in substitutional systems

International Nuclear Information System (INIS)

Magri, R.; Zunger, A.

1991-01-01

The goal of ''band-gap engineering'' in substitutional lattices is to identify atomic configurations that would give rise to a desired value of the band gap. Yet, current theoretical approaches to the problems, based largely on compilations of band structures for various latice configurations, have not yielded simple rules relating structural motifs to band gaps. We show that the band gap of substitutional AlAs/GaAs lattices can be usefully expanded in terms of a hierarchy of contributions from real-space ''atomic figures'' (pairs, triplets, quadruplets) detemined from first-principles band-structure calculations. Pair figures (up to fourth neighbors) and three-body figures are dominant. In analogy with similar cluster expansions of the total energy, this permits a systematic search among all lattice configurations for those having ''special'' band gaps. This approach enables the design of substitutional systems with certain band-gap properties by assembling atomic figures. As an illustration, we predict that the [0 bar 12]-oriented (AlAs) 1 /(GaAs) 4 /(AlAs) 1 /(GaAs) 2 superlattice has the largest band gap among all Al 0.25 Ga 0.75 As lattices with a maximum of ten cations per unit cell

A Global Network Alignment Method Using Discrete Particle Swarm Optimization.

Science.gov (United States)

Huang, Jiaxiang; Gong, Maoguo; Ma, Lijia

2016-10-19

Molecular interactions data increase exponentially with the advance of biotechnology. This makes it possible and necessary to comparatively analyse the different data at a network level. Global network alignment is an important network comparison approach to identify conserved subnetworks and get insight into evolutionary relationship across species. Network alignment which is analogous to subgraph isomorphism is known to be an NP-hard problem. In this paper, we introduce a novel heuristic Particle-Swarm-Optimization based Network Aligner (PSONA), which optimizes a weighted global alignment model considering both protein sequence similarity and interaction conservations. The particle statuses and status updating rules are redefined in a discrete form by using permutation. A seed-and-extend strategy is employed to guide the searching for the superior alignment. The proposed initialization method "seeds" matches with high sequence similarity into the alignment, which guarantees the functional coherence of the mapping nodes. A greedy local search method is designed as the "extension" procedure to iteratively optimize the edge conservations. PSONA is compared with several state-of-art methods on ten network pairs combined by five species. The experimental results demonstrate that the proposed aligner can map the proteins with high functional coherence and can be used as a booster to effectively refine the well-studied aligners.

Differential evolution-simulated annealing for multiple sequence alignment

Science.gov (United States)

Addawe, R. C.; Addawe, J. M.; Sueño, M. R. K.; Magadia, J. C.

2017-10-01

Multiple sequence alignments (MSA) are used in the analysis of molecular evolution and sequence structure relationships. In this paper, a hybrid algorithm, Differential Evolution - Simulated Annealing (DESA) is applied in optimizing multiple sequence alignments (MSAs) based on structural information, non-gaps percentage and totally conserved columns. DESA is a robust algorithm characterized by self-organization, mutation, crossover, and SA-like selection scheme of the strategy parameters. Here, the MSA problem is treated as a multi-objective optimization problem of the hybrid evolutionary algorithm, DESA. Thus, we name the algorithm as DESA-MSA. Simulated sequences and alignments were generated to evaluate the accuracy and efficiency of DESA-MSA using different indel sizes, sequence lengths, deletion rates and insertion rates. The proposed hybrid algorithm obtained acceptable solutions particularly for the MSA problem evaluated based on the three objectives.

Kinetics-Driven Superconducting Gap in Underdoped Cuprate Superconductors Within the Strong-Coupling Limit

Directory of Open Access Journals (Sweden)

Yucel Yildirim

2011-09-01

Full Text Available A generic theory of the quasiparticle superconducting gap in underdoped cuprates is derived in the strong-coupling limit, and found to describe the experimental “second gap” in absolute scale. In drastic contrast to the standard pairing gap associated with Bogoliubov quasiparticle excitations, the quasiparticle gap is shown to originate from anomalous kinetic (scattering processes, with a size unrelated to the pairing strength. Consequently, the k dependence of the gap deviates significantly from the pure d_{x^{2}-y^{2}} wave of the order parameter. Our study reveals a new paradigm for the nature of the superconducting gap, and is expected to reconcile numerous apparent contradictions among existing experiments and point toward a more coherent understanding of high-temperature superconductivity.

Measuring the Alignment between States' Finance and Accountability Policies: The Opportunity Gap

Science.gov (United States)

Della Sala, Matthew R.; Knoeppel, Robert C.

2015-01-01

The research described in this paper expands on attempts to conceptualize, measure, and evaluate the degree to which states have aligned their finance systems with their respective accountability policies. State education finance and accountability policies serve as levers to provide equal educational opportunities for all students--scholars have…

The Effects of a Roommate-Pairing Program on International Student Satisfaction and Academic Success

OpenAIRE

Tolman, Steven

2017-01-01

While great attention has been given to the growth of international students at U.S. institutions, there is a gap in the literature examining support for this student population within residence halls. To address the gap, this quantitative study evaluated an international roommate-pairing program (IRP) by comparing the residential experience of IRP participants with a control group. The results showed the roommate-pairing program had a positive impact on the residential expe...

Broadband illumination of superconducting pair breaking photon detectors

International Nuclear Information System (INIS)

Guruswamy, T; Goldie, D J; Withington, S

2016-01-01

Understanding the detailed behaviour of superconducting pair breaking photon detectors such as Kinetic Inductance Detectors (KIDs) requires knowledge of the nonequilibrium quasiparticle energy distributions. We have previously calculated the steady state distributions resulting from uniform absorption of monochromatic sub gap and above gap frequency radiation by thin films. In this work, we use the same methods to calculate the effect of illumination by broadband sources, such as thermal radiation from astrophysical phenomena or from the readout system. Absorption of photons at multiple above gap frequencies is shown to leave unchanged the structure of the quasiparticle energy distribution close to the superconducting gap. Hence for typical absorbed powers, we find the effects of absorption of broadband pair breaking radiation can simply be considered as the sum of the effects of absorption of many monochromatic sources. Distribution averaged quantities, like quasiparticle generation efficiency η, match exactly a weighted average over the bandwidth of the source of calculations assuming a monochromatic source. For sub gap frequencies, however, distributing the absorbed power across multiple frequencies does change the low energy quasiparticle distribution. For moderate and high absorbed powers, this results in a significantly larger η–a higher number of excess quasiparticles for a broadband source compared to a monochromatic source of equal total absorbed power. Typically in KIDs the microwave power absorbed has a very narrow bandwidth, but in devices with broad resonance characteristics (low quality factors), this increase in η may be measurable. (paper)

Sequence embedding for fast construction of guide trees for multiple sequence alignment

LENUS (Irish Health Repository)

Blackshields, Gordon

2010-05-14

Abstract Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from http:\\/\\/www.clustal.org\\/mbed.tgz.

Josephson junction analog and quasiparticle-pair current

DEFF Research Database (Denmark)

Bak, Christen Kjeldahl; Pedersen, Niels Falsig

1973-01-01

A close analogy exists between a Josephson junction and a phase-locked loop. A new type of electrical analog based on this principle is presented. It is shown that the inclusion in this analog of a low-pass filter gives rise to a current of the same form as the Josephson quasiparticle-pair current....... A simple picture of the quasiparticle-pair current, which gives the right dependences, is obtained by assuming a junction cutoff frequency to be at the energy gap. ©1973 American Institute of Physics...

Magnetic Fluctuations in Pair-Density-Wave Superconductors

Science.gov (United States)

Christensen, Morten H.; Jacobsen, Henrik; Maier, Thomas A.; Andersen, Brian M.

2016-04-01

Pair-density-wave superconductivity constitutes a novel electronic condensate proposed to be realized in certain unconventional superconductors. Establishing its potential existence is important for our fundamental understanding of superconductivity in correlated materials. Here we compute the dynamical magnetic susceptibility in the presence of a pair-density-wave ordered state and study its fingerprints on the spin-wave spectrum including the neutron resonance. In contrast to the standard case of d -wave superconductivity, we show that the pair-density-wave phase exhibits neither a spin gap nor a magnetic resonance peak, in agreement with a recent neutron scattering experiment on underdoped La1.905 Ba0.095 CuO4 [Z. Xu et al., Phys. Rev. Lett. 113, 177002 (2014)].

Future Directions for Dissemination and Implementation Science: Aligning Ecological Theory and Public Health to Close the Research to Practice Gap.

Science.gov (United States)

Atkins, Marc S; Rusch, Dana; Mehta, Tara G; Lakind, Davielle

2016-01-01

Dissemination and implementation science (DI) has evolved as a major research model for children's mental health in response to a long-standing call to integrate science and practice and bridge the elusive research to practice gap. However, to address the complex and urgent needs of the most vulnerable children and families, future directions for DI require a new alignment of ecological theory and public health to provide effective, sustainable, and accessible mental health services. We present core principles of ecological theory to emphasize how contextual factors impact behavior and allow for the reciprocal impact individuals have on the settings they occupy, and an alignment of these principles with a public health model to ensure that services span the prevention to intervention continuum. We provide exemplars from our ongoing work in urban schools and a new direction for research to address the mental health needs of immigrant Latino families. Through these examples we illustrate how DI can expand its reach by embedding within natural settings to build on local capacity and indigenous resources, incorporating the local knowledge necessary to more substantively address long-standing mental health disparities. This paradigm shift for DI, away from an overemphasis on promoting program adoption, calls for fitting interventions within settings that matter most to children's healthy development and for utilizing and strengthening available community resources. In this way, we can meet the challenge of addressing our nation's mental health burden by supporting the needs and values of families and communities within their own unique social ecologies.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

OpenAIRE

Maréchal Eric; Ortet Philippe; Roy Sylvaine; Bastien Olivier

2005-01-01

Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic recon...

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng

2015-06-13

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

Alignment of the VISA Undulator

International Nuclear Information System (INIS)

Ruland, Robert E.

2000-01-01

As part of the R and D program towards a fourth generation light source, a Self-Amplified Spontaneous Emission (SASE) demonstration is being prepared. The Visible-Infrared SASE Amplifier (VISA) undulator is being installed at Brookhaven National Laboratory. The VISA undulator is an in-vacuum, 4-meter long, 1.8 cm period, pure-permanent magnet device, with a novel, strong focusing, permanent magnet FODO array included within the fixed, 6 mm undulator gap. The undulator is constructed of 99 cm long segments. To attain maximum SASE gain requires establishing overlap of electron and photon beams to within 50 pm rms. This imposes challenging tolerances on mechanical fabrication and magnetic field quality, and necessitates use of laser straightness interferometry for calibration and alignment of the magnetic axes of the undulator segments. This paper describes the magnetic centerline determination, and the fiducialization and alignment processes, which were performed to meet the tolerance goal

The formation of Cooper pairs and the nature of superconducting currents

International Nuclear Information System (INIS)

Weisskopf, V.F.

1979-12-01

A simple physical explanation is given for the formation of Cooper pairs in a superconducting metal, for the origin of the attractive force causing the binding of the pairs, for the forming of a degenerate Bose gas by the Cooper pairs, for the finite energy gap that prevents the ensemble of electrons to change its quantum state at low temperatures, and for the existence of permanent currents in a superconducting wire. (orig.)

The formation of Cooper pairs and the nature of superconducting currents

International Nuclear Information System (INIS)

Weisskopf, V.F.

1981-01-01

A simple physical explanation is given for the formation of Cooper pairs in a superconducting metal, for the origin of the attractive force causing the binding of the pairs, for the forming of a degenerate Bose gas by the Cooper pairs, for the finite energy gap that prevents the ensemble of electrons from changing its quantum state at low temperatures, and for the existence of permanent currents in a superconducting wire. (author)

Optical and x-ray alignment approaches for off-plane reflection gratings

Science.gov (United States)

Allured, Ryan; Donovan, Benjamin D.; DeRoo, Casey T.; Marlowe, Hannah R.; McEntaffer, Randall L.; Tutt, James H.; Cheimets, Peter N.; Hertz, Edward; Smith, Randall K.; Burwitz, Vadim; Hartner, Gisela; Menz, Benedikt

2015-09-01

Off-plane reflection gratings offer the potential for high-resolution, high-throughput X-ray spectroscopy on future missions. Typically, the gratings are placed in the path of a converging beam from an X-ray telescope. In the off-plane reflection grating case, these gratings must be co-aligned such that their diffracted spectra overlap at the focal plane. Misalignments degrade spectral resolution and effective area. In-situ X-ray alignment of a pair of off-plane reflection gratings in the path of a silicon pore optics module has been performed at the MPE PANTER beamline in Germany. However, in-situ X-ray alignment may not be feasible when assembling all of the gratings required for a satellite mission. In that event, optical methods must be developed to achieve spectral alignment. We have developed an alignment approach utilizing a Shack-Hartmann wavefront sensor and diffraction of an ultraviolet laser. We are fabricating the necessary hardware, and will be taking a prototype grating module to an X-ray beamline for performance testing following assembly and alignment.

CORAL: aligning conserved core regions across domain families.

Science.gov (United States)

Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

Hohlraum Target Alignment from X-ray Detector Images using Starburst Design Patterns

International Nuclear Information System (INIS)

Leach, R.R.; Conder, A.; Edwards, O.; Kroll, J.; Kozioziemski, B.; Mapoles, E.; McGuigan, D.; Wilhelmsen, K.

2010-01-01

National Ignition Facility (NIF) is a high-energy laser facility comprised of 192 laser beams focused with enough power and precision on a hydrogen-filled spherical, cryogenic target to initiate a fusion reaction. The target container, or hohlraum, must be accurately aligned to an x-ray imaging system to allow careful monitoring of the frozen fuel layer in the target. To achieve alignment, x-ray images are acquired through starburst-shaped windows cut into opposite sides of the hohlraum. When the hohlraum is in alignment, the starburst pattern pairs match nearly exactly and allow a clear view of the ice layer formation on the edge of the target capsule. During the alignment process, x-ray image analysis is applied to determine the direction and magnitude of adjustment required. X-ray detector and source are moved in concert during the alignment process. The automated pointing alignment system described here is both accurate and efficient. In this paper, we describe the control and associated image processing that enables automation of the starburst pointing alignment.

A sensitive short read homology search tool for paired-end read sequencing data.

Science.gov (United States)

Techa-Angkoon, Prapaporn; Sun, Yanni; Lei, Jikai

2017-10-16

Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search. Short-Pair is best used for next-generation sequencing (NGS) data that lack reference genomes. It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/ .

Dual origin of pairing in nuclei

Energy Technology Data Exchange (ETDEWEB)

Idini, A. [University of Jyvaskyla, Department of Physics (Finland); Potel, G. [Michigan State University, National Superconducting Cyclotron Laboratory (United States); Barranco, F. [Escuela Superior de Ingenieros, Universidad de Sevilla, Departamento de Fìsica Aplicada III (Spain); Vigezzi, E., E-mail: enrico.vigezzi@mi.infn.it [INFN Sezione di Milano (Italy); Broglia, R. A. [Università di Milano, Dipartimento di Fisica (Italy)

2016-11-15

The pairing correlations of the nucleus {sup 120}Sn are calculated by solving the Nambu–Gor’kov equations, including medium polarization effects resulting from the interweaving of quasiparticles, spin and density vibrations, taking into account, within the framework of nuclear field theory (NFT), processes leading to self-energy and vertex corrections and to the induced pairing interaction. From these results one can not only demonstrate the inevitability of the dual origin of pairing in nuclei, but also extract information which can be used at profit to quantitatively disentangle the contributions to the pairing gap Δ arising from the bare and from the induced pairing interaction. The first is the strong {sup 1}S{sub 0} short-range NN potential resulting from meson exchange between nucleons moving in time reversal states within an energy range of hundreds of MeV from the Fermi energy. The second results from the exchange of vibrational modes between nucleons moving within few MeV from the Fermi energy. Short- (v{sub p}{sup bare}) and long-range (v{sub p}{sup ind}) pairing interactions contribute essentially equally to nuclear Cooper pair stability. That is to the breaking of gauge invariance in open-shell superfluid nuclei and thus to the order parameter, namely to the ground state expectation value of the pair creation operator. In other words, to the emergent property of generalized rigidity in gauge space, and associated rotational bands and Cooper pair tunneling between members of these bands.

Dual origin of pairing in nuclei

Science.gov (United States)

Idini, A.; Potel, G.; Barranco, F.; Vigezzi, E.; Broglia, R. A.

2016-11-01

The pairing correlations of the nucleus 120Sn are calculated by solving the Nambu-Gor'kov equations, including medium polarization effects resulting from the interweaving of quasiparticles, spin and density vibrations, taking into account, within the framework of nuclear field theory (NFT), processes leading to self-energy and vertex corrections and to the induced pairing interaction. From these results one can not only demonstrate the inevitability of the dual origin of pairing in nuclei, but also extract information which can be used at profit to quantitatively disentangle the contributions to the pairing gap Δ arising from the bare and from the induced pairing interaction. The first is the strong 1 S 0 short-range NN potential resulting from meson exchange between nucleons moving in time reversal states within an energy range of hundreds of MeV from the Fermi energy. The second results from the exchange of vibrational modes between nucleons moving within few MeV from the Fermi energy. Short- ( v p bare) and long-range ( v p ind) pairing interactions contribute essentially equally to nuclear Cooper pair stability. That is to the breaking of gauge invariance in open-shell superfluid nuclei and thus to the order parameter, namely to the ground state expectation value of the pair creation operator. In other words, to the emergent property of generalized rigidity in gauge space, and associated rotational bands and Cooper pair tunneling between members of these bands.

Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tail

Directory of Open Access Journals (Sweden)

Burghardt Bernd

2007-07-01

Full Text Available Abstract Background The optimal score for ungapped local alignments of infinitely long random sequences is known to follow a Gumbel extreme value distribution. Less is known about the important case, where gaps are allowed. For this case, the distribution is only known empirically in the high-probability region, which is biologically less relevant. Results We provide a method to obtain numerically the biologically relevant rare-event tail of the distribution. The method, which has been outlined in an earlier work, is based on generating the sequences with a parametrized probability distribution, which is biased with respect to the original biological one, in the framework of Metropolis Coupled Markov Chain Monte Carlo. Here, we first present the approach in detail and evaluate the convergence of the algorithm by considering a simple test case. In the earlier work, the method was just applied to one single example case. Therefore, we consider here a large set of parameters: We study the distributions for protein alignment with different substitution matrices (BLOSUM62 and PAM250 and affine gap costs with different parameter values. In the logarithmic phase (large gap costs it was previously assumed that the Gumbel form still holds, hence the Gumbel distribution is usually used when evaluating p-values in databases. Here we show that for all cases, provided that the sequences are not too long (L > 400, a "modified" Gumbel distribution, i.e. a Gumbel distribution with an additional Gaussian factor is suitable to describe the data. We also provide a "scaling analysis" of the parameters used in the modified Gumbel distribution. Furthermore, via a comparison with BLAST parameters, we show that significance estimations change considerably when using the true distributions as presented here. Finally, we study also the distribution of the sum statistics of the k best alignments. Conclusion Our results show that the statistics of gapped and ungapped local

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

Science.gov (United States)

Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

2009-07-01

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

Science.gov (United States)

Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

2015-01-01

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

Aligned fibers direct collective cell migration to engineer closing and nonclosing wound gaps.

Science.gov (United States)

Sharma, Puja; Ng, Colin; Jana, Aniket; Padhi, Abinash; Szymanski, Paige; Lee, Jerry S H; Behkam, Bahareh; Nain, Amrinder S

2017-09-15

Cell emergence onto damaged or organized fibrous extracellular matrix (ECM) is a crucial precursor to collective cell migration in wound closure and cancer metastasis, respectively. However, there is a fundamental gap in our quantitative understanding of the role of local ECM size and arrangement in cell emergence-based migration and local gap closure. Here, using ECM-mimicking nanofibers bridging cell monolayers, we describe a method to recapitulate and quantitatively describe these in vivo behaviors over multispatial (single cell to cell sheets) and temporal (minutes to weeks) scales. On fiber arrays with large interfiber spacing, cells emerge (invade) either singularly by breaking cell-cell junctions analogous to release of a stretched rubber band (recoil), or in groups of few cells (chains), whereas on closely spaced fibers, multiple chains emerge collectively. Advancing cells on fibers form cell streams, which support suspended cell sheets (SCS) of various sizes and curvatures. SCS converge to form local gaps that close based on both the gap size and shape. We document that cell stream spacing of 375 µm and larger hinders SCS advancement, thus providing abilities to engineer closing and nonclosing gaps. Altogether we highlight the importance of studying cell-fiber interactions and matrix structural remodeling in fundamental and translational cell biology. © 2017 Sharma et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Magnetic field alignment for a 20 MeV linear induction accelerator

International Nuclear Information System (INIS)

Zhang Wenwei; Pan Haifeng; Li Hong; Liu Yunlong; Zhang Linwen

2002-01-01

'Dragon-1' accelerator now is being constructed in CAEP. It will produce high current pulse electron beams. The main components of the accelerator include 72 induction accelerating cells and 18 connection cells with ports for beam di gnostic hardware and vacuum pump. In order to acquire high quality beams, a lot of problems have to be addressed such as to reduce the emittance, to control the increase of corkscrew and so on. The alignment of the focus magnetic field is the most concerned. A laser track has been used for mechanical alignment, magnetic alignment is performed by using pulsed-wire technique, and the natural tilt errors is corrected by a pair of steering coil, which is located inside the cell

IS ENVIRONMENTAL ALIGNMENT AND BUSINESS PERFORMANCE: A CONCEPTUAL APPROACH

Directory of Open Access Journals (Sweden)

K. Garg

2012-01-01

Full Text Available

ENGLISH ABSTRACT: This paper proposes a conceptual model termed "IS environmental alignment" that focuses on the support provided by IS strategy to minimize the gap between perceived environmental uncertainty and realized/objective environmental conditions. The model uses the Chan et al [9] alignment measurement method to measure IS strategic alignment as it provides a quantitative measure. In due course the proposed model would be tested in industry and would examine the affect of IS environmental alignment on business performance. The implication of the model lies in the effective use of deployed IS systems by organizations.

AFRIKAANSE OPSOMMING: 'n Konsepmodel word voorgelê wat handel oor "IS-omgewingsaanpassing". IS-strategie-ondersteuning by die minimisering van die gaping tussen waargenome omgewingsonsekerheid en gerealiseerde/objektiewe omgewingstoestande. Die model maak gebruik van die Chan et al [9] aanpassingsmeetmetode om IS-strategie-aanpassing op 'n kwantitatiewe basis te bepaal. Met die verloop van tyd sal die konsepmodel in die praktyk getoets word om te toon hoe IS-strategie-aanpassing sakevertoning affekteer. Die effektiewe ontplooiing van IS-stelsels by ondernemings word voorgehou.

A transcript finishing initiative for closing gaps in the human transcriptome

DEFF Research Database (Denmark)

Sogayar, Mari Cleide; Camargo, Anamaria A; Bettoni, Fabiana

2004-01-01

We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected...

Comparative study of the requantization of the time-dependent mean field for the dynamics of nuclear pairing

Science.gov (United States)

Ni, Fang; Nakatsukasa, Takashi

2018-04-01

To describe quantal collective phenomena, it is useful to requantize the time-dependent mean-field dynamics. We study the time-dependent Hartree-Fock-Bogoliubov (TDHFB) theory for the two-level pairing Hamiltonian, and compare results of different quantization methods. The one constructing microscopic wave functions, using the TDHFB trajectories fulfilling the Einstein-Brillouin-Keller quantization condition, turns out to be the most accurate. The method is based on the stationary-phase approximation to the path integral. We also examine the performance of the collective model which assumes that the pairing gap parameter is the collective coordinate. The applicability of the collective model is limited for the nuclear pairing with a small number of single-particle levels, because the pairing gap parameter represents only a half of the pairing collective space.

GapCoder automates the use of indel characters in phylogenetic analysis.

Science.gov (United States)

Young, Nelson D; Healy, John

2003-02-19

Several ways of incorporating indels into phylogenetic analysis have been suggested. Simple indel coding has two strengths: (1) biological realism and (2) efficiency of analysis. In the method, each indel with different start and/or end positions is considered to be a separate character. The presence/absence of these indel characters is then added to the data set. We have written a program, GapCoder to automate this procedure. The program can input PIR format aligned datasets, find the indels and add the indel-based characters. The output is a NEXUS format file, which includes a table showing what region each indel characters is based on. If regions are excluded from analysis, this table makes it easy to identify the corresponding indel characters for exclusion. Manual implementation of the simple indel coding method can be very time-consuming, especially in data sets where indels are numerous and/or overlapping. GapCoder automates this method and is therefore particularly useful during procedures where phylogenetic analyses need to be repeated many times, such as when different alignments are being explored or when various taxon or character sets are being explored. GapCoder is currently available for Windows from http://www.home.duq.edu/~youngnd/GapCoder.

HAL-2 promotes homologous pairing during Caenorhabditis elegans meiosis by antagonizing inhibitory effects of synaptonemal complex precursors.

Science.gov (United States)

Zhang, Weibin; Miley, Natasha; Zastrow, Michael S; MacQueen, Amy J; Sato, Aya; Nabeshima, Kentaro; Martinez-Perez, Enrique; Mlynarczyk-Evans, Susanna; Carlton, Peter M; Villeneuve, Anne M

2012-01-01

During meiosis, chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex (SC). Since the SC assembles cooperatively yet is indifferent to homology, pairing and SC assembly must be tightly coordinated. We identify HAL-2 as a key mediator in this coordination, showing that HAL-2 promotes pairing largely by preventing detrimental effects of SC precursors (SYP proteins). hal-2 mutants fail to establish pairing and lack multiple markers of chromosome movement mediated by pairing centers (PCs), chromosome sites that link chromosomes to cytoplasmic microtubules through nuclear envelope-spanning complexes. Moreover, SYP proteins load inappropriately along individual unpaired chromosomes in hal-2 mutants, and markers of PC-dependent movement and function are restored in hal-2; syp double mutants. These and other data indicate that SYP proteins can impede pairing and that HAL-2 promotes pairing predominantly but not exclusively by counteracting this inhibition, thereby enabling activation and regulation of PC function. HAL-2 concentrates in the germ cell nucleoplasm and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented. We propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing untimely interactions between SC precursors and chromosomes and allowing sufficient accumulation of precursors for rapid cooperative assembly upon homology verification.

Evidence for Consistency of the Glycation Gap in Diabetes

OpenAIRE

Nayak, Ananth U.; Holland, Martin R.; Macdonald, David R.; Nevill, Alan; Singh, Baldev M.

2011-01-01

OBJECTIVE Discordance between HbA1c and fructosamine estimations in the assessment of glycemia is often encountered. A number of mechanisms might explain such discordance, but whether it is consistent is uncertain. This study aims to coanalyze paired glycosylated hemoglobin (HbA1c)-fructosamine estimations by using fructosamine to determine a predicted HbA1c, to calculate a glycation gap (G-gap) and to determine whether the G-gap is consistent over time. RESEARCH DESIGN AND METHODS We include...

Angle-resolved photoemission studies of the superconducting gap symmetry in Fe-based superconductors

Directory of Open Access Journals (Sweden)

Y.-B. Huang

2012-12-01

Full Text Available The superconducting gap is the fundamental parameter that characterizes the superconducting state, and its symmetry is a direct consequence of the mechanism responsible for Cooper pairing. Here we discuss about angle-resolved photoemission spectroscopy measurements of the superconducting gap in the Fe-based high-temperature superconductors. We show that the superconducting gap is Fermi surface dependent and nodeless with small anisotropy, or more precisely, a function of the momentum location in the Brillouin zone. We show that while this observation seems inconsistent with weak coupling approaches for superconductivity in these materials, it is well supported by strong coupling models and global superconducting gaps. We also suggest that a smaller lifetime of the superconducting Cooper pairs induced by the momentum dependent interband scattering inherent to these materials could affect the residual density of states at low energies, which is critical for a proper evaluation of the superconducting gap.

RNA structure alignment by a unit-vector approach.

Science.gov (United States)

Capriotti, Emidio; Marti-Renom, Marc A

2008-08-15

The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

Statistical alignment: computational properties, homology testing and goodness-of-fit

DEFF Research Database (Denmark)

Hein, J; Wiuf, Carsten; Møller, Martin

2000-01-01

The model of insertions and deletions in biological sequences, first formulated by Thorne, Kishino, and Felsenstein in 1991 (the TKF91 model), provides a basis for performing alignment within a statistical framework. Here we investigate this model.Firstly, we show how to accelerate the statistical...... alignment algorithms several orders of magnitude. The main innovations are to confine likelihood calculations to a band close to the similarity based alignment, to get good initial guesses of the evolutionary parameters and to apply an efficient numerical optimisation algorithm for finding the maximum...... analysis.Secondly, we propose a new homology test based on this model, where homology means that an ancestor to a sequence pair can be found finitely far back in time. This test has statistical advantages relative to the traditional shuffle test for proteins.Finally, we describe a goodness-of-fit test...

Pairing in hadron structure

International Nuclear Information System (INIS)

Chela-Flores, J.

1981-08-01

A many-body approach to hadron structure is presented, in which we consider two parton species: spin-0 (b-partons), and spin-1/2 (f-partons). We extend a boson and a fermion pairing scheme for the b-, and f-partons respectively, into a Yang-Mills gauge theory. The main feature of this theory is that the gauge field is not identified with the usual gluon field variable in QCD. We study the confinement problem of the hadron constituents, and obtain, for low temperatures, partons that are confined by energy gaps. As the critical temperatures for the corresponding phase transitions are approached, the energy gap gradually disappears, and confinement is lost. The theory goes beyond the non-relativistic harmonic oscillator quark model, in the sense of giving physical reasons why a non-relativistic approximation is adequate in describing the internal dynamics of hadron structure. (author)

A Thin Lens Model for Charged-Particle RF Accelerating Gaps

Energy Technology Data Exchange (ETDEWEB)

Allen, Christopher K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-07-01

Presented is a thin-lens model for an RF accelerating gap that considers general axial fields without energy dependence or other a priori assumptions. Both the cosine and sine transit time factors (i.e., Fourier transforms) are required plus two additional functions; the Hilbert transforms the transit-time factors. The combination yields a complex-valued Hamiltonian rotating in the complex plane with synchronous phase. Using Hamiltonians the phase and energy gains are computed independently in the pre-gap and post-gap regions then aligned using the asymptotic values of wave number. Derivations of these results are outlined, examples are shown, and simulations with the model are presented.

Creating a medical English-Swedish dictionary using interactive word alignment

Directory of Open Access Journals (Sweden)

Zweigenbaum Pierre

2006-10-01

Full Text Available Abstract Background This paper reports on a parallel collection of rubrics from the medical terminology systems ICD-10, ICF, MeSH, NCSP and KSH97-P and its use for semi-automatic creation of an English-Swedish dictionary of medical terminology. The methods presented are relevant for many other West European language pairs than English-Swedish. Methods The medical terminology systems were collected in electronic format in both English and Swedish and the rubrics were extracted in parallel language pairs. Initially, interactive word alignment was used to create training data from a sample. Then the training data were utilised in automatic word alignment in order to generate candidate term pairs. The last step was manual verification of the term pair candidates. Results A dictionary of 31,000 verified entries has been created in less than three man weeks, thus with considerably less time and effort needed compared to a manual approach, and without compromising quality. As a side effect of our work we found 40 different translation problems in the terminology systems and these results indicate the power of the method for finding inconsistencies in terminology translations. We also report on some factors that may contribute to making the process of dictionary creation with similar tools even more expedient. Finally, the contribution is discussed in relation to other ongoing efforts in constructing medical lexicons for non-English languages. Conclusion In three man weeks we were able to produce a medical English-Swedish dictionary consisting of 31,000 entries and also found hidden translation errors in the utilized medical terminology systems.

Creating a medical English-Swedish dictionary using interactive word alignment

Science.gov (United States)

Nyström, Mikael; Merkel, Magnus; Ahrenberg, Lars; Zweigenbaum, Pierre; Petersson, Håkan; Åhlfeldt, Hans

2006-01-01

Background This paper reports on a parallel collection of rubrics from the medical terminology systems ICD-10, ICF, MeSH, NCSP and KSH97-P and its use for semi-automatic creation of an English-Swedish dictionary of medical terminology. The methods presented are relevant for many other West European language pairs than English-Swedish. Methods The medical terminology systems were collected in electronic format in both English and Swedish and the rubrics were extracted in parallel language pairs. Initially, interactive word alignment was used to create training data from a sample. Then the training data were utilised in automatic word alignment in order to generate candidate term pairs. The last step was manual verification of the term pair candidates. Results A dictionary of 31,000 verified entries has been created in less than three man weeks, thus with considerably less time and effort needed compared to a manual approach, and without compromising quality. As a side effect of our work we found 40 different translation problems in the terminology systems and these results indicate the power of the method for finding inconsistencies in terminology translations. We also report on some factors that may contribute to making the process of dictionary creation with similar tools even more expedient. Finally, the contribution is discussed in relation to other ongoing efforts in constructing medical lexicons for non-English languages. Conclusion In three man weeks we were able to produce a medical English-Swedish dictionary consisting of 31,000 entries and also found hidden translation errors in the utilized medical terminology systems. PMID:17034649

Creating a medical English-Swedish dictionary using interactive word alignment.

Science.gov (United States)

Nyström, Mikael; Merkel, Magnus; Ahrenberg, Lars; Zweigenbaum, Pierre; Petersson, Håkan; Ahlfeldt, Hans

2006-10-12

This paper reports on a parallel collection of rubrics from the medical terminology systems ICD-10, ICF, MeSH, NCSP and KSH97-P and its use for semi-automatic creation of an English-Swedish dictionary of medical terminology. The methods presented are relevant for many other West European language pairs than English-Swedish. The medical terminology systems were collected in electronic format in both English and Swedish and the rubrics were extracted in parallel language pairs. Initially, interactive word alignment was used to create training data from a sample. Then the training data were utilised in automatic word alignment in order to generate candidate term pairs. The last step was manual verification of the term pair candidates. A dictionary of 31,000 verified entries has been created in less than three man weeks, thus with considerably less time and effort needed compared to a manual approach, and without compromising quality. As a side effect of our work we found 40 different translation problems in the terminology systems and these results indicate the power of the method for finding inconsistencies in terminology translations. We also report on some factors that may contribute to making the process of dictionary creation with similar tools even more expedient. Finally, the contribution is discussed in relation to other ongoing efforts in constructing medical lexicons for non-English languages. In three man weeks we were able to produce a medical English-Swedish dictionary consisting of 31,000 entries and also found hidden translation errors in the utilized medical terminology systems.

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

Directory of Open Access Journals (Sweden)

Claros M Gonzalo

2010-06-01

Full Text Available Abstract Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used

Photoluminescence of heterostructures with GaP1−xNx and GaP1−x−yNxAsy layers grown on GaP and Si substrates by molecular-beam epitaxy

International Nuclear Information System (INIS)

Lazarenko, A. A.; Nikitina, E. V.; Sobolev, M. S.; Pirogov, E. V.; Denisov, D. V.; Egorov, A. Yu.

2015-01-01

The structural and optical properties of heterostructures containing GaP 1−x N x ternary and GaP 1−x−y N x As y quaternary alloy layers are discussed. The heterostructures are grown by molecular-beam epitaxy on GaP and Si substrates. The structures are studied by the high-resolution X-ray diffraction technique and photoluminescence measurements in a wide temperature range from 10 to 300 K. In the low-temperature photoluminescence spectra of the alloys with a low nitrogen fraction (x < 0.007), two clearly resolved narrow lines attributed to the localized states of nitrogen pairs and the phonon replicas of these lines are observed

The two-proton shell gap in Sn isotopes

International Nuclear Information System (INIS)

Fleischer, P.; Kluepfel, P.; Reinhard, P.-G.; Cornelius, T.; Schramm, S.; Maruhn, J.A.; Buervenich, T.J.

2004-01-01

We present an analysis of two-proton shell gaps in Sn isotopes. As theoretical tool we use self-consistent mean-field models, namely the relativistic mean-field model and the Skyrme-Hartree-Fock approach, both with two different pairing forces, a delta interaction (DI) model and a density-dependent delta interaction (DDDI). We investigate the influence of nuclear deformation as well as collective correlations and find that both effects contribute significantly. Moreover, we find a further significant dependence on the pairing force used. The inclusion of deformation plus correlation effects and the use of DDDI pairing provides agreement with the data. (orig.)

Synergistic Instance-Level Subspace Alignment for Fine-Grained Sketch-Based Image Retrieval.

Science.gov (United States)

Li, Ke; Pang, Kaiyue; Song, Yi-Zhe; Hospedales, Timothy M; Xiang, Tao; Zhang, Honggang

2017-08-25

We study the problem of fine-grained sketch-based image retrieval. By performing instance-level (rather than category-level) retrieval, it embodies a timely and practical application, particularly with the ubiquitous availability of touchscreens. Three factors contribute to the challenging nature of the problem: (i) free-hand sketches are inherently abstract and iconic, making visual comparisons with photos difficult, (ii) sketches and photos are in two different visual domains, i.e. black and white lines vs. color pixels, and (iii) fine-grained distinctions are especially challenging when executed across domain and abstraction-level. To address these challenges, we propose to bridge the image-sketch gap both at the high-level via parts and attributes, as well as at the low-level, via introducing a new domain alignment method. More specifically, (i) we contribute a dataset with 304 photos and 912 sketches, where each sketch and image is annotated with its semantic parts and associated part-level attributes. With the help of this dataset, we investigate (ii) how strongly-supervised deformable part-based models can be learned that subsequently enable automatic detection of part-level attributes, and provide pose-aligned sketch-image comparisons. To reduce the sketch-image gap when comparing low-level features, we also (iii) propose a novel method for instance-level domain-alignment, that exploits both subspace and instance-level cues to better align the domains. Finally (iv) these are combined in a matching framework integrating aligned low-level features, mid-level geometric structure and high-level semantic attributes. Extensive experiments conducted on our new dataset demonstrate effectiveness of the proposed method.

Cooper-pair size and binding energy for unconventional superconducting systems

Science.gov (United States)

Dinóla Neto, F.; Neto, Minos A.; Salmon, Octavio D. Rodriguez

2018-06-01

The main proposal of this paper is to analyze the size of the Cooper pairs composed by unbalanced mass fermions from different electronic bands along the BCS-BEC crossover and study the binding energy of the pairs. We are considering an interaction between fermions with different masses leading to an inter-band pairing. In addiction to the attractive interaction we have an hybridization term to couple both bands, which in general acts unfavorable for the pairing between the electrons. We get first order phase transitions as the hybridization breaks the Cooper pairs for the s-wave symmetry of the gap amplitude. The results show the dependence of the Cooper-pair size as a function of the hybridization for T = 0 . We also propose the structure of the binding energy of the inter-band system as a function of the two-bands quasi-particle energies.

Design of a magnetic field alignment diagnostic for the MFTF-B magnet system

International Nuclear Information System (INIS)

Deadrick, F.J.; House, P.A.; Frye, R.W.

1985-01-01

Magnet alignment in tandem mirror fusion machines plays a crucial role in achieving and maintaining plasma confinement. Various visual alignment tools have been described by Post et al. to align the Tara magnet system. We have designed and installed a remotely operated magnetic field alignment (MFA) diagnostic system as a part of the Mirror Fusion Test Facility (MFTF-B). It measures critical magnetic field alignment parameters of the MFTF-B coil set while under full-field operating conditions. The MFA diagnostic employs a pair of low-energy, electron beam guns on a remotely positionable probe to trace and map selected magnetic field lines. An array of precision electrical detector paddles locates the position of the electron beam, and thus the magnetic field line, at several critical points. The measurements provide a means to compute proper compensating currents to correct for mechanical misalignments of the magnets with auxiliary trim coils if necessary. This paper describes both the mechanical and electrical design of the MFA diagnostic hardware

Absence of paired crossing in the positive parity bands of 124Cs

Science.gov (United States)

Singh, A. K.; Basu, A.; Nag, Somnath; Hübel, H.; Domscheit, J.; Ragnarsson, I.; Al-Khatib, A.; Hagemann, G. B.; Herskind, B.; Elema, D. R.; Wilson, J. N.; Clark, R. M.; Cromaz, M.; Fallon, P.; Görgen, A.; Lee, I.-Y.; Ward, D.; Ma, W. C.

2018-02-01

High-spin states in 124Cs were populated in the 64Ni(64Ni,p 3 n ) reaction and the Gammasphere detector array was used to measure γ -ray coincidences. Both positive- and negative-parity bands, including bands with chiral configurations, have been extended to higher spin, where a shape change has been observed. The configurations of the bands before and after the alignment are discussed within the framework of the cranked Nilsson-Strutinsky model. The calculations suggest that the nucleus undergoes a shape transition from triaxial to prolate around spin I ≃22 of the positive-parity states. The alignment gain of 8 ℏ , observed in the positive-parity bands, is due to partial alignment of several valence nucleons. This indicates the absence of band crossing due to paired nucleons in the bands.

Movement of anterior teeth using clear aligners: a three-dimensional, retrospective evaluation.

Science.gov (United States)

Tepedino, Michele; Paoloni, Valeria; Cozza, Paola; Chimenti, Claudio

2018-04-02

Clear aligner treatment offers several advantages, but the available literature shows that some kind of tooth movements are unpredictable. In addition, the majority of the studies are focused on one clear aligner system, while different characteristics of various systems can provide different treatment outcomes. The aim of the present retrospective cohort study was to evaluate the predictability of Nuvola® aligner system in achieving torque movements of anterior teeth. Thirty-nine adult patients, who were consecutively treated with clear aligners, were retrospectively selected, and digital models pre-treatment (T0), post-treatment (T1) and the digital setup models (TS) were collected. Only the first phase of treatment made of 12 aligners was considered for the present study. Torque of anterior teeth was measured as labiolingual inclination on digital models at T0, T1, and TS using VAM software. Any difference between the predicted and achieved torque movements was evaluated using Wilcoxon signed-rank test or paired sample t test. First-type error was set as p clear aligner system was able to produce clinical outcomes comparable to the planning of the digital setup relative to torque movements of the anterior teeth.

Application of monorail fixator for femoral gap nonunion.

Science.gov (United States)

Agrawal, Hemendra-Kumar; Jaiman, Ashish; Khatkar, Vipin; Sharma, Vinod-Kumar

2014-01-01

Difficult femoral nonunion takes account of infective nonunion and aseptic gap nonunion. Limb length discrepancy and nonunion need to be tackled simultaneously. Conventionally Ilizarov ring fixator is in vogue but it has some limitations. To overcome these, monorail fixator is an effective alternative. Persistent good results can be obtained if we can get a perfect anatomical alignment and good regeneration.

Role of superconducting energy gap in extended BCS-Bose crossover theory

Science.gov (United States)

Chávez, I.; García, L. A.; de Llano, M.; Grether, M.

2017-10-01

The generalized Bose-Einstein condensation (GBEC) theory of superconductivity (SC) is briefly surveyed. It hinges on three distinct new ingredients: (i) Treatment of Cooper pairs (CPs) as actual bosons since they obey Bose statistics, in contrast to BCS pairs which do not obey Bose commutation relations; (ii) inclusion of two-hole Cooper pairs (2hCPs) on an equal footing with two-electron Cooper pairs (2eCPs), thus making this a complete boson-fermion (BF) model; and (iii) inclusion in the resulting ternary ideal BF gas with particular BF vertex interactions that drive boson formation/disintegration processes. GBEC subsumes as special cases both BCS (having its 50-50 symmetry of both kinds of CPs) and ordinary BEC theories (having no 2hCPs), as well as the now familiar BCS-Bose crossover theory. We extended the crossover theory with the explicit inclusion of 2hCPs and construct a phase diagram of Tc/TF versus n/nf, where Tc and TF are the critical and Fermi temperatures, n is the total number density and nf that of unbound electrons at T = 0. Also, with this extended crossover one can construct the energy gap Δ(T)/Δ(0) versus T/Tc for some elemental SCs by solving at least two equations numerically: a gap-like and a number equation. In 50-50 symmetry, the energy gap curve agrees quite well with experimental data. But ignoring 2hCPs altogether leads to the gap curve falling substantially below that with 50-50 symmetry which already fits the data quite well, showing that 2hCPs are indispensable to describe SCs.

Cooper pair splitters beyond the Coulomb blockade regime

Energy Technology Data Exchange (ETDEWEB)

Amitai, Ehud; Tiwari, Rakesh P.; Nigg, Simon E. [Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel (Switzerland); Walter, Stefan [Institute for Theoretical Physics, University Erlangen Nuernberg, Staudtstrasse 7, 91058 Erlangen (Germany); Schmidt, Thomas L. [Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg (Luxembourg)

2016-07-01

We consider the setup of a conventional s-wave Cooper pair splitter. However, we consider the charging energies in the quantum dots to be finite and smaller than the superconducting gap. We find analytically that at low energies the superconductor mediates an inter-dot tunneling term, the spin symmetry of which is influenced by a finite Zeeman field. This effect, together with an electrical tuning scheme of the quantum dot levels, can be used to engineer a non local triplet state on the two quantum dots, thereby extending the non-local state engineering capabilities of the Cooper pair splitter system.

High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

Science.gov (United States)

Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

2017-07-01

This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

Aligning the unalignable: bacteriophage whole genome alignments.

Science.gov (United States)

Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

2016-01-13

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

Science.gov (United States)

Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

Directory of Open Access Journals (Sweden)

Maréchal Eric

2005-03-01

Full Text Available Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. Conclusion The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

Directory of Open Access Journals (Sweden)

Sven Warris

Full Text Available To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.With the Parallel SW Alignment Software (PaSWAS it is possible (a to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs to perform high-speed sequence alignments, and (b retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1 tag recovery in next generation sequence data and (2 isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

Science.gov (United States)

Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

2015-01-01

To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

Sub-cell turning to accomplish micron-level alignment of precision assemblies

Science.gov (United States)

Kumler, James J.; Buss, Christian

2017-08-01

Higher performance expectations for complex optical systems demand tighter alignment requirements for lens assembly alignment. In order to meet diffraction limited imaging performance over wide spectral bands across the UV and visible wavebands, new manufacturing approaches and tools must be developed if the optical systems will be produced consistently in volume production. This is especially applicable in the field of precision microscope objectives for life science, semiconductor inspection and laser material processing systems. We observe a rising need for the improvement in the optical imaging performance of objective lenses. The key challenge lies in the micron-level decentration and tilt of each lens element. One solution for the production of high quality lens systems is sub-cell assembly with alignment turning. This process relies on an automatic alignment chuck to align the optical axis of a mounted lens to the spindle axis of the machine. Subsequently, the mount is cut with diamond tools on a lathe with respect to the optical axis of the mount. Software controlled integrated measurement technology ensures highest precision. In addition to traditional production processes, further dimensions can be controlled in a very precise manner, e.g. the air gaps between the lenses. Using alignment turning simplifies further alignment steps and reduces the risk of errors. This paper describes new challenges in microscope objective design and manufacturing, and addresses difficulties with standard production processes. A new measurement and alignment technique is described, and strengths and limitations are outlined.

Alignment measurements uncertainties for large assemblies using probabilistic analysis techniques

CERN Document Server

AUTHOR|(CDS)2090816; Almond, Heather

Big science and ambitious industrial projects continually push forward with technical requirements beyond the grasp of conventional engineering techniques. Example of those are ultra-high precision requirements in the field of celestial telescopes, particle accelerators and aerospace industry. Such extreme requirements are limited largely by the capability of the metrology used, namely, it’s uncertainty in relation to the alignment tolerance required. The current work was initiated as part of Maria Curie European research project held at CERN, Geneva aiming to answer those challenges as related to future accelerators requiring alignment of 2 m large assemblies to tolerances in the 10 µm range. The thesis has found several gaps in current knowledge limiting such capability. Among those was the lack of application of state of the art uncertainty propagation methods in alignment measurements metrology. Another major limiting factor found was the lack of uncertainty statements in the thermal errors compensatio...

Controlled Deposition and Alignment of Carbon Nanotubes

Science.gov (United States)

Smits, Jan M. (Inventor); Wincheski, Russell A. (Inventor); Patry, JoAnne L. (Inventor); Watkins, Anthony Neal (Inventor); Jordan, Jeffrey D. (Inventor)

2012-01-01

A carbon nanotube (CNT) attraction material is deposited on a substrate in the gap region between two electrodes on the substrate. An electric potential is applied to the two electrodes. The CNT attraction material is wetted with a solution defined by a carrier liquid having carbon nanotubes (CNTs) suspended therein. A portion of the CNTs align with the electric field and adhere to the CNT attraction material. The carrier liquid and any CNTs not adhered to the CNT attraction material are then removed.

Baryonic 3P2-dominant superfluidity under combined pion condensation with Δ isobar. II). Properties of pairing interaction and numerical results

International Nuclear Information System (INIS)

Tamagaki, Ryozo

2007-01-01

According to the formulation developed in I, we calculate energy gaps of the baryonic 3 P 2 -dominant superfluidity under the combined pion condensation with Δ-mixing at moderately high density in neutron star interior. Adopting a baryon-baryon potential extended from a 'root' NN potential to be workable in the N+Δ space, we obtain the concrete form of the pairing interaction matrix elements between the quasi-baryon pairs, which constitute a two-dimensional angular-momentum stretched state and a charge triplet. With use of OPEG-B as a 'root' NN potential and an available set of the parameters representing the combined pion condensation, we study the properties of two-dimensional pairing potentials and the matrix elements of pairing interaction. We find that the strong attraction of pairing interaction for the quasi-neutron pairs is brought about by the spin-orbit potential and the spin- and isospin-dependent core terms of the central potential, whose effects are enhanced due to the pion condensation. The quasi-neutron pair plays a decisive role to bring about meaningful energy gaps, while the coupling between different quasi-baryon pairs plays no important role, as a consequence of a unique feature of the combined pion condensation we adopt. We numerically solve the energy gap equation for baryon density of (2-6) times the nuclear density and clarify substantial aspects of resulting superfluid energy gaps, and discuss related problems by taking into account possible change in the factors affecting the energy gaps, such as baryon-baryon potentials, some of the pion condensation parameters and an effective mass of the quasi-particle. Standing on these results, we can say that the 3 P 2 -dominant superfluid is realized with the critical temperatures T c of the order of 10 9 K, equivalent to the energy gaps of the order of 0.1 MeV, under the combined pion condensation in neutron star matter. The key point of the recognition lies in the aspects that the �

Baryonic 3 P2-Dominant Superfluidity under Combined Pion Condensation with Δ Isobar. II --- Properties of Pairing Interaction and Numerical Results ---

Science.gov (United States)

Tamagaki, R.; Takatsuka, T.

2007-05-01

According to the formulation developed in I, we calculate energy gaps of the baryonic (3) P_2-dominant superfluidity under the combined pion condensation with Delta-mixing at moderately high density in neutron star interior. Adopting a baryon-baryon potential extended from a ``root" NN potential to be workable in the N + Delta space, we obtain the concrete form of the pairing interaction matrix elements between the quasi-baryon pairs, which constitute a two-dimensional angular-momentum stretched state and a charge triplet. With use of OPEG-B as a ``root" NN potential and an available set of the parameters representing the combined pion condensation, we study the properties of two-dimensional pairing potentials and the matrix elements of pairing interaction. We find that the strong attraction of pairing interaction for the quasi-neutron pairs is brought about by the spin-orbit potential and the spin- and isospin-dependent core terms of the central potential, whose effects are enhanced due to the pion condensation. The quasi-neutron pair plays a decisive role to bring about meaningful energy gaps, while the coupling between different quasi-baryon pairs plays no important role, as a consequence of a unique feature of the combined pion condensation we adopt. We numerically solve the energy gap equation for baryon density of (2-6) times the nuclear density and clarify substantial aspects of resulting superfluid energy gaps, and discuss related problems by taking into account possible change in the factors affecting the energy gaps, such as baryon-baryon potentials, some of the pion condensation parameters and an effective mass of the quasi-particle. Standing on these results, we can say that the (3) P_2-dominant superfluid is realized with the critical temperatures T_c of the order of 10(9) K, equivalent to the energy gaps of the order of 0.1 MeV, under the combined pion condensation in neutron star matter. The key point of the recognition lies in the aspects that the

Visualizing pair formation on the atomic scale in high-Tc superconductors

International Nuclear Information System (INIS)

Pasupathy, A.

2008-01-01

Full text: Unlike traditional superconductors, the density of states (DOS) of the high-T c superconductor Bi-2212 shows large nanoscale variations that have been detected using scanning tunneling microscopy (STM). Such variations are seen in the low temperature superconducting gap and in features associated with the coupling of pairs to boson modes. In order to understand these variations in the spectra, we perform atomic resolution STM measurements of Bi-2212 as a function of temperature. Using newly developed experimental techniques, we measure the evolution of the DOS from low temperature (T c ) to temperatures where all gaps in the spectrum have disappeared (T>T*). Such measurements show that the pairing gap nucleates in nanoscale regions at temperatures between T c and T*. By normalizing the low temperature DOS (T c ) to the DOS at high temperature, we are able to fit the superconducting DOS to the d-wave BCS form. We find that the experimental spectrum deviations from a simple d-wave fit indicating a strong coupling between electrons and bosonic modes. We will discuss the temperature evolution of these as well as other features in the DOS and correlate such measurements with the inhomogeneity seen in the gap magnitude at low temperature

Non-magnetic impurity effect on suppression of Tc and gap evolution in the two-gap superconductor Lu2Fe3Si5

International Nuclear Information System (INIS)

Nakajima, Y.; Hidaka, H.; Tamegai, T.

2013-01-01

Highlights: ► Non-magnetic impurities suppress T c and the amplitude of gaps in Lu 2 Fe 3 Si 5 . ► Critical scattering rate is higher than that expected in s ± -pairing scenario. ► The evolution of two distinct gaps dose not show merging the amplitude of gaps. -- Abstract: We report the suppression of T c and the evolution of amplitudes of the two gaps with the introduction of non-magnetic impurities in a two-gap superconductor Lu 2 Fe 3 Si 5 . While T c rapidly decreases by a small amount of substitution of Sc for Lu, the suppression of T c is more than ten times slower than that expected from the Abrikosov–Gor’kov equation describing the reduction of T c in a superconductor with sign reversal in the gap function. The evolution of two distinct gaps by the introduction of non-magnetic impurities does not show merging the amplitude of two gaps, which is strikingly different from the typical two-gap superconductor MgB 2

Radiographic assessment of knee-ankle alignment after total knee arthroplasty for varus and valgus knee osteoarthritis.

Science.gov (United States)

Gao, Fuqiang; Ma, Jinhui; Sun, Wei; Guo, Wanshou; Li, Zirong; Wang, Weiguo

2017-01-01

There are unanswered questions about knee-ankle alignment after total knee arthroplasty (TKA) for varus and valgus osteoarthritis (OA) of the knee. The aim of this retrospective study was to assess knee-ankle alignment after TKA. The study consisted of 149 patients who had undergone TKA due to varus and valgus knee OA. The alignment and angles in the selected knees and ankles were measured on full-length standing anteroposterior radiographs, both pre-operatively and post-operatively. The paired t-test and Pearson's correlation tests were used for statistical analysis. The results showed that ankle alignment correlated with knee alignment both pre-operatively and postoperatively (Pknee was corrected (Pknee-ankle alignment on the non-operative side (P>0.05). These findings indicated that routine TKA could correct the varus or valgus deformity of a knee, and improve the tilt of the ankle. Ankle alignment correlated with knee alignment both pre-operatively and postoperatively. Both pre-operative knee and ankle malalignment can be simultaneously corrected following TKA. Level III. Copyright © 2016 Elsevier B.V. All rights reserved.

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

Science.gov (United States)

Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

2010-07-01

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

The Effects of a Roommate-Pairing Program on International Student Satisfaction and Academic Success

Science.gov (United States)

Tolman, Steven

2017-01-01

While great attention has been given to the growth of international students at U.S. institutions, there is a gap in the literature examining support for this student population within residence halls. To address the gap, this quantitative study evaluated an international roommate-pairing program (IRP) by comparing the residential experience of…

Study on the wide-angle Michelson interferometer with large air gap.

Science.gov (United States)

Gao, Haiyang; Tang, Yuanhe; Hua, Dengxin; Liu, Hanchen

2011-10-10

A wide-angle Michelson interferometer with large air gap is proposed to effectively reduce the size of the glass arms and constraint on material. It provides a novel and practical instrument for ground based wind measurement of the upper atmosphere. The field widening conditions for the large air gap are calculated in theory. For the five spectral lines of 557.7 nm, 630.0 nm, 732.0 nm, 834.6 nm, and 865.7 nm, the optimal results under ideal condition are obtained with air gaps of 1.0 cm, 1.5 cm, and 2.0 cm, respectively. With the fixed optical path difference (OPD) of 7.495 cm, three pairs of glass arms are optimized. The pair with length of 1.5 cm for air gap, 5.765 cm for H-ZF12, and 2.956 cm for H-ZLaF54, has better effect of field widening than the other two pairs and its OPD variation is only within 0.30 wavelengths at incident angle of 3°. For developing a more practical wide-angle Michelson interferometer, the H-K9L glass with size of 4.445 cm is employed as the arm material of solid interferometer. The experiment for field of view of 3° is designed and the data processing and analysis for 60 images show the agreement between experimental results and theoretical simulation. The OPD variations are only within 0.27 wavelengths for image edge. The feasibility and practicality of the wide-angle Michelson interferometer with large air gap is proved by means of theory and experiment. © 2011 Optical Society of America

Are the strategic stars aligned for your corporate brand?

Science.gov (United States)

Hatch, M J; Schultz, M

2001-02-01

In recent years, companies have increasingly seen the benefits of creating a corporate brand. Rather than spend marketing dollars on branding individual products, giants like Disney and Microsoft promote a single umbrella image that casts one glow over all their products. A company must align three interdependent elements--call them strategic stars--to create a strong corporate brand: vision, culture, and image. Aligning the stars takes concentrated managerial skill and will, the authors say, because each element is driven by a different constituency: management, employees, or stakeholders. To effectively build a corporate brand, executives must identify where their strategic stars fall out of line. The authors offer a series of diagnostic questions designed to reveal misalignments in corporate vision, culture, and image. The first set of questions looks for gaps between vision and culture; for example, when management establishes a vision that is too ambitious for the organization to implement. The second set addresses culture and image, uncovering possible gaps between the attitudes of employees and the perceptions of the outside world. The last set of questions explores the vision-image gap--is management taking the company in a direction that its stake-holders support? The authors discuss the benefits of a corporate brand, such as reducing marketing costs and building a sense of community among customers. But they also point to cases in which a corporate brand doesn't make sense--for instance, if you are a product incubator, if you've recently experienced M&A activity, or if you are expecting fallout from risky ventures.

Drive the Dirac electrons into Cooper pairs in SrxBi2Se3

Science.gov (United States)

Du, Guan; Shao, Jifeng; Yang, Xiong; Du, Zengyi; Fang, Delong; Wang, Jinghui; Ran, Kejing; Wen, Jinsheng; Zhang, Changjin; Yang, Huan; Zhang, Yuheng; Wen, Hai-Hu

2017-01-01

Topological superconductors are a very interesting and frontier topic in condensed matter physics. Despite the tremendous efforts in exploring topological superconductivity, its presence is however still under heavy debate. The Dirac electrons have been proven to exist on the surface of a topological insulator. It remains unclear whether and how the Dirac electrons fall into Cooper pairing in an intrinsic superconductor with the topological surface states. Here we show the systematic study of scanning tunnelling microscope/spectroscopy on the possible topological superconductor SrxBi2Se3. We first demonstrate that only the intercalated Sr atoms can induce superconductivity. Then we show the full superconducting gaps without any in-gap density of states as expected theoretically for a bulk topological superconductor. Finally, we find that the surface Dirac electrons will simultaneously condense into the superconducting state within the superconducting gap. This vividly demonstrates how the surface Dirac electrons are driven into Cooper pairs. PMID:28198378

Maglev guideway route alignment and right-of-way requirements

Science.gov (United States)

Carlton, S.; Andriola, T.

1992-12-01

The use of existing rights-of-way (ROW) is assessed for maglev systems by estimating trip times and land acquisition requirements for potential maglev corridors while meeting passenger comfort limits. Right-of-way excursions improve trip time but incur a cost for purchasing land. The final report documents findings of the eight tasks in establishing right-of-way feasibility by examining three city-pair corridors in detail and developing an approximation method for estimating route length and travel times in 20 additional city-pair corridor portions and 21 new corridors. The use of routes independent of existing railroad or highway right-of-way have trip time advantages and significantly reduce the need for aggressive guideway geometries on intercity corridors. Selection of the appropriate alignment is determined by many corridor specific issues. Use of existing intercity rights-of-way may be appropriate for parts of routes on a corridor-specific basis and for urban penetration where vehicle speeds are likely to be reduced by policy due to noise and safety considerations, and where land acquisition costs are high. Detailed aspects of available rights-of-way, land acquisition costs, geotechnical issues, land use, and population centers must be examined in more detail on a specific corridor basis before the proper or best maglev alignment can be chosen.

Fabrication of uniaxially aligned 3D electrospun scaffolds for neural regeneration

Energy Technology Data Exchange (ETDEWEB)

Subramanian, Anuradha; Krishnan, Uma Maheswari; Sethuraman, Swaminathan, E-mail: swami@sastra.edu [Center for Nanotechnology and Advanced Biomaterials, SASTRA University, Thanjavur 613 401, Tamil Nadu (India)

2011-04-15

Nanofibrous scaffolds are very promising physical guidance substrates for regenerating nerves to traverse larger nerve gaps. In this study, we have attempted to develop 2D random and 3D longitudinally oriented nanofibers of poly(lactide-co-glycolide) (PLGA) by the modified electrospinning process and characterized the surface morphology, mechanical properties, porosity, degradation and wettability. The orientation of aligned fibers was optimized by varying the speed of the rotating mandrel in the electrospinning process. The mean diameter of random PLGA nanofibers was 197 {+-} 72 nm, whereas that of the aligned PLGA fiber was 187 {+-} 121 nm. The pore size of aligned PLGA nanofibers (3.5 {+-} 1.1 {mu}m) was significantly lower than their respective random nanofibers (8.0 {+-} 2.0 {mu}m) (p < 0.05). However, the percentage porosity of both scaffolds was comparable (p > 0.05). The mass loss percentage and molecular weight loss percentage due to degradation was higher in random PLGA fibers when compared to aligned PLGA after 5 weeks (p < 0.05). The tensile strength and Young's modulus of random PLGA fibers were significantly higher than those of the aligned PLGA nanofibers (p < 0.05). Both random and longitudinally aligned scaffolds were used for the in vitro culture of Schwann cells. Morphology and cell proliferation results demonstrated that the aligned fibers assist the direction of Schwann cells and a better proliferation rate than their random fibers. The results confirmed that aligned nanofibers have better deformability, slow degradation, comparable porosity and orientation cues than random nanofibers. Hence the longitudinally aligned nanofibers may be ideal scaffolds for nerve regeneration.

Improving model construction of profile HMMs for remote homology detection through structural alignment

Directory of Open Access Journals (Sweden)

Zaverucha Gerson

2007-11-01

Full Text Available Abstract Background Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. Results We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. Conclusion We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

Improving model construction of profile HMMs for remote homology detection through structural alignment.

Science.gov (United States)

Bernardes, Juliana S; Dávila, Alberto M R; Costa, Vítor S; Zaverucha, Gerson

2007-11-09

Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

Structural change of cooper pairs in color superconductivity. Crossover from weak coupling to strong coupling

Energy Technology Data Exchange (ETDEWEB)

Abuki, Hiroaki; Hatsuda, Tetsuo [Tokyo Univ., Dept. of Physics, Tokyo (Japan); Itakura, Kazunori [Brookhaven National Laboratory, RIKEN BNL Research Center, Upton, NY (United States)

2002-09-01

The two-flavor color superconductivity is studied over a wide range of baryon density with a single model. We pay a special attention to the spatial-momentum dependence of the gap and to the spatial-structure of Cooper pairs. At extremely high baryon density ({approx}O(10{sup 10} {rho}{sub 0}) with {rho}{sub 0} being the normal nuclear matter density), our model becomes equivalent to the usual perturbative QCD treatment and the gap is shown to have a sharp peak near the Fermi surface due to the weak-coupling nature of QCD. On the other hand, the gap is a smooth function of the momentum at lower densities ({approx}O(10{sup 10} {rho}{sub 0})) due to strong color magnetic and electric interactions. To study the structural change of Cooper pairs from high density to lower density, quark correlation in the color superconductor is studied both in the momentum space and in the coordinate space. The size of the Cooper pair is shown to become comparable to the averaged inter-quark distance at low densities. Also, effects of the momentum-dependent running coupling and the antiquark pairing, which are both small at high density, are shown to be non-negligible at low densities. These features are highly contrasted to the standard BCS superconductivity in metals. (author)

Dispersion analysis of the Pn -Pn-1DG mixed finite element pair for atmospheric modelling

Science.gov (United States)

Melvin, Thomas

2018-02-01

Mixed finite element methods provide a generalisation of staggered grid finite difference methods with a framework to extend the method to high orders. The ability to generate a high order method is appealing for applications on the kind of quasi-uniform grids that are popular for atmospheric modelling, so that the method retains an acceptable level of accuracy even around special points in the grid. The dispersion properties of such schemes are important to study as they provide insight into the numerical adjustment to imbalance that is an important component in atmospheric modelling. This paper extends the recent analysis of the P2 - P1DG pair, that is a quadratic continuous and linear discontinuous finite element pair, to higher polynomial orders and also spectral element type pairs. In common with the previously studied element pair, and also with other schemes such as the spectral element and discontinuous Galerkin methods, increasing the polynomial order is found to provide a more accurate dispersion relation for the well resolved part of the spectrum but at the cost of a number of unphysical spectral gaps. The effects of these spectral gaps are investigated and shown to have a varying impact depending upon the width of the gap. Finally, the tensor product nature of the finite element spaces is exploited to extend the dispersion analysis into two-dimensions.

Conductance of Conjugated Molecular Wires: Length Dependence, Anchoring Groups, and Band Alignment

DEFF Research Database (Denmark)

Peng, Guowen; Strange, Mikkel; Thygesen, Kristian Sommer

2009-01-01

, is not solely determined by the intrinsic band gap of the molecular wire but also depends on the anchoring group. This is because the alignment of the metal Fermi level with respect to the molecular levels is controlled by charge transfer and interface dipoles which in turn are determined by the local chemistry...

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

Directory of Open Access Journals (Sweden)

Michal Brylinski

2014-09-01

Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

Measuring the distance between multiple sequence alignments.

Science.gov (United States)

Blackburne, Benjamin P; Whelan, Simon

2012-02-15

Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses. We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them. MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/.

Gap-Balancing versus Measured Resection Technique in Total Knee Arthroplasty: A Comparison Study.

Science.gov (United States)

Churchill, Jessica L; Khlopas, Anton; Sultan, Assem A; Harwin, Steven F; Mont, Michael A

2018-01-01

Proper femoral component alignment in the axial plane during total knee arthroplasty (TKA) depends on accurate bone cuts and soft tissue balancing. Two methods that are used to achieve this are "measured resection" and "gap balancing." However, a controversy exists as to which method is more accurate and leads to better outcomes. Therefore, the purpose of this study was to evaluate: (1) implant survivorship, (2) patient outcomes, (3) complications, and (4) radiographic analysis comparing patients who underwent TKA with either gap-balancing or measured resection techniques. A total of 214 consecutive patients (221 knees) underwent primary TKA by a single surgeon between 2011 and 2012. Component alignment was achieved by using measured resection in 116 knees and gap balancing was used in 105 knees. The patients had a mean age of 66 years (range, 44-86 years) and a mean body mass index of 32 kg/m 2 (range, 22-52 kg/m 2 ). Patient range-of-motion (ROM) and Knee Society (KS) function and pain scores, and radiographic assessment, were assessed preoperatively and postoperatively at ∼6 weeks, 3 months, 1 year, and then annually. The mean follow-up time was 3 years. A Kaplan-Meier's analysis was performed to calculate the survivorship. The aseptic survivorship was 98% in both the measured resection and gap-balancing groups. The mean ROM was not significantly different between the measured resection and gap-balancing groups (123 vs. 123 degrees, p  = 0.990). There were no significant differences between the two groups in terms of the KS function scores (86 vs. 85 points, p  = 0.829) or the KS pain scores (93 vs. 92 points, p  = 0.425). Otherwise, the radiographic evaluation at latest follow-up did not demonstrate any evidence of progressive radiolucencies or loosening, of any prosthesis. The results of this study found that at a mean follow-up of 3 years, both the measured resection and gap-balancing techniques achieved excellent survivorship and

GraphAlignment: Bayesian pairwise alignment of biological networks

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Kolář Michal

2012-11-01

Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates

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Sergei Kuchin

2011-03-01

Full Text Available Explaining base pairing is an important element in teaching undergraduate genetics. I propose a teaching approach that aims to close the gap between the mantra “A pairs with T, and G pairs with C” and the “intimidating” chemical diagrams. The approach offers a set of simple “shorthands” for the key bases that can be used to quickly deduce all canonical and wobble pairs that the students need to know. The approach can be further developed to analyze mutagenic mismatch pairing.

Gap solitons in a chain of split-ring resonator dimers

Energy Technology Data Exchange (ETDEWEB)

Cui, Wei-na, E-mail: cuiweinaa@163.com [Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094 (China); Li, Hong-xia, E-mail: hxli@njust.edu.cn [Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094 (China); Sun, Min [Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094 (China); Bu, Ling-bing [Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Key Laboratory for Aerosol-Cloud-Precipitation of China Meteorological Administration, Key Laboratory of Meteorological Disaster of Ministry of Education, Nanjing University of Information Science and Technology, Nanjing 210044 (China)

2017-06-21

Dynamics of a chain of split-ring resonator dimers with Kerr nonlinear interaction are investigated. A dimer is built as a pair of coupled split-ring resonators with different size. It is shown that the gap solitons with frequency lying in the gap exist due to the interaction of the discreteness and nonlinearity. Such localized structures are studied in the phase plane and analytical and numerical expressions are also obtained. - Highlights: • The coupling of the two modes is studied in the chain of split-ring resonator dimers with Kerr nonlinear interaction. • The evolution of the localized structures is studied in the phase plane. • This system supports gap solitons with the frequencies lying in the gap.

Precise synaptic efficacy alignment suggests potentiation dominated learning

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Christoph eHartmann

2016-01-01

Full Text Available Recent evidence suggests that parallel synapses from the same axonal branch onto the same dendritic branch have almost identical strength. It has been proposed that this alignment is only possible through learning rules that integrate activity over long time spans. However, learning mechanisms such as spike-timing-dependent plasticity (STDP are commonly assumed to be temporally local. Here, we propose that the combination of temporally local STDP and a multiplicative synaptic normalization mechanism is sufficient to explain the alignment of parallel synapses.To address this issue, we introduce three increasingly complex models: First, we model the idealized interaction of STDP and synaptic normalization in a single neuron as a simple stochastic process and derive analytically that the alignment effect can be described by a so-called Kesten process. From this we can derive that synaptic efficacy alignment requires potentiation-dominated learning regimes. We verify these conditions in a single-neuron model with independent spiking activities but more realistic synapses. As expected, we only observe synaptic efficacy alignment for long-term potentiation-biased STDP. Finally, we explore how well the findings transfer to recurrent neural networks where the learning mechanisms interact with the correlated activity of the network. We find that due to the self-reinforcing correlations in recurrent circuits under STDP, alignment occurs for both long-term potentiation- and depression-biased STDP, because the learning will be potentiation dominated in both cases due to the potentiating events induced by correlated activity. This is in line with recent results demonstrating a dominance of potentiation over depression during waking and normalization during sleep. This leads us to predict that individual spine pairs will be more similar in the morning than they are after sleep depriviation.In conclusion, we show that synaptic normalization in conjunction with

Two Influential Primate Classifications Logically Aligned.

Science.gov (United States)

Franz, Nico M; Pier, Naomi M; Reeder, Deeann M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-07-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments

Coupling of a single quantum emitter to end-to-end aligned silver nanowires

DEFF Research Database (Denmark)

Kumar, Shailesh; Huck, Alexander; Chen, Yuntian

2013-01-01

We report on the observation of coupling a single nitrogen vacancy (NV) center in a nanodiamond crystal to a propagating plasmonic mode of silver nanowires. The nanocrystal is placed either near the apex of a single silver nanowire or in the gap between two end-to-end aligned silver nanowires. We...

InP quantum dots embedded in GaP: Optical properties and carrier dynamics

International Nuclear Information System (INIS)

Hatami, F.; Masselink, W.T.; Schrottke, L.; Tomm, J.W.; Talalaev, V.; Kristukat, C.; Goni, A.R.

2003-01-01

The optical emission and dynamics of carriers in Stranski-Krastanow self-organized InP quantum dots embedded in a GaP matrix are studied. InP deposited on GaP (001) using gas-source molecular-beam epitaxy forms quantum dots for InP coverage greater than 1.8 monolayers. Strong photoluminescence from the quantum dots is observed up to room temperature at about 2 eV; photoluminescence from the two-dimensional InP wetting layer is measured at about 2.2 eV. Modeling based on the 'model-solid theory' indicates that the band alignment for the InP quantum dots is direct and type I. Furthermore, low-temperature time-resolved photoluminescence measurements indicate that the carrier lifetime in the quantum dots is about 2 ns, typical for type-I quantum dots. Pressure-dependent photoluminescence measurements provide further evidence for a type-I band alignment for InP/GaP quantum dots at normal pressure with the GaP X states lying about 30 meV higher than the Γ states in the InP quantum dots, but indicate that they become type II under hydrostatic pressures of about 1.2 GPa

Electrostatically Induced Carbon Nanotube Alignment for Polymer Composite Applications

Science.gov (United States)

Chapkin, Wesley Aaron

finding matches an electrostatic potential energy model for CNT rotation. Lastly, we investigate the effects of conductive carbon fibers on electrostatically induced alignment of CNTs within carbon fiber composites. The relative electric field strength throughout the composite is modeled using COMSOL Multiphysics. We show the ability to generate enhanced electric field gradients within the gaps between carbon fibers for various fiber orientations. Using polarized Raman spectroscopy, increased levels of CNT alignment are observed between carbon fiber tows, which is consistent with the modeled higher electric field strengths in these regions. These findings could potentially lead to the development of carbon fiber composites with CNT additions that selectively enhance the composite properties outside the carbon fiber interphase in the neat epoxy.

Paired quasars near NGC 2639: Evidence for quasars in superclusters

International Nuclear Information System (INIS)

Ford, H.; Ciardullo, R.; Harms, R.

1983-01-01

Arp found 10 quasars near a low-redshift galaxy 27' SSE of NGC 2639. Six of the quasars can be grouped into three redshift pairs which align across the anonymous galaxy. The large number of quasars and pairings could show an association with the low-redshift galaxy, or alternatively, might be due to superclusters seen along the line of sight. We tested the latter hypothesis by using deep, red-sensitive Lick 3 m prime focus plates to search for a supercluster associated with the z = 0.3 quasar pair. The plates show extended nebulosity associated with the quasar U10 (thetaapprox.7'', or 20 kpc at z = 0.3) and a richness class 1, Bautz-Morgan type III cluster 4' NW of U10. A spectrum of one the cluster's brightest galaxies gives z = 0.34, suggesting that the cluster and quasar are unassociated. We obtained spectra of eight of the quasars and find that (i) two of the quasars have very strong absorption shortward of Lyα, and (ii) two of Arp's redshifts (including one which Arp considered uncertain) are incorrect. Our redshifts break two of the redshift pairs, including the pair at z = 0.3. We use the redshift distribution of optically selected quasars to argue that the third pair has no statistical significance, and conclude that there is no basis for associating the quasars with the low-redshift anonymous galaxy. The disappearance of the redshift pairs vitiates the possibility of testing the paired-quasars-in-superclusters hypothesis in the NGC 2639 field

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez.

Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

Sequence comparison and phylogenetic analysis of core gene of ...

African Journals Online (AJOL)

STORAGESEVER

2010-07-19

Jul 19, 2010 ... and antisense primers, a single band of 573 base pairs .... Amino acid sequence alignment of Cluster I and Cluster II of phylogenetic tree. First ten sequences ... sequence weighting, postion-spiecific gap penalties and weight.

Angle alignment evokes perceived depth and illusory surfaces.

Science.gov (United States)

Shapley, Robert; Maertens, Marianne

2008-01-01

There is a distinct visual process that triggers the perception of illusory surfaces and contours along the intersections of aligned, zigzag line patterns. Such illusory contours and surfaces are qualitatively different from illusory contours of the Kanizsa type. The illusory contours and surfaces in this case are not the product of occlusion and do not imply occlusion of one surface by another. Rather, the aligned angles in the patterns are combined by the visual system into the perception of a fold or a 3-D corner, as of stairs on a staircase or a wall ending on a floor. The depth impression is ambiguous and reversible like the Necker cube. Such patterns were used by American Indian artists of the Akimel O'odham (Pima) tribe in basketry, and also by modern European and American artists like Josef Albers, Bridget Riley, Victor Vasarely, and Frank Stella. Our research aims to find out what manipulations of the visual image affect perceived depth in such patterns in order to learn about the perceptual mechanisms. Using paired comparisons, we find that human observers perceive depth in such patterns if, and only if, lines in adjacent regions of the patterns join to form angles, and also if, and only if, the angles are aligned precisely to be consistent with a fold or 3-D corner. The amount of perceived depth is graded, depending on the steepness and the density of angles in the aligned-angle pattern. The required precision of the alignment implies that early retinotopic visual cortical areas may be involved in this perceptual behavior, but the linkage of form with perceived depth suggests involvement of higher cortical areas as well.

Estimation of the contribution of gaps to tritium retention in the divertor of ITER

International Nuclear Information System (INIS)

Matveev, D; Kirschner, A; Litnovsky, A; Borodin, D; Samm, U; Schmid, K; Komm, M; Van Oost, G

2014-01-01

An estimation of the contribution of gaps to beryllium deposition and resulting tritium retention in the divertor of ITER is presented. Deposition of beryllium layers in gaps of the full tungsten divertor is simulated with the 3D-GAPS code. For gaps aligned along the poloidal direction, non-shaped and shaped solutions are compared. Plasma and impurity ion fluxes from Schmid (2008 Nucl. Fusion 48 105004) are used as input. Ion penetration into gaps is considered to be geometrical along magnetic field lines. The effect of realistic ion penetration into gaps is discussed. In total, gaps in the divertor are estimated to contribute about 0.3 mgT s −1 to the overall tritium retention dominated by toroidal gaps, which are not shaped. This amount corresponds to about 7800 ITER discharges up to the safety limit of 1 kg in-vessel tritium; excluding, however, tritium release during wall baking and retention at plasma-wetted and remote areas. (paper)

Application of monorail fixator for femoral gap nonunion

Directory of Open Access Journals (Sweden)

Agrawal Hemendra Kumar

2014-07-01

Full Text Available 【Abstract】Difficult femoral nonunion takes account of infective nonunion and aseptic gap nonunion. Limb length discrepancy and nonunion need to be tackled simultaneously. Conventionally Ilizarov ring fixator is in vogue but it has some limitations. To overcome these, monorail fixator is an effective alternative. Persistent good results can be obtained if we can get a perfect anatomical alignment and good regeneration. Key words: Femur; Ilizarov technique; External fixators

Effects of the particle-number projection on the isovector pairing energy

International Nuclear Information System (INIS)

Allal, N.H.; Fellah, M.; Oudih, M.R.; Benhamouda, N.

2006-01-01

The usual neutron-proton BCS wave function is simultaneously projected on both the good neutron and proton numbers using a discrete projection operator. The projected energy of the system is deduced as a limit of rapidly convergent sequence. It is numerically studied for the N=Z nuclei of which ''experimental'' pairing gaps may be deduced from the experimental odd-even mass differences. It then appears that the particle-number fluctuation effect is even more important than in the case of pairing between like-particles. (orig.)

Accurate and robust brain image alignment using boundary-based registration.

Science.gov (United States)

Greve, Douglas N; Fischl, Bruce

2009-10-15

The fine spatial scales of the structures in the human brain represent an enormous challenge to the successful integration of information from different images for both within- and between-subject analysis. While many algorithms to register image pairs from the same subject exist, visual inspection shows that their accuracy and robustness to be suspect, particularly when there are strong intensity gradients and/or only part of the brain is imaged. This paper introduces a new algorithm called Boundary-Based Registration, or BBR. The novelty of BBR is that it treats the two images very differently. The reference image must be of sufficient resolution and quality to extract surfaces that separate tissue types. The input image is then aligned to the reference by maximizing the intensity gradient across tissue boundaries. Several lower quality images can be aligned through their alignment with the reference. Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial-brain images to whole-brain images, a domain in which existing registration algorithms frequently fail. Even in the limit of registering a single slice, we show the BBR results to be robust and accurate.

Importance of interlayer pair tunneling: A variational perspective

International Nuclear Information System (INIS)

Medhi, Amal; Basu, Saurabh

2011-01-01

We study the effect of interlayer pair tunneling in a bilayer superconductor where each layer is described by a two dimensional t-J model and the two layers are connected by the Josephson pair tunneling term. We study this model using a grand canonical variational Monte Carlo (GVMC) method, for which we develop a new algorithm to perform Monte Carlo simulation of a system with fluctuating particle number. The variational wavefunction is taken to be the product of two Gutzwiller projected d-wave BCS wavefunctions with variable particle densities, one for each layer. We calculate the energy of the above state as a function of the d-wave superconducting gap parameter, Δ. We find that the interlayer pair tunneling energy, E perpendicular shows interesting variation with Δ. E perpendicular tends to enhance the optimal value of Δ, thereby the superconducting pairing. However the magnitude of the tunneling energy is found to be too small to have any appreciable effect on the physical properties. While the result is supported by early experiments and hence may appear known to the community, the current work presents a new approach to the problem and confirms the diminished role of interlayer pair tunneling by directly calculating its contribution to superconducting condensation energy.

An efficient multi-resolution GA approach to dental image alignment

Science.gov (United States)

Nassar, Diaa Eldin; Ogirala, Mythili; Adjeroh, Donald; Ammar, Hany

2006-02-01

Automating the process of postmortem identification of individuals using dental records is receiving an increased attention in forensic science, especially with the large volume of victims encountered in mass disasters. Dental radiograph alignment is a key step required for automating the dental identification process. In this paper, we address the problem of dental radiograph alignment using a Multi-Resolution Genetic Algorithm (MR-GA) approach. We use location and orientation information of edge points as features; we assume that affine transformations suffice to restore geometric discrepancies between two images of a tooth, we efficiently search the 6D space of affine parameters using GA progressively across multi-resolution image versions, and we use a Hausdorff distance measure to compute the similarity between a reference tooth and a query tooth subject to a possible alignment transform. Testing results based on 52 teeth-pair images suggest that our algorithm converges to reasonable solutions in more than 85% of the test cases, with most of the error in the remaining cases due to excessive misalignments.

Energy level alignment at hybridized organic-metal interfaces from a GW projection approach

Science.gov (United States)

Chen, Yifeng; Tamblyn, Isaac; Quek, Su Ying

Energy level alignments at organic-metal interfaces are of profound importance in numerous (opto)electronic applications. Standard density functional theory (DFT) calculations generally give incorrect energy level alignments and missing long-range polarization effects. Previous efforts to address this problem using the many-electron GW method have focused on physisorbed systems where hybridization effects are insignificant. Here, we use state-of-the-art GW methods to predict the level alignment at the amine-Au interface, where molecular levels do hybridize with metallic states. This non-trivial hybridization implies that DFT result is a poor approximation to the quasiparticle states. However, we find that the self-energy operator is approximately diagonal in the molecular basis, allowing us to use a projection approach to predict the level alignments. Our results indicate that the metallic substrate reduces the HOMO-LUMO gap by 3.5 4.0 eV, depending on the molecular coverage/presence of Au adatoms. Our GW results are further compared with those of a simple image charge model that describes the level alignment in physisorbed systems. Syq and YC acknowledge Grant NRF-NRFF2013-07 and the medium-sized centre program from the National Research Foundation, Singapore.

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

Directory of Open Access Journals (Sweden)

Daniels Noah M

2012-10-01

Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

Size and strain tunable band alignment of black-blue phosphorene lateral heterostructures.

Science.gov (United States)

Li, Yan; Ma, Fei

2017-05-17

Single-element lateral heterostructures composed of black and blue phosphorene are not only free from lattice mismatch but also exhibit rich physical properties related to the seamlessly stitched interfaces, providing the building blocks for designing atomically thin devices. Using first-principles calculations, we investigate the influence of interface structure, size effect and strain engineering on the electronic structure, effective masses and band alignment of black-blue phosphorene lateral heterostructures. The lateral heterostructure with an octatomic-ring interface presents a strong metallic feature due to the interface states, while a metal-semiconductor transition takes place in the system with a hexatomic-ring interface upon hydrogen passivation. Following a reciprocal scaling law, the band gap is tuned in a wide energy range by synchronously increasing the widths of black and blue phosphorene or by only widening that of black phosphorene. Moreover, type-II band alignment is observed in the width ranges of 2.0-3.1 nm and 3.7-4.2 nm, out of which it is type-I. However, the band gap and effective masses show small changes if only the width of blue phosphorene is altered. When the lateral heterostructure is tensile loaded, the effective mass ratio of hole to electron is enlarged by an order of magnitude at a strain of 4% along the zigzag direction. Meanwhile, the band alignment undergoes a crossover from type-I to type-II at a strain of 2%, facilitating efficient electron-hole separation for light detection and harvesting.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez

2010-01-01

The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

Envisaging quantum transport phenomenon in a muddled base pair of DNA

Science.gov (United States)

Vohra, Rajan; Sawhney, Ravinder Singh

2018-05-01

The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au-AT base pair-Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T( E) and HOMO-LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.

S-pairing in neutron matter: I. Correlated basis function theory

International Nuclear Information System (INIS)

Fabrocini, Adelchi; Fantoni, Stefano; Illarionov, Alexey Yu.; Schmidt, Kevin E.

2008-01-01

S-wave pairing in neutron matter is studied within an extension of correlated basis function (CBF) theory to include the strong, short range spatial correlations due to realistic nuclear forces and the pairing correlations of the Bardeen, Cooper and Schrieffer (BCS) approach. The correlation operator contains central as well as tensor components. The correlated BCS scheme of [S. Fantoni, Nucl. Phys. A 363 (1981) 381], developed for simple scalar correlations, is generalized to this more realistic case. The energy of the correlated pair condensed phase of neutron matter is evaluated at the two-body order of the cluster expansion, but considering the one-body density and the corresponding energy vertex corrections at the first order of the Power Series expansion. Based on these approximations, we have derived a system of Euler equations for the correlation factors and for the BCS amplitudes, resulting in correlated nonlinear gap equations, formally close to the standard BCS ones. These equations have been solved for the momentum independent part of several realistic potentials (Reid, Argonne v 14 and Argonne v 8 ' ) to stress the role of the tensor correlations and of the many-body effects. Simple Jastrow correlations and/or the lack of the density corrections enhance the gap with respect to uncorrelated BCS, whereas it is reduced according to the strength of the tensor interaction and following the inclusion of many-body contributions

Pairing correlations. II. Microscopic analysis of odd-even mass staggering in nuclei

International Nuclear Information System (INIS)

Duguet, T.; Bonche, P.; Heenen, P.-H.; Meyer, J.

2002-01-01

The odd-even mass staggering in nuclei is analyzed in the context of self-consistent mean-field calculations, for spherical as well as for deformed nuclei. For these nuclei, the respective merits of the energy differences Δ (3) and Δ (5) to extract both the pairing gap and the time-reversal symmetry breaking effect at the same time are extensively discussed. The usual mass formula Δ (3) is shown to contain additional mean-field contributions when realistic pairing is used in the calculation. A simple tool is proposed in order to remove the time-reversal symmetry breaking effects from Δ (5) . Extended comparisons with the odd-even mass staggering obtained in the zero-pairing limit (schematic model and self-consistent calculations) show the nonperturbative contribution of pairing correlations on this observable

Rotation of intramedullary alignment rods affects distal femoral cutting plane in total knee arthroplasty.

Science.gov (United States)

Maderbacher, Günther; Matussek, Jan; Keshmiri, Armin; Greimel, Felix; Baier, Clemens; Grifka, Joachim; Maderbacher, Hermann

2018-02-17

Intramedullary rods are widely used to align the distal femoral cut in total knee arthroplasty. We hypothesised that both coronal (varus/valgus) and sagittal (extension/flexion) cutting plane are affected by rotational changes of intramedullary femoral alignment guides. Distal femoral cuts using intramedullary alignment rods were simulated by means of a computer-aided engineering software in 4°, 6°, 8°, 10°, and 12° of valgus in relation to the femoral anatomical axis and 4° extension, neutral, as well as 4°, 8°, and 12° of flexion in relation to the femoral mechanical axis. This reflects the different angles between anatomical and mechanical axis in coronal and sagittal planes. To assess the influence of rotation of the alignment guide on the effective distal femoral cutting plane, all combinations were simulated with the rod gradually aligned from 40° of external to 40° of internal rotation. Rotational changes of the distal femoral alignment guides affect both the coronal and sagittal cutting planes. When alignment rods are intruded neutrally with regards to sagittal alignment, external rotation causes flexion, while internal rotation causes extension of the sagittal cutting plane. Simultaneously the coronal effect (valgus) decreases resulting in an increased varus of the cutting plane. However, when alignment rods are intruded in extension or flexion partly contradictory effects are observed. Generally the effect increases with the degree of valgus preset, rotation and flexion. As incorrect rotation of intramedullary alignment guides for distal femoral cuts causes significant cutting errors, exact rotational alignment is crucial. Coronal cutting errors in the distal femoral plane might result in overall leg malalignment, asymmetric extension gaps and subsequent sagittal cutting errors.

Magnet-assisted device-level alignment for the fabrication of membrane-sandwiched polydimethylsiloxane microfluidic devices

International Nuclear Information System (INIS)

Lu, J-C; Liao, W-H; Tung, Y-C

2012-01-01

Polydimethylsiloxane (PDMS) microfluidic device is one of the most essential techniques that advance microfluidics research in recent decades. PDMS is broadly exploited to construct microfluidic devices due to its unique and advantageous material properties. To realize more functionalities, PDMS microfluidic devices with multi-layer architectures, especially those with sandwiched membranes, have been developed for various applications. However, existing alignment methods for device fabrication are mainly based on manual observations, which are time consuming, inaccurate and inconsistent. This paper develops a magnet-assisted alignment method to enhance device-level alignment accuracy and precision without complicated fabrication processes. In the developed alignment method, magnets are embedded into PDMS layers at the corners of the device. The paired magnets are arranged in symmetric positions at each PDMS layer, and the magnetic attraction force automatically pulls the PDMS layers into the aligned position during assembly. This paper also applies the method to construct a practical microfluidic device, a tunable chaotic micromixer. The results demonstrate the successful operation of the device without failure, which suggests the accurate alignment and reliable bonding achieved by the method. Consequently, the fabrication method developed in this paper is promising to be exploited to construct various membrane-sandwiched PDMS microfluidic devices with more integrated functionalities to advance microfluidics research. (paper)

Photon-pair generation in nonlinear metal-dielectric one-dimensional photonic structures

Czech Academy of Sciences Publication Activity Database

Javůrek, D.; Svozilík, J.; Peřina ml., Jan

2014-01-01

Roč. 90, č. 5 (2014), "053813-1"-"053813-14" ISSN 1050-2947 R&D Projects: GA ČR GAP205/12/0382 Institutional support: RVO:68378271 Keywords : photon pairs * nonlinear metal-dielectric * one-dimensional photonic structures Subject RIV: BH - Optics, Masers, Lasers Impact factor: 2.808, year: 2014

Self-aligned metallization on organic semiconductor through 3D dual-layer thermal nanoimprint

International Nuclear Information System (INIS)

Jung, Y; Cheng, X

2014-01-01

High-resolution patterning of metal structures on organic semiconductors is important to the realization of high-performance organic transistors for organic integrated circuit applications. The traditional shadow mask technique has a limited resolution, precluding sub-micron metal structures on organic semiconductors. Thus organic transistors cannot benefit from scaling into the deep sub-micron region to improve their dc and ac performances. In this work, we report an efficient multiple-level metallization on poly (3-hexylthiophene) (P3HT) with a deep sub-micron lateral gap. By using a 3D nanoimprint mold in a dual-layer thermal nanoimprint process, we achieved self-aligned two-level metallization on P3HT. The 3D dual-layer thermal nanoimprint enables the first metal patterns to have suspending side-wings that can clearly define a distance from the second metal patterns. Isotropic and anisotropic side-wing structures can be fabricated through two different schemes. The process based on isotropic side-wings achieves a lateral-gap in the order of 100 nm (scheme 1). A gap of 60 nm can be achieved from the process with anisotropic side-wings (scheme 2). Because of the capability of nanoscale metal patterning on organic semiconductors with high overlay accuracy, this self-aligned metallization technique can be utilized to fabricate high-performance organic metal semiconductor field-effect transistor. (paper)

Shape evolution in 76,78Kr nuclei at high spins in tilted axis ...

Indian Academy of Sciences (India)

band with J = 20–30 lying below the observed ground band is predicted. ... a given value of the quadrupole deformation parameter and pairing gaps for the ... about the oblate symmetry axis, i.e., the spin generated by rotation alignment of.

Optical study of the band structure of wurtzite GaP nanowires

OpenAIRE

Assali, S.; Greil, J.; Zardo, I.; Belabbes, A.; de Moor, M.W.A.; Kölling, S.; Koenraad, P.M.; Bechstedt, F.; Bakkers, E.P.A.M.; Haverkort, J.E.M.

2016-01-01

We investigated the optical properties of wurtzite (WZ) GaP nanowires by performing photoluminescence (PL) and time-resolved PL measurements in the temperature range from 4 K to 300 K, together with atom probe tomography to identify residual impurities in the nanowires. At low temperature, the WZ GaP luminescence shows donor-acceptor pair emission at 2.115 eV and 2.088 eV, and Burstein-Moss band-filling continuum between 2.180 and 2.253 eV, resulting in a direct band gap above 2.170 eV. Sharp...

Structural and electronic properties of GaAs and GaP semiconductors

Energy Technology Data Exchange (ETDEWEB)

Rani, Anita [Guru Nanak College for girls, Sri Muktsar Sahib, Punjab (India); Kumar, Ranjan [Department of Physics, Panjab University, Chandigarh-160014 (India)

2015-05-15

The Structural and Electronic properties of Zinc Blende phase of GaAs and GaP compounds are studied using self consistent SIESTA-code, pseudopotentials and Density Functional Theory (DFT) in Local Density Approximation (LDA). The Lattice Constant, Equillibrium Volume, Cohesive Energy per pair, Compressibility and Band Gap are calculated. The band gaps calcultated with DFT using LDA is smaller than the experimental values. The P-V data fitted to third order Birch Murnaghan equation of state provide the Bulk Modulus and its pressure derivatives. Our Structural and Electronic properties estimations are in agreement with available experimental and theoretical data.

Transition from Sign-Reversed to Sign-Preserved Cooper-Pairing Symmetry in Sulfur-Doped Iron Selenide Superconductors.

Science.gov (United States)

Wang, Qisi; Park, J T; Feng, Yu; Shen, Yao; Hao, Yiqing; Pan, Bingying; Lynn, J W; Ivanov, A; Chi, Songxue; Matsuda, M; Cao, Huibo; Birgeneau, R J; Efremov, D V; Zhao, Jun

2016-05-13

An essential step toward elucidating the mechanism of superconductivity is to determine the sign or phase of the superconducting order parameter, as it is closely related to the pairing interaction. In conventional superconductors, the electron-phonon interaction induces attraction between electrons near the Fermi energy and results in a sign-preserved s-wave pairing. For high-temperature superconductors, including cuprates and iron-based superconductors, prevalent weak coupling theories suggest that the electron pairing is mediated by spin fluctuations which lead to repulsive interactions, and therefore that a sign-reversed pairing with an s_{±} or d-wave symmetry is favored. Here, by using magnetic neutron scattering, a phase sensitive probe of the superconducting gap, we report the observation of a transition from the sign-reversed to sign-preserved Cooper-pairing symmetry with insignificant changes in T_{c} in the S-doped iron selenide superconductors K_{x}Fe_{2-y}(Se_{1-z}S_{z})_{2}. We show that a rather sharp magnetic resonant mode well below the superconducting gap (2Δ) in the undoped sample (z=0) is replaced by a broad hump structure above 2Δ under 50% S doping. These results cannot be readily explained by simple spin fluctuation-exchange pairing theories and, therefore, multiple pairing channels are required to describe superconductivity in this system. Our findings may also yield a simple explanation for the sometimes contradictory data on the sign of the superconducting order parameter in iron-based materials.

The importance of triaxial shapes in spin aligned configurations in the A = 170-180 mass region

International Nuclear Information System (INIS)

Bengtsson, R.

1990-01-01

Deformations determined from total routhian surfaces (TRS) for the yrast states of even-even isotopes of W, Os, and Pt are presented. The calculated deformations imply a number of specific features for the yrast line, resulting from deformation changes and the alignment of specific pairs of quasiparticles. The triaxial shapes predicted from the TRS are important for determining the character of the aligning particles as well as for making a correct interpretation of the strength of the interaction between crossing bands and the bandcrossing frequencies. 19 refs., 9 figs

Influence of solvent and salt concentration on the alignment properties of acrylamide copolymer gels for the measurement of RDC.

Science.gov (United States)

Trigo-Mouriño, Pablo; Navarro-Vázquez, Armando; Sánchez-Pedregal, Víctor M

2012-12-01

The dependence of molecular alignment with solvent nature and salt concentration has been investigated for mechanically stretched polyacrylamide copolymer gels. Residual dipolar couplings (RDCs) were recorded for D(2)O, DMSO-d(6), and DMSO-d(6)/D(2)O solutions containing different proportions of the solvents and different sodium chloride concentrations. Alignment tensors were determined by fitting the experimental RDCs to the DFT-computed structure of N-methylcodeinium ion. Analysis of the tensors shows that the degree of alignment decreases with the proportion of DMSO-d(6) as well as with the concentration of sodium chloride, most likely due to enhanced ion-pair aggregation. Furthermore, rotation of the alignment tensor is observed when increasing the salt concentration. Copyright © 2012 John Wiley & Sons, Ltd.

Initial experience with megavoltage (MV) CT guidance for daily prostate alignments

International Nuclear Information System (INIS)

Langen, Katja M.; Zhang Yashan; Andrews, Rhonda D.; Hurley, Monica E.; Meeks, Sanford L.; Poole, Darrell O.; Willoughby, Twyla R.; Kupelian, Patrick A.

2005-01-01

Purpose: The on-board megavoltage (MV) computed tomography (CT) capabilities of a TomoTherapy Hi*ART unit were used to obtain daily MVCT images of prostate cancer patients. For patient alignment the daily MVCT image needs to be registered with the planning CT image to calculate couch shifts. Three manual techniques of registering the MVCT images with the planning kilovoltage (kV) CT images were evaluated. The techniques are based on visual alignment of (1) fiducial prostate markers (2) CT anatomy, and (3) kVCT contours. Methods and Materials: One hundred and twelve alignments from 3 patients were available for analysis. The radiation therapists visually registered the MVCT images with the planning kVCT images based on fiducial markers for actual patient alignment. Retrospectively, the therapists registered each image set using anatomy and contour-based techniques. In addition to the therapists, a physician retrospectively registered each image set based on each of the three techniques. For each MVCT to kVCT image pair a reference alignment was computed from the center-of-mass (COM) of the three fiducial markers. All registration results were compared with these reference alignments. The physician's image registrations were compared with the radiation therapists' registrations to assess the user variability of the different techniques. Results: The marker-based registration results agree best with the reference alignments, while the contour-based registrations show the least degree of agreement. Using anatomy and contour-based registrations, the radiation therapist's alignments differed by ≥ 3 mm from the reference alignments in 24%, 33%, and 3% and 55%, 48%, and 21% of all registrations in the anterior-posterior, superior-inferior, and lateral directions, respectively. The respective values for the marker-based alignments were 3%, 6%, and 3%. The physician's registrations showed the same general trend. The marker-based registrations showed the least amount of

Gaps between jets in hadronic collisions

Czech Academy of Sciences Publication Activity Database

Kepka, Oldřich; Marquet, C.; Royon, C.

2011-01-01

Roč. 83, č. 3 (2011), 034036/1-034036/7 ISSN 1550-7998 R&D Projects: GA MŠk LC527; GA MŠk LA08015; GA MŠk LA08032 Institutional research plan: CEZ:AV0Z10100502 Keywords : pp inclusive reaction * anti-p p annihilation * jet pair production * rapidity gap * quantum chromodynamics perturbation theory * color singlet Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 4.558, year: 2011

Measurement of Coherent Emission and Linear Polarization of Photons by Electrons in the Strong Fields of Aligned Crystals

CERN Document Server

Apyan, A.; Badelek, B.; Ballestrero, S.; Biino, C.; Birol, I.; Cenci, P.; Connell, S.H.; Eichblatt, S.; Fonseca, T.; Freund, A.; Gorini, B.; Groess, R.; Ispirian, K.; Ketel, T.J.; Kononets, Yu.V.; Lopez, A.; Mangiarotti, A.; van Rens, B.; Sellschop, J.P.F.; Shieh, M.; Sona, P.; Strakhovenko, V.; Uggerhoj, E.; Uggerhj, Ulrik Ingerslev; Unel, G.; Velasco, M.; Vilakazi, Z.Z.; Wessely, O.; Kononets, Yu.V.

2004-01-01

We present new results regarding the features of high energy photon emission by an electron beam of 178 GeV penetrating a 1.5 cm thick single Si crystal aligned at the Strings-Of-Strings (SOS) orientation. This concerns a special case of coherent bremsstrahlung where the electron interacts with the strong fields of successive atomic strings in a plane and for which the largest enhancement of the highest energy photons is expected. The polarization of the resulting photon beam was measured by the asymmetry of electron-positron pair production in an aligned diamond crystal analyzer. By the selection of a single pair the energy and the polarization of individual photons could be measured in an the environment of multiple photons produced in the radiator crystal. Photons in the high energy region show less than 20% linear polarization at the 90% confidence level.

Limitations of the dual voltage clamp method in assaying conductance and kinetics of gap junction channels

NARCIS (Netherlands)

Wilders, R.; Jongsma, H. J.

1992-01-01

The electrical properties of gap junctions in cell pairs are usually studied by means of the dual voltage clamp method. The voltage across the junctional channels, however, cannot be controlled adequately due to an artificial resistance and a natural resistance, both connected in series with the gap

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez

2010-01-01

Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

Linear to Circular Polarisation Conversion using Birefringent Properties of Aligned Crystals for Multi-GeV Photons

CERN Document Server

Apyan, A.; Badelek, B.; Ballestrero, S.; Biino, C.; Birol, I.; Cenci, P.; Connell, S.H.; Eichblatt, S.; Fonseca, T.; Freund, A.; Gorini, B.; Groess, R.; Ispirian, K.; Ketel, T.J.; Kononets, Yu.V.; Lopez, A.; Mangiarotti, A.; van Rens, B.; Sellschop, J.P.F.; Shieh, M.; Sona, P.; Strakhovenko, V.; Uggerhoj, E.; Uggerhj, Ulrik Ingerslev; Unel, G.; Velasco, M.; Vilakazi, Z.Z.; Wessely, O.; Kononets, Yu.V.

2003-01-01

We present the first experimental results on the use of a thick aligned Si crystal acting as a quarter wave plate to induce a degree of circular polarisation in a high energy linearly polarised photon beam. The linearly polarised photon beam is produced from coherent bremsstrahlung radiation by 178 GeV unpolarised electrons incident on an aligned Si crystal, acting as a radiator. The linear polarisation of the photon beam is characterised by measuring the asymmetry in electron-positron pair production in a Ge crystal, for different crystal orientations. The Ge crystal therefore acts as an analyser. The birefringence phenomenon, which converts the linear polarisation to circular polarisation, is observed by letting the linearly polarised photons beam pass through a thick Si quarter wave plate crystal, and then measuring the asymmetry in electron-positron pair production again for a selection of relative angles between the crystallographic planes of the radiator, analyser and quarter wave plate. The systematics...

A finite range pairing force for density functional theory in superfluid nuclei

International Nuclear Information System (INIS)

Tian, Y.; Ma, Z.Y.; Ring, P.

2009-01-01

The problem of pairing in the 1 S 0 channel of finite nuclei is revisited. In nuclear matter forces of separable form can be adjusted to the bare nuclear force, to any phenomenological pairing interaction such as the Gogny force or to exact solutions of the gap equation. In finite nuclei, because of translational invariance, such forces are no longer separable. Using well-known techniques of Talmi and Moshinsky we expand the matrix elements in a series of separable terms, which converges quickly preserving translational invariance and finite range. In this way the complicated problem of a cut-off at large momenta or energies inherent in other separable or zero range pairing forces is avoided. Applications in the framework of the relativistic Hartree-Bogoliubov approach show that the pairing properties are depicted on almost the same footing as by the original pairing interaction not only in nuclear matter, but also in finite nuclei. This simple separable force can be easily applied for the investigation of pairing properties in nuclei far from stability as well as for further investigations going beyond mean field theory.

Band alignment of two-dimensional metal monochalcogenides MXs (M=Ga,In; X=S,Se,Te

Directory of Open Access Journals (Sweden)

Huazheng Sun

2017-09-01

Full Text Available Monolayer metal monochalcogenides MXs (M=Ga,In; X=S,Se,Te form a new class of two-dimensional semiconductors with indirect band gaps, and their band alignment information is investigated via first principles calculations. The dependence of band gap, valence-band maximum, conduction band minimum, and charge transfer on the M or X element has been obtained and can be understood from the orbital analysis of the band edges. Potential applications of metal monochalcogenides to design van der Waals heterostructures and catalyse the photo-splitting reaction of water have been discussed.

Twisted injectivity in projected entangled pair states and the classification of quantum phases

Energy Technology Data Exchange (ETDEWEB)

Buerschaper, Oliver, E-mail: obuerschaper@perimeterinstitute.ca

2014-12-15

We introduce a class of projected entangled pair states (PEPS) which is based on a group symmetry twisted by a 3-cocycle of the group. This twisted symmetry is expressed as a matrix product operator (MPO) with bond dimension greater than 1 and acts on the virtual boundary of a PEPS tensor. We show that it gives rise to a new standard form for PEPS from which we construct a family of local Hamiltonians which are gapped, frustration-free and include fixed points of the renormalization group flow. Based on this insight, we advance the classification of 2D gapped quantum spin systems by showing how this new standard form for PEPS determines the emergent topological order of these local Hamiltonians. Specifically, we identify their universality class as DIJKGRAAF–WITTEN topological quantum field theory (TQFT). - Highlights: • We introduce a new standard form for projected entangled pair states via a twisted group symmetry which is given by nontrivial matrix product operators. • We construct a large family of gapped, frustration-free Hamiltonians in two dimensions from this new standard form. • We rigorously show how this new standard form for low energy states determines the emergent topological order.

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

Science.gov (United States)

Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

2018-01-01

Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

Effect of anitiferromagnetism on superconducting gap of cuprates

International Nuclear Information System (INIS)

Rout, G.C.; Panda, B.N.; Bishoyi, K.C.

2000-01-01

The interplay between superconductivity (SC) and antiferromagnetism (AF) is studied in strongly correlated systems: R 2-x M x CuO 4 (R = Nd, La, Pr, Gd; M = Sr, Ge). It is assumed that superconductivity arises due to BCS pairing mechanism in presence of AF in Cu lattices of Cu-O planes. Temperature dependence of SC gap as well as staggered magnetic field are calculated analytically and solved self-consistently with respect to half-filled band situation for different model parameters λ 1 , and λ 2 being SC and AF coupling parameters respectively. The SC gap is studied in the coexistent phase of SC and AFM. (author)

Energy level alignment at C{sub 60}/DTDCTB/PEDOT:PSS interfaces in organic photovoltaics

Energy Technology Data Exchange (ETDEWEB)

Yoo, Jisu; Jung, Kwanwook; Jeong, Junkyeong; Hyun, Gyeongho [Institute of Physics and Applied Physics, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722 (Korea, Republic of); Lee, Hyunbok, E-mail: hyunbok@kangwon.ac.kr [Department of Physics, Kangwon National University, Chuncheon-si, Gangwon-do 24341 (Korea, Republic of); Yi, Yeonjin, E-mail: yeonjin@yonsei.ac.kr [Institute of Physics and Applied Physics, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722 (Korea, Republic of)

2017-04-30

Highlights: • The interfacial energy level alignment of C{sub 60}/DTDCTB/PEDOT:PSS was determined via in situ UPS and IPES measurements. • A large photovoltaic gap of 1.30 eV was evaluated between the DTDCTB donor and C{sub 60} acceptor. • A low hole extraction barrier of 0.42 eV from DTDCTB to PEDOT:PSS was evaluated. • The excellent electronic properties of DTDCTB with a narrow band gap were the source of its high OPV power conversion efficiencies. - Abstract: The electronic structure of a narrow band gap small molecule ditolylaminothienyl–benzothiadiazole–dicyanovinylene (DTDCTB), possessing a donor-acceptor-acceptor configuration, was investigated with regard to its application as an efficient donor material in organic photovoltaics (OPVs). The interfacial orbital alignment of C{sub 60}/DTDCTB/poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) was determined using in situ ultraviolet photoelectron and inverse photoelectron spectroscopic methods. The ionization energy and electron affinity values of DTDCTB were measured to be 5.27 eV and 3.65 eV, respectively, and thus a very small transport gap of 1.62 eV was evaluated. Large band bending of DTDCTB on PEDOT:PSS was observed, resulting in a low hole extraction barrier. Additionally, the photovoltaic gap between the highest occupied molecular orbital level of the DTDCTB donor and the lowest unoccupied molecular orbital level of the C{sub 60} acceptor was estimated to be 1.30 eV, which is known to be the theoretical maximum open-circuit voltage in OPVs employing the C{sub 60}/DTDCTB active layer. The unique electronic structures of DTDCTB contributed toward the recently reported excellent power conversion efficiencies of OPVs containing a DTDCTB donor material.

Implementation of large area CMOS image sensor module using the precision align inspection

International Nuclear Information System (INIS)

Kim, Byoung Wook; Kim, Toung Ju; Ryu, Cheol Woo; Lee, Kyung Yong; Kim, Jin Soo; Kim, Myung Soo; Cho, Gyu Seong

2014-01-01

This paper describes a large area CMOS image sensor module Implementation using the precision align inspection program. This work is needed because wafer cutting system does not always have high precision. The program check more than 8 point of sensor edges and align sensors with moving table. The size of a 2×1 butted CMOS image sensor module which except for the size of PCB is 170 mm×170 mm. And the pixel size is 55 μm×55 μm and the number of pixels is 3,072×3,072. The gap between the two CMOS image sensor module was arranged in less than one pixel size

Implementation of large area CMOS image sensor module using the precision align inspection

Energy Technology Data Exchange (ETDEWEB)

Kim, Byoung Wook; Kim, Toung Ju; Ryu, Cheol Woo [Radiation Imaging Technology Center, JBTP, Iksan (Korea, Republic of); Lee, Kyung Yong; Kim, Jin Soo [Nano Sol-Tech INC., Iksan (Korea, Republic of); Kim, Myung Soo; Cho, Gyu Seong [Dept. of Nuclear and Quantum Engineering, KAIST, Daejeon (Korea, Republic of)

2014-12-15

This paper describes a large area CMOS image sensor module Implementation using the precision align inspection program. This work is needed because wafer cutting system does not always have high precision. The program check more than 8 point of sensor edges and align sensors with moving table. The size of a 2×1 butted CMOS image sensor module which except for the size of PCB is 170 mm×170 mm. And the pixel size is 55 μm×55 μm and the number of pixels is 3,072×3,072. The gap between the two CMOS image sensor module was arranged in less than one pixel size.

Role of the Band Gap for the Interaction Energy of Coadsorbed Fragments

DEFF Research Database (Denmark)

Castelli, Ivano Eligio; Man, Isabela-Costinela; Soriga, Stefan-Gabriel

2017-01-01

on semiconductors. We propose here a correlation between the cooperative interaction energy, i.e., the energy difference between the adsorption energies of coadsorbed electron donor–acceptor pair and isolated fragments and the band gap of the clean oxide surface. We demonstrate this effect for a number of oxides...... and donor–acceptor pairs and explain it with the shift in the Fermi level before and after the adsorption. The conclusion is that the adsorption of acceptor–donor pairs is considerably more favorable compared to unpaired fragments,and this energy difference is approximately equal to the value of the band...

MUON DETECTORS: ALIGNMENT

CERN Multimedia

Z. Szillasi and G. Gomez.

2013-01-01

When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

Energy Technology Data Exchange (ETDEWEB)

Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

2015-11-01

Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

Layer-dependent band alignment and work function of few-layer phosphorene.

Science.gov (United States)

Cai, Yongqing; Zhang, Gang; Zhang, Yong-Wei

2014-10-20

Using first-principles calculations, we study the electronic properties of few-layer phosphorene focusing on layer-dependent behavior of band gap, work function band alignment and carrier effective mass. It is found that few-layer phosphorene shows a robust direct band gap character, and its band gap decreases with the number of layers following a power law. The work function decreases rapidly from monolayer (5.16 eV) to trilayer (4.56 eV), and then slowly upon further increasing the layer number. Compared to monolayer phosphorene, there is a drastic decrease of hole effective mass along the ridge (zigzag) direction for bilayer phosphorene, indicating a strong interlayer coupling and screening effect. Our study suggests that 1). Few-layer phosphorene with a layer-dependent band gap and a robust direct band gap character is promising for efficient solar energy harvest. 2). Few-layer phosphorene outperforms monolayer counterpart in terms of a lighter carrier effective mass, a higher carrier density and a weaker scattering due to enhanced screening. 3). The layer-dependent band edges and work functions of few-layer phosphorene allow for modification of Schottky barrier with enhanced carrier injection efficiency. It is expected that few-layer phosphorene will present abundant opportunities for a plethora of new electronic applications.

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

Energy Technology Data Exchange (ETDEWEB)

Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha; Luo, Shujun; Schroth, Gary P.; Rokhsar, Daniel S.; Salzberg, Steven L.

2011-08-18

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ~280 bp or ~3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.

RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)

Czech Academy of Sciences Publication Activity Database

Réblová, Martina; Réblová, K.

2013-01-01

Roč. 12, č. 2 (2013), s. 305-319 ISSN 1617-416X R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 Keywords : 2D structure * 2D mask * alignment Subject RIV: EF - Botanics Impact factor: 1.543, year: 2013

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez and J. Pivarski

2011-01-01

Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

MUON DETECTORS: ALIGNMENT

CERN Multimedia

Gervasio Gomez

The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

Nonmagnetic impurity in the spin-gap state

International Nuclear Information System (INIS)

Nagaosa, N.; Ng, T.

1995-01-01

The effects of nonmagnetic strong scatterers (unitary limit) on magnetic and transport properties are studied for resonating-valence-bond states in both the slave-boson and slave-fermion mean-field theories with the gap for the triplet excitations. In the d-wave pairing state of the slave-boson mean-field theory in two dimensions, there is no true gap for spinons, but the Anderson localization occurs, which leads to the local moment when the repulsive interaction is taken into account. In the slave-fermion mean-field theory, local moments are found bound to nonmagnetic impurities as a result of (staggered) gauge interaction. However, in both theories, localization of spinon does not appear in the resistivity, which shows the classical value for the holon

Practice Patterns of School-Based Occupational Therapists Targeting Handwriting: A Knowledge-to-Practice Gap

Science.gov (United States)

Cramm, Heidi; Egan, Mary

2015-01-01

Poor handwriting is a common reason for referral to school-based occupational therapy. A survey was used to explore the extent to which current practice patterns in Ontario, Canada, align with evidence on effective intervention for handwriting. Knowledge-to-practice gaps were identified related to focus on performance components versus…

Band Alignment in MoS2/WS2 Transition Metal Dichalcogenide Heterostructures Probed by Scanning Tunneling Microscopy and Spectroscopy.

Science.gov (United States)

Hill, Heather M; Rigosi, Albert F; Rim, Kwang Taeg; Flynn, George W; Heinz, Tony F

2016-08-10

Using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS), we examine the electronic structure of transition metal dichalcogenide heterostructures (TMDCHs) composed of monolayers of MoS2 and WS2. STS data are obtained for heterostructures of varying stacking configuration as well as the individual monolayers. Analysis of the tunneling spectra includes the influence of finite sample temperature, yield information about the quasi-particle bandgaps, and the band alignment of MoS2 and WS2. We report the band gaps of MoS2 (2.16 ± 0.04 eV) and WS2 (2.38 ± 0.06 eV) in the materials as measured on the heterostructure regions and the general type II band alignment for the heterostructure, which shows an interfacial band gap of 1.45 ± 0.06 eV.

Transformation of the superconducting gap to an insulating pseudogap at a critical hole density in the cuprates

Science.gov (United States)

Liu, Ye-Hua; Wang, Wan-Sheng; Wang, Qiang-Hua; Zhang, Fu-Chun; Rice, T. M.

2017-07-01

We apply the recent wave-packet formalism developed by Ossadnik to describe the origin of the short-range ordered pseudogap state as the hole doping is lowered through a critical density in cuprates. We argue that the energy gain that drives this precursor state to Mott localization, follows from maximizing umklapp scattering near the Fermi energy. To this end, we show how energy gaps driven by umklapp scattering can open on an appropriately chosen surface, as proposed earlier by Yang, Rice, and Zhang. The key feature is that the pairing instability includes umklapp scattering, leading to an energy gap not only in the single-particle spectrum but also in the pair spectrum. As a result the superconducting gap at overdoping is turned into an insulating pseudogap in the antinodal parts of the Fermi surface.

Intrinsically aligned chemo-mechanical functionalization of twin cantilever structures

International Nuclear Information System (INIS)

Toffoli, V; Esch, F; Melli, M; Pozzato, A; Tormen, M; Lazzarino, M; Cataruzza, F; Carrato, S; Scoles, G

2008-01-01

Mechanical oscillators became a main focus of research in recent years for potential applications in biomolecule detectors. We recently demonstrated the feasibility of a scheme based on twin cantilevers with a sensitivity down to the single molecule. This approach is extremely promising under the condition that the two terminals of the device can be functionalized with high selectivity and nanometric accuracy by linker molecules. Here we demonstrate a chemo-mechanical method to achieve the intrinsically aligned functionalization of two silicon surfaces, which can be separated by a gap controllable with nanometric precision. The chemical binding of the target molecules in the selected position is obtained through a cycloaddition reaction which exploits the reactivity of the freshly cleaved surfaces that form when the cantilever gap is created. The general validity of this approach is shown by the use in different chemical environments of two compounds with different reactive functional groups.

Aid alignment for global health research: the role of HIROs

Directory of Open Access Journals (Sweden)

Viergever Roderik F

2011-03-01

Full Text Available Abstract The lack of a mechanism that aligns financial flows for global health research towards public health priorities limits the impact of health research on health and health equity. Collaborative groups of health research funders appear to be particularly well situated to ameliorate this situation and to initiate discussion on aid alignment for global health research. One such group is the Heads of International Research Organizations (HIROs, which brings together a large number of major government and philanthropic funders of biomedical research. Surprisingly, there is hardly any information publicly available on HIROs' objectives, or on how it aims to achieve more harmonization in the field of research for health. Greater transparency on HIROs' objectives and on its current efforts towards addressing the gap between global health research needs and investments would be desirable, given the enormous potential benefits of more coordination by this group.

Boron/nitrogen pairs Co-doping in metallic carbon nanotubes: a first-principle study

International Nuclear Information System (INIS)

Ouyang Fang-Ping; Peng Sheng-Lin; Chen Ling-Na; Sun Shu-Yuan; Xu Hui

2011-01-01

By using the first-principles calculations, the electronic structure and quantum transport properties of metallic carbon nanotubes with B/N pairs co-doping have been investigated. It is shown that the total energies of metallic carbon nanotubes are sensitive to the doping sites of the B/N pairs. The energy gaps of the doped metallic carbon nanotubes decrease with decreasing the concentration of the B/N pair not only along the tube axis but also around the tube. Moreover, the I—V characteristics and transmissions of the doped tubes are studied. Our results reveal that the conducting ability of the doped tube decreases with increasing the concentrations of the B/N pairs due to symmetry breaking of the system. This fact opens a new way to modulate band structures of metallic carbon nanotubes by doping B/N pair with suitable concentration and the novel characteristics are potentially useful in future applications. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez

2011-01-01

The Muon Alignment work now focuses on producing a new track-based alignment with higher track statistics, making systematic studies between the results of the hardware and track-based alignment methods and aligning the barrel using standalone muon tracks. Currently, the muon track reconstruction software uses a hardware-based alignment in the barrel (DT) and a track-based alignment in the endcaps (CSC). An important task is to assess the muon momentum resolution that can be achieved using the current muon alignment, especially for highly energetic muons. For this purpose, cosmic ray muons are used, since the rate of high-energy muons from collisions is very low and the event statistics are still limited. Cosmics have the advantage of higher statistics in the pT region above 100 GeV/c, but they have the disadvantage of having a mostly vertical topology, resulting in a very few global endcap muons. Only the barrel alignment has therefore been tested so far. Cosmic muons traversing CMS from top to bottom are s...

Interplay of antiferromagnetism and superconductivity in cuprates with impurity effect and d-wave pairing

Energy Technology Data Exchange (ETDEWEB)

Mohapatra, Rasmita, E-mail: rmrmmohapatra@gmail.com [P.G. Department of Applied Physics and Ballistics, F.M. University, Balasore, Odisha 756019 (India); Rout, G.C., E-mail: gcr@iopb.res.in [Physics Enclave, Plot no-664/4825, Lane-4A, Shree Vihar, Patia, Bhubaneswar, Odisha 751024 (India)

2015-05-15

Highlights: • We considered here the interplay of antiferromagnetism (AFM) and Superconductivity (SC) with d-wave pairing symmetry in presence of impurity effect. • The tunneling conductance explains the multiple peaks and dip-hump structure. • It is observed that AFM coupling enhances the superconducting transition temperature. • The low temperature specific heat anomaly due to impurity atoms. - Abstract: We present here a model Hamiltonian to study the interplay between staggered magnetic field and the superconductivity with d-wave pairing symmetry in presence of hybridization between impurity f-electrons of rare-earth ions and 3d-electrons of copper ions. The staggered field and superconducting (SC) gaps are calculated by Green’s function technique and solved self-consistently. The coupling constants are compared using s-wave and d-wave pairings. The strength of hybridization suppresses the magnitude of the gaps; while antiferromagnetic coupling enhances the superconducting transition temperature, but suppresses the Neel temperature. The density of states (DOS) representing tunneling conductance shows complex character with impurity level lying at the Fermi level. The electronic specific heat explains prototype heavy fermion behavior in cuprate systems at low temperatures.

Interplay of antiferromagnetism and superconductivity in cuprates with impurity effect and d-wave pairing

International Nuclear Information System (INIS)

Mohapatra, Rasmita; Rout, G.C.

2015-01-01

Highlights: • We considered here the interplay of antiferromagnetism (AFM) and Superconductivity (SC) with d-wave pairing symmetry in presence of impurity effect. • The tunneling conductance explains the multiple peaks and dip-hump structure. • It is observed that AFM coupling enhances the superconducting transition temperature. • The low temperature specific heat anomaly due to impurity atoms. - Abstract: We present here a model Hamiltonian to study the interplay between staggered magnetic field and the superconductivity with d-wave pairing symmetry in presence of hybridization between impurity f-electrons of rare-earth ions and 3d-electrons of copper ions. The staggered field and superconducting (SC) gaps are calculated by Green’s function technique and solved self-consistently. The coupling constants are compared using s-wave and d-wave pairings. The strength of hybridization suppresses the magnitude of the gaps; while antiferromagnetic coupling enhances the superconducting transition temperature, but suppresses the Neel temperature. The density of states (DOS) representing tunneling conductance shows complex character with impurity level lying at the Fermi level. The electronic specific heat explains prototype heavy fermion behavior in cuprate systems at low temperatures

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

Science.gov (United States)

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

Alignment-Annotator web server: rendering and annotating sequence alignments.

Science.gov (United States)

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The role of spatial organization in preference for color pairs.

Science.gov (United States)

Schloss, Karen B; Palmer, Stephen E

2011-01-01

We investigated how spatial organization influences color-pair preference asymmetries: differential preference for one color pair over another when the pairs contain the same colors in opposite spatial configurations. Schloss and Palmer (2011, Attention, Perception, & Psychophysics 73 55-571) found weak figure ground preference asymmetries for small squares centered on large squares in aesthetic ratings. Here, we found robust preference asymmetries using a more sensitive forced-choice task: participants strongly prefer pairs with yellower, lighter figures on bluer, darker grounds (experiment 1). We also investigated which spatial factors influence these preference asymmetries. Relative area of the two component regions is clearly important, and perceived 3-D area of the 2-D displays (ie after the ground is amodally completed behind the figure) is more influential than 2-D area (experiment 2). Surroundedness is not required, because yellowness blueness effects were comparable for pairs in which the figure was surrounded by the ground, and for mosaic arrangements in which the regions were adjacent and separated by a gap (experiment 3). Lightness darkness effects, however, were opposite for figure ground versus mosaic organizations: people prefer figure-ground organizations in which smaller regions are lighter, but prefer mosaic organizations in which smaller regions are darker. Physiological, phenomenological, and ecological explanations of the reported results are discussed.

The essential role of vibronic interactions in electron pairing in the micro- and macroscopic sized materials

International Nuclear Information System (INIS)

Kato, Takashi

2010-01-01

Graphical abstract: The electron-phonon interactions destroy the electron pairs formed by Coulomb interactions, and at the same time, form the energy gap by which the electron pairs become stable. - Abstract: In order to discuss how the nondissipative delocalized diamagnetic currents in the microscopic sized materials are closely related to the conventional superconductivity in the macroscopic sized materials, the unified theory, by which various sized superconductivity can be explained, is suggested. It has been believed for a long time that the electron-phonon interactions play an essential role in the attractive electron-electron interactions, as described in the Bardeen-Cooper-Schrieffer (BCS) theory in the conventional superconductivity. However, it is suggested in this paper that the electron-phonon interactions do not play an essential role in the attractive electron-electron interactions but play an essential role in the forming of energy gap by which the electron pairs formed by the attractive Coulomb interactions in the conventional superconducting states become more stable than those in the normal metallic states at low temperatures.

Multi-pair states in electron–positron pair creation

Directory of Open Access Journals (Sweden)

Anton Wöllert

2016-09-01

Full Text Available Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron–positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron–positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron–positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron–positron pairs.

Multi-pair states in electron–positron pair creation

Energy Technology Data Exchange (ETDEWEB)

Wöllert, Anton, E-mail: woellert@mpi-hd.mpg.de; Bauke, Heiko, E-mail: heiko.bauke@mpi-hd.mpg.de; Keitel, Christoph H.

2016-09-10

Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron–positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron–positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron–positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron–positron pairs.

Multi-pair states in electron–positron pair creation

International Nuclear Information System (INIS)

Wöllert, Anton; Bauke, Heiko; Keitel, Christoph H.

2016-01-01

Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron–positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron–positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron–positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron–positron pairs.

PriFi - Using a Multiple Alignment of Related Sequences to Find Primers for  Amplification of Homologs

DEFF Research Database (Denmark)

Fredslund, Jakob; Schauser, Leif; Madsen, Lene Heegaard

2005-01-01

Using a comparative approach, the web program PriFi (http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main) designs pairs of primers useful for PCR amplification of genomic DNA in species where prior sequence information is not available. The program works with an alignment of DNA sequences from phylog...

Spin-polaron theory of high-Tc superconductivity: I, spin polarons and high-Tc pairing

International Nuclear Information System (INIS)

Wood, R.F.

1993-06-01

The concept of a spin polaron is introduced and contrasted with the more familiar ionic polaron picture. A brief review of aspects of ionic bipolaronic superconductivity is given with particular emphasis on the real-space pairing and true Bose condensation characteristics. The formation energy of spin polarons is then calculated in analogy with ionic polarons. The spin-flip energy of a Cu spin in an antiferromagnetically aligned CuO 2 plane is discussed. It is shown that the introduction of holes into the CuO 2 planes will always lead to the destruction of long-range AF ordering due to the formation of spin polarons. The pairing of two spin polarons can be expected because of the reestablishment of local (short-range) AF ordering; the magnitude of the pairing energy is estimated using a simplified model. The paper closes with a brief discussion of the formal theory of spin polarons

Keeping in Touch With the Visual System: Spatial Alignment and Multisensory Integration of Visual-Somatosensory Inputs

Directory of Open Access Journals (Sweden)

Jeannette Rose Mahoney

2015-08-01

Full Text Available Correlated sensory inputs coursing along the individual sensory processing hierarchies arrive at multisensory convergence zones in cortex where inputs are processed in an integrative manner. The exact hierarchical level of multisensory convergence zones and the timing of their inputs are still under debate, although increasingly, evidence points to multisensory integration at very early sensory processing levels. The objective of the current study was to determine, both psychophysically and electrophysiologically, whether differential visual-somatosensory integration patterns exist for stimuli presented to the same versus opposite hemifields. Using high-density electrical mapping and complementary psychophysical data, we examined multisensory integrative processing for combinations of visual and somatosensory inputs presented to both left and right spatial locations. We assessed how early during sensory processing visual-somatosensory (VS interactions were seen in the event-related potential and whether spatial alignment of the visual and somatosensory elements resulted in differential integration effects. Reaction times to all VS pairings were significantly faster than those to the unisensory conditions, regardless of spatial alignment, pointing to engagement of integrative multisensory processing in all conditions. In support, electrophysiological results revealed significant differences between multisensory simultaneous VS and summed V+S responses, regardless of the spatial alignment of the constituent inputs. Nonetheless, multisensory effects were earlier in the aligned conditions, and were found to be particularly robust in the case of right-sided inputs (beginning at just 55ms. In contrast to previous work on audio-visual and audio-somatosensory inputs, the current work suggests a degree of spatial specificity to the earliest detectable multisensory integrative effects in response to visual-somatosensory pairings.

Further test of new pairing scheme used in overhaul of BCS theory

International Nuclear Information System (INIS)

Zheng, X.H.; Walmsley, D.G.

2014-01-01

Highlights: • Explanation of a new pairing scheme to overhaul BCS theory. • Prediction of superconductor properties from normal state resistivity. • Applications to Nb, Pb, Al, Ta, Mo, Ir and W, T c between 9.5 and 0.012 K. • High accuracy compared with measured energy gap of Nb, Pb, Al and Ta. • Prediction of energy gap for Mo, Ir and W (so far not measured). - Abstract: A new electron pairing scheme, rectifying a fundamental flaw of the BCS theory, is tested extensively. It postulates that superconductivity arises solely from residual umklapp scattering when it is not in competition for the same destination electron states with normal scattering. It reconciles a long standing theoretical discrepancy in the strength of the electron–phonon interaction between the normal and superconductive states. The new scheme is exploited to calculate the superconductive electron–phonon spectral density, α 2 F(ν), entirely on the basis of normal state electrical resistivity. This leads to first principles superconductive properties (zero temperature energy gap and tunnelling conductance) in seven metals which turn out to be highly accurate when compared with known data; in other cases experimental verification is invited. The transition temperatures involved vary over almost three orders of magnitude: from 9.5 K for niobium to 0.012 K for tungsten

The nuclear receptor E75A has a novel pair-rule-like function in patterning the milkweed bug, Oncopeltus fasciatus.

Science.gov (United States)

Erezyilmaz, Deniz F; Kelstrup, Hans C; Riddiford, Lynn M

2009-10-01

Genetic studies of the fruit fly Drosophila have revealed a hierarchy of segmentation genes (maternal, gap, pair-rule and HOX) that subdivide the syncytial blastoderm into sequentially finer-scale coordinates. Within this hierarchy, the pair-rule genes translate gradients of information into periodic stripes of expression. How pair-rule genes function during the progressive mode of segmentation seen in short and intermediate-germ insects is an ongoing question. Here we report that the nuclear receptor Of'E75A is expressed with double segment periodicity in the head and thorax. In the abdomen, Of'E75A is expressed in a unique pattern during posterior elongation, and briefly resembles a sequence that is typical of pair-rule genes. Depletion of Of'E75A mRNA caused loss of a subset of odd-numbered parasegments, as well as parasegment 6. Because these parasegments straddle segment boundaries, we observe fusions between adjacent segments. Finally, expression of Of'E75A in the blastoderm requires even-skipped, which is a gap gene in Oncopeltus. These data show that the function of Of'E75A during embryogenesis shares many properties with canonical pair-rule genes in other insects. They further suggest that parasegment specification may occur through irregular and episodic pair-rule-like activity.

Partial preferential chromosome pairing is genotype dependent in tetraploid rose.

Science.gov (United States)

Bourke, Peter M; Arens, Paul; Voorrips, Roeland E; Esselink, G Danny; Koning-Boucoiran, Carole F S; Van't Westende, Wendy P C; Santos Leonardo, Tiago; Wissink, Patrick; Zheng, Chaozhi; van Geest, Geert; Visser, Richard G F; Krens, Frans A; Smulders, Marinus J M; Maliepaard, Chris

2017-04-01

It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

DEFF Research Database (Denmark)

Wernersson, Rasmus; Pedersen, Anders Gorm

2003-01-01

The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

Hopping ladder and power relaxation due to donor-acceptor pairs

International Nuclear Information System (INIS)

Kostadinov, I.Z.

1985-11-01

Hopping between donor-acceptor pairs leads to peculiar temperature dependence of the conductivity and the photoconductivity under subband gap illumination in the form of non-linear activation energies ladder. The correlated and uncorrelated distributions of pairs are considered and the conditions for the ladder existence are determined. The relaxation of the carrier concentration fluctuations is studied and power type decay is found. The temperature dependence of the exponent is calculated in agreement with the non-exponential decay of the pulse excited luminescence observed by Dean et al. The temperature dependence of the luminescence intensity also shows variable activation energy as found here. The exponent value α=1.316 is also in agreement with the data for crystalline and amorphous materials. (author)

Band Alignment Determination of Two-Dimensional Heterojunctions and Their Electronic Applications

KAUST Repository

Chiu, Ming-Hui

2018-05-09

Two-dimensional (2D) layered materials such as MoS2 have been recognized as high on-off ratio semiconductors which are promising candidates for electronic and optoelectronic devices. In addition to the use of individual 2D materials, the accelerated field of 2D heterostructures enables even greater functionalities. Device designs differ, and they are strongly controlled by the electronic band alignment. For example, photovoltaic cells require type II heterostructures for light harvesting, and light-emitting diodes benefit from multiple quantum wells with the type I band alignment for high emission efficiency. The vertical tunneling field-effect transistor for next-generation electronics depends on nearly broken-gap band alignment for boosting its performance. To tailor these 2D layered materials toward possible future applications, the understanding of 2D heterostructure band alignment becomes critically important. In the first part of this thesis, we discuss the band alignment of 2D heterostructures. To do so, we firstly study the interlayer coupling between two dissimilar 2D materials. We conclude that a post-anneal process could enhance the interlayer coupling of as-transferred 2D heterostructures, and heterostructural stacking imposes similar symmetry changes as homostructural stacking. Later, we precisely determine the quasi particle bandgap and band alignment of the MoS2/WSe2 heterostructure by using scan tunneling microscopy/spectroscopy (STM/S) and micron-beam X-ray photoelectron spectroscopy (μ-XPS) techniques. Lastly, we prove that the band alignment of 2D heterojunctions can be accurately predicted by Anderson’s model, which has previously failed to predict conventional bulk heterostructures. In the second part of this thesis, we develop a new Chemical Vapor Deposition (CVD) method capable of precisely controlling the growth area of p- and n-type transition metal dichalcogenides (TMDCs) and further form lateral or vertical 2D heterostructures. This

Excitons and Cooper pairs two composite bosons in many-body physics

CERN Document Server

Combescot, Monique

2015-01-01

This book bridges a gap between two major communities of Condensed Matter Physics, Semiconductors and Superconductors, that have thrived independently. Through an original perspective that their key particles, excitons and Cooper pairs, are composite bosons, the authors raise fundamental questions of current interest: how does the Pauli exclusion principle wield its power on the fermionic components of bosonic particles at a microscopic level and how this affects the macroscopic physics? What can we learn from Wannier and Frenkel excitons and from Cooper pairs that helps us understand "bosonic condensation" of composite bosons and its difference from Bose-Einstein condensation of elementary bosons? The authors start from solid mathematical and physical foundation to derive excitons and Cooper pairs. They further introduce Shiva diagrams as a graphic support to grasp the many-body physics induced by fermion exchange - a novel mechanism not visualized by standard Feynman diagrams. Advanced undergraduate or grad...

Approximating local observables on projected entangled pair states

Science.gov (United States)

Schwarz, M.; Buerschaper, O.; Eisert, J.

2017-06-01

Tensor network states are for good reasons believed to capture ground states of gapped local Hamiltonians arising in the condensed matter context, states which are in turn expected to satisfy an entanglement area law. However, the computational hardness of contracting projected entangled pair states in two- and higher-dimensional systems is often seen as a significant obstacle when devising higher-dimensional variants of the density-matrix renormalization group method. In this work, we show that for those projected entangled pair states that are expected to provide good approximations of such ground states of local Hamiltonians, one can compute local expectation values in quasipolynomial time. We therefore provide a complexity-theoretic justification of why state-of-the-art numerical tools work so well in practice. We finally turn to the computation of local expectation values on quantum computers, providing a meaningful application for a small-scale quantum computer.

SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

Science.gov (United States)

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

A simple method for fabrication of electrospun fibers with controlled degree of alignment having potential for nerve regeneration applications

Energy Technology Data Exchange (ETDEWEB)

Vimal, Sunil Kumar; Ahamad, Nadim; Katti, Dhirendra S., E-mail: dsk@iitk.ac.in

2016-06-01

In peripheral nerve injuries where direct suturing of nerve endings is not feasible, nerve regeneration has been facilitated through the use of artificially aligned fibrous scaffolds that provide directional growth of neurons to bridge the gap. The degree of fiber alignment is crucial and can impact the directionality of cells in a fibrous scaffold. While there have been multiple approaches that have been used for controlling fiber alignment, however, they have been associated with a compromised control on other properties, such as diameter, morphology, curvature, and topology of fibers. Therefore, the present study demonstrates a modified electrospinning set-up, that enabled fabrication of electrospun fibers with controlled degree of alignment from non-aligned (NA), moderately aligned (MA, 75%) to highly aligned (HA, 95%) sub-micron fibers while keeping other physical properties unchanged. The results demonstrate that the aligned fibers (MA and HA) facilitated directional growth of human astrocytoma cells (U373), wherein the aspect ratio of cells was found to increase with an increase in degree of fibers alignment. In contrast to NA and MA fibers, the HA fibers showed improved contact guidance to U373 cells that was demonstrated by a significantly higher cell aspect ratio and nuclear aspect ratio. In conclusion, the present study demonstrated a modified electrospinning setup to fabricate differentially aligned fibrous scaffolds with the HA fibers showing potential for use in neural tissue engineering. - Highlights: • Modified electrospinning set-up for fabrication of fibers with controlled alignment • Three parameter-based control on the degree of alignment of fibers • The aligned fibers enhanced cell elongation and cell-cell contact. • The aligned fibers show potential for use in nerve regeneration.

Type II band alignment in Ge1-x-ySixSny/Ge1-α-βSiαSnβ heterojunctions

Science.gov (United States)

Dey, Swagata; Mukhopadhyay, Bratati; Sen, Gopa; Basu, P. K.

2018-02-01

We have examined type II band alignment in Ge1-x-ySixSny/Ge1-α-βSiαSβ heterojunctions grown on virtual substrates in Si platform. It is found that, for different values of x, y, α and β, direct band gap type II band line up can be achieved for both tensile and compressive strains. The calculated band gap energy corresponds to the mid infrared to far infrared regions in the electromagnetic spectrum.

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Gorodkin, Jan; Backofen, Rolf

2008-01-01

Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single...... the corresponding probability of being single stranded. Furthermore, we found that structurally conserved RNA motifs are mostly supported by folding energies. Other problems (e.g. RNA-folding kinetics) may also benefit from employing the principles of the model we introduce. Our implementation, PETfold, was tested...

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.

Science.gov (United States)

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2012-11-21

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

Directory of Open Access Journals (Sweden)

Flemington Erik

2011-01-01

Full Text Available Abstract Background Next Generation Sequencing (NGS technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM or Binary SAM (BAM format is now standard, biomedical researchers still have difficulty accessing this information. Results We have developed a Graphical User Interface (GUI software tool named SAMMate. SAMMate allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate also automates some standard procedures in DNA-seq and RNA-seq data analysis. Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression abundance scores for customized genomic intervals using short reads originating from both exons and exon-exon junctions. Furthermore, SAMMate can quickly calculate a whole-genome signal map at base-wise resolution allowing researchers to solve an array of bioinformatics problems. Finally, SAMMate can export both a wiggle file for alignment visualization in the UCSC genome browser and an alignment statistics report. The biological impact of these features is demonstrated via several case studies that predict miRNA targets using short read alignment information files. Conclusions With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net.

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

Directory of Open Access Journals (Sweden)

Lyngsø Rune

2010-04-01

Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

Internal alignment and position resolution of the silicon tracker of DAMPE determined with orbit data

Science.gov (United States)

Tykhonov, A.; Ambrosi, G.; Asfandiyarov, R.; Azzarello, P.; Bernardini, P.; Bertucci, B.; Bolognini, A.; Cadoux, F.; D'Amone, A.; De Benedittis, A.; De Mitri, I.; Di Santo, M.; Dong, Y. F.; Duranti, M.; D'Urso, D.; Fan, R. R.; Fusco, P.; Gallo, V.; Gao, M.; Gargano, F.; Garrappa, S.; Gong, K.; Ionica, M.; La Marra, D.; Lei, S. J.; Li, X.; Loparco, F.; Marsella, G.; Mazziotta, M. N.; Peng, W. X.; Qiao, R.; Salinas, M. M.; Surdo, A.; Vagelli, V.; Vitillo, S.; Wang, H. Y.; Wang, J. Z.; Wang, Z. M.; Wu, D.; Wu, X.; Zhang, F.; Zhang, J. Y.; Zhao, H.; Zimmer, S.

2018-06-01

The DArk Matter Particle Explorer (DAMPE) is a space-borne particle detector designed to probe electrons and gamma-rays in the few GeV to 10 TeV energy range, as well as cosmic-ray proton and nuclei components between 10 GeV and 100 TeV. The silicon-tungsten tracker-converter is a crucial component of DAMPE. It allows the direction of incoming photons converting into electron-positron pairs to be estimated, and the trajectory and charge (Z) of cosmic-ray particles to be identified. It consists of 768 silicon micro-strip sensors assembled in 6 double layers with a total active area of 6.6 m2. Silicon planes are interleaved with three layers of tungsten plates, resulting in about one radiation length of material in the tracker. Internal alignment parameters of the tracker have been determined on orbit, with non-showering protons and helium nuclei. We describe the alignment procedure and present the position resolution and alignment stability measurements.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

S. Szillasi

2013-01-01

The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

Pair breaking and charge relaxation in superconductors

International Nuclear Information System (INIS)

Nielson, J.B.; Pethick, C.J.; Rammer, J.; Smith, H.

1982-01-01

We present a general formalism based on the quasiclassical Green's function for calculating charge imbalance in nonequilibrium superconductors. Our discussion is sufficiently general that it applies at arbitrary temperatures, and under conditions when the width of quasiparticle states are appreciable due to pair breaking processes, and when strong coupling effects are significant. As a first application we demonstrate in detail how in the limit of smallpair breaking and for a weak coupling superconductor the collision term in the formalism reduces to the one in the quasiparticle Boltzmann equation. We next treat the case of charge imbalance generated by tunnel injection, with pair breaking by phonons and magnetic impurities. Over the range of temperatures investigated exerimentally to date, the calculated charge imbalance is rather close to that evaluated using the Boltzmann equation, even if pair braeking is so strong as almost to destroy superconductivity. Finally we consider charge imbalance generated by the combined influence of a supercurrent and a temperature gradient. We give calculations for a dirty superconductor with scattering by phonons as the pair breaking mechanism, and the results give a reasonable account of the experimental data of Clarke, Fjordboge, and Lindelof. We carry out calculations for the case of impurity scattering along which are valid not only in the clean and dirty limits, but also for intermediate situations. These enable us to see how the large contribution to the charge imbalance found for energies close to the gap edge in the clean case is reduced with increasing impurity scattering

CdSe/CdTe interface band gaps and band offsets calculated using spin-orbit and self-energy corrections

Energy Technology Data Exchange (ETDEWEB)

Ribeiro, M. [Centro de Pesquisas Avancadas Wernher von Braun, Av. Alice de Castro P.N. Mattosinho 301, CEP 13098-392 Campinas, SP (Brazil); Ferreira, L.G. [Departamento de Fisica dos Materiais e Mecanica, Instituto de Fisica, Universidade de Sao Paulo, 05315-970 Sao Paulo, SP (Brazil); Fonseca, L.R.C. [Center for Semiconductor Components, State University of Campinas, R. Pandia Calogeras 90, 13083-870 Campinas, SP (Brazil); Ramprasad, R. [Department of Chemical, Materials and Biomolecular Engineering, Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Storrs, CT 06269 (United States)

2012-09-20

We performed ab initio calculations of the electronic structures of bulk CdSe and CdTe, and their interface band alignments on the CdSe in-plane lattice parameters. For this, we employed the LDA-1/2 self-energy correction scheme to obtain corrected band gaps and band offsets. Our calculations include the spin-orbit effects for the bulk cases, which have shown to be of importance for the equilibrium systems and are possibly degraded in these strained semiconductors. Therefore, the SO showed reduced importance for the band alignment of this particular system. Moreover, the electronic structure calculated along the transition region across the CdSe/CdTe interface shows an interesting non-monotonic variation of the band gap in the range 0.8-1.8 eV, which may enhance the absorption of light for corresponding frequencies at the interface between these two materials in photovoltaic applications.

Three-Nucleon Forces and Triplet Pairing in Neutron Matter

Science.gov (United States)

Papakonstantinou, P.; Clark, J. W.

2017-12-01

The existence of superfluidity of the neutron component in the core of a neutron star, associated specifically with triplet P-wave pairing, is currently an open question that is central to interpretation of the observed cooling curves and other neutron-star observables. Ab initio theoretical calculations aimed at resolving this issue face unique challenges in the relevant high-density domain, which reaches beyond the saturation density of symmetrical nuclear matter. These issues include uncertainties in the three-nucleon (3N) interaction and in the effects of strong short-range correlations—and more generally of in-medium modification of nucleonic self-energies and interactions. A survey of existing solutions of the gap equations in the triplet channel demonstrates that the net impact on the gap magnitude of 3N forces, coupled channels, and mass renormalization shows extreme variation dependent on specific theoretical inputs, in some cases even pointing to the absence of a triplet gap, thus motivating a detailed analysis of competing effects within a well-controlled model. In the present study, we track the effects of the 3N force and in-medium modifications in the representative case of the ^3P_2 channel, based on the Argonne v_{18} two-nucleon (2N) interaction supplemented by 3N interactions of the Urbana IX family. Sensitivity of the results to the input interaction is clearly demonstrated. We point out consistency issues with respect to the simultaneous treatment of 3N forces and in-medium effects, which warrant further investigation. We consider this pilot study as the first step toward a systematic and comprehensive exploration of coupled-channel ^3P F_2 pairing using a broad range of 2N and 3N interactions from the current generation of refined semi-phenomenological models and models derived from chiral effective field theory.

Band alignment in organic devices: Photoemission studies of model oligomers on In2O3

International Nuclear Information System (INIS)

Blyth, R. I. R.; Duschek, R.; Koller, G.; Netzer, F. P.; Ramsey, M. G.

2001-01-01

The interfaces of In 2 O 3 , a model for indium - tin - oxide (ITO), with benzene, thiophene, and benzaldehyde, models for technologically important organic molecules, are studied using angle resolved ultraviolet photoemission and work function measurements. Band alignment diagrams for hypothetical Al/organic/ITO devices have been drawn, using values determined from this work and previously published studies of these molecules on Al(111). The similarity between the bonding of benzene and thiophene on Al(111) and In 2 O 3 , i.e., largely electrostatic, leads to near identical alignment at both metal and oxide interfaces. This indicates that clean Al and ITO will make a very poor electron/hole injecting pair. We suggest that the apparent efficiency of Al as an electron injecting contact in real devices is due to the presence of oxygen at the Al/organic interface. For benzaldehyde the interaction with In 2 O 3 is largely electrostatic, in contrast to the covalent bonds formed on Al(111). This leads to very different alignment at the Al and oxide interfaces, showing the importance of the particular organic - inorganic interaction in determining band alignment. [copyright] 2001 American Institute of Physics

MaxAlign: maximizing usable data in an alignment

DEFF Research Database (Denmark)

Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

2007-01-01

Align. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. CONCLUSION: We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also...

Aligning for Innovation - Alignment Strategy to Drive Innovation

Science.gov (United States)

Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

2010-01-01

With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

Band alignment of type I at (100ZnTe/PbSe interface

Directory of Open Access Journals (Sweden)

Igor Konovalov

2016-06-01

Full Text Available A junction of lattice-matched cubic semiconductors ZnTe and PbSe results in a band alignment of type I so that the narrow band gap of PbSe is completely within the wider band gap of ZnTe. The valence band offset of 0.27 eV was found, representing a minor barrier during injection of holes from PbSe into ZnTe. Simple linear extrapolation of the valence band edge results in a smaller calculated band offset, but a more elaborate square root approximation was used instead, which accounts for parabolic bands. PbSe was electrodeposited at room temperature with and without Cd2+ ions in the electrolyte. Although Cd adsorbs at the surface, the presence of Cd in the electrolyte does not influence the band offset.

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Richter, Andreas S.; Gorodkin, Jan

2010-01-01

of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our approach (in contrast to other RNARNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base...... pairs. As a proof of concept, we show an example and discuss the strengths and weaknesses of the approach....

Control rod housing alignment

International Nuclear Information System (INIS)

Dixon, R.C.; Deaver, G.A.; Punches, J.R.; Singleton, G.E.; Erbes, J.G.; Offer, H.P.

1990-01-01

This patent describes a process for measuring the vertical alignment between a hole in a core plate and the top of a corresponding control rod drive housing within a boiling water reactor. It comprises: providing an alignment apparatus. The alignment apparatus including a lower end for fitting to the top of the control rod drive housing; an upper end for fitting to the aperture in the core plate, and a leveling means attached to the alignment apparatus to read out the difference in angularity with respect to gravity, and alignment pin registering means for registering to the alignment pin on the core plate; lowering the alignment device on a depending support through a lattice position in the top guide through the hole in the core plate down into registered contact with the top of the control rod drive housing; registering the upper end to the sides of the hole in the core plate; registering the alignment pin registering means to an alignment pin on the core plate to impart to the alignment device the required angularity; and reading out the angle of the control rod drive housing with respect to the hole in the core plate through the leveling devices whereby the angularity of the top of the control rod drive housing with respect to the hole in the core plate can be determined

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

2012-01-01

  A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

Simulation of beamline alignment operations

International Nuclear Information System (INIS)

Annese, C; Miller, M G.

1999-01-01

The CORBA-based Simulator was a Laboratory Directed Research and Development (LDRD) project that applied simulation techniques to explore critical questions about distributed control systems. The simulator project used a three-prong approach that studied object-oriented distribution tools, computer network modeling, and simulation of key control system scenarios. The National Ignition Facility's (NIF) optical alignment system was modeled to study control system operations. The alignment of NIF's 192 beamlines is a large complex operation involving more than 100 computer systems and 8000 mechanized devices. The alignment process is defined by a detailed set of procedures; however, many of the steps are deterministic. The alignment steps for a poorly aligned component are similar to that of a nearly aligned component; however, additional operations/iterations are required to complete the process. Thus, the same alignment operations will require variable amounts of time to perform depending on the current alignment condition as well as other factors. Simulation of the alignment process is necessary to understand beamline alignment time requirements and how shared resources such as the Output Sensor and Target Alignment Sensor effect alignment efficiency. The simulation has provided alignment time estimates and other results based on documented alignment procedures and alignment experience gained in the laboratory. Computer communication time, mechanical hardware actuation times, image processing algorithm execution times, etc. have been experimentally determined and incorporated into the model. Previous analysis of alignment operations utilized average implementation times for all alignment operations. Resource sharing becomes rather simple to model when only average values are used. The time required to actually implement the many individual alignment operations will be quite dynamic. The simulation model estimates the time to complete an operation using

Ultrawide band gap amorphous oxide semiconductor, Ga–Zn–O

Energy Technology Data Exchange (ETDEWEB)

Kim, Junghwan, E-mail: JH.KIM@lucid.msl.titech.ac.jp [Materials and Structures Laboratory, Tokyo Institute of Technology, Mailbox R3-4, 4259 Nagatsuta, Midori-ku, Yokohama (Japan); Miyokawa, Norihiko; Sekiya, Takumi; Ide, Keisuke [Materials and Structures Laboratory, Tokyo Institute of Technology, Mailbox R3-4, 4259 Nagatsuta, Midori-ku, Yokohama (Japan); Toda, Yoshitake [Materials Research Center for Element Strategy, Tokyo Institute of Technology, Mailbox SE-6, 4259 Nagatsuta, Midori-ku, Yokohama (Japan); Hiramatsu, Hidenori; Hosono, Hideo; Kamiya, Toshio [Materials and Structures Laboratory, Tokyo Institute of Technology, Mailbox R3-4, 4259 Nagatsuta, Midori-ku, Yokohama (Japan); Materials Research Center for Element Strategy, Tokyo Institute of Technology, Mailbox SE-6, 4259 Nagatsuta, Midori-ku, Yokohama (Japan)

2016-09-01

We fabricated amorphous oxide semiconductor films, a-(Ga{sub 1–x}Zn{sub x})O{sub y}, at room temperature on glass, which have widely tunable band gaps (E{sub g}) ranging from 3.47–4.12 eV. The highest electron Hall mobility ~ 7 cm{sup 2} V{sup −1} s{sup −1} was obtained for E{sub g} = ~ 3.8 eV. Ultraviolet photoemission spectroscopy revealed that the increase in E{sub g} with increasing the Ga content comes mostly from the deepening of the valence band maximum level while the conduction band minimum level remains almost unchanged. These characteristics are explained by their electronic structures. As these films can be fabricated at room temperature on plastic, this achievement extends the applications of flexible electronics to opto-electronic integrated circuits associated with deep ultraviolet region. - Highlights: • Incorporation of H/H{sub 2}O stabilizes the amorphous phase. • Ultrawide band gap (~ 3.8 eV) amorphous oxide semiconductor was fabricated. • The increase in band gap comes mostly from the deepening of the valence band maximum level. • Donor level is more likely aligned to the valence band maximum level.

Prediction of molecular alignment of nucleic acids in aligned media

International Nuclear Information System (INIS)

Wu Bin; Petersen, Michael; Girard, Frederic; Tessari, Marco; Wijmenga, Sybren S.

2006-01-01

We demonstrate - using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined - that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request

A new prosthetic alignment device to read and record prosthesis alignment data.

Science.gov (United States)

Pirouzi, Gholamhossein; Abu Osman, Noor Azuan; Ali, Sadeeq; Davoodi Makinejad, Majid

2017-12-01

Prosthetic alignment is an essential process to rehabilitate patients with amputations. This study presents, for the first time, an invented device to read and record prosthesis alignment data. The digital device consists of seven main parts: the trigger, internal shaft, shell, sensor adjustment button, digital display, sliding shell, and tip. The alignment data were read and recorded by the user or a computer to replicate prosthesis adjustment for future use or examine the sequence of changes in alignment and its effect on the posture of the patient. Alignment data were recorded at the anterior/posterior and medial/lateral positions for five patients. Results show the high level of confidence to record alignment data and replicate adjustments. Therefore, the device helps patients readjust their prosthesis by themselves, or prosthetists to perform adjustment for patients and analyze the effects of malalignment.

Single-gap multi-harmonic buncher for NSC pelletron

International Nuclear Information System (INIS)

Sarkar, A.; Ghosh, S.; Barua, P.

2001-01-01

A single-gap multi-harmonic buncher, developed in collaboration with Argonne National Laboratory, has been installed in the pre-acceleration region of NSC Pelletron. This buncher is required for injecting bunched beam into the booster LINAC, presently under construction. A saw-tooth voltage generated across a single gap formed by a closely spaced pair of grids is used for bunching the dc ion beam produced by the Pelletron accelerator. This saw-tooth voltage is produced by adding a sine wave with its three higher harmonics in proper phase and amplitude. 28 Si beam has been bunched successfully using this buncher. The best FWHM of the bunched beam was 1.5 ns and the maximum efficiency of bunching was 50%. The bunching voltage had no steering effect on the beam. (author)

Graphene-induced band gap renormalization in polythiophene: a many-body perturbation study

Science.gov (United States)

Marsusi, F.; Fedorov, I. A.; Gerivani, S.

2018-01-01

Density functional theory and many-body perturbation theory at the G0W0 level are employed to study the electronic properties of polythiophene (PT) adsorbed on the graphene surface. Analysis of the charge density difference shows that substrate-adsorbate interaction leads to a strong physisorption and interfacial electric dipole moment formation. The electrostatic potential displays a  -0.19 eV shift in the graphene work function from its initial value of 4.53 eV, as the result of the interaction. The LDA band gap of the polymer does not show any change. However, the band structure exhibits weak orbital hybridizations resulting from slight overlapping between the polymer and graphene states wave functions. The interfacial polarization effects on the band gap and levels alignment are investigated at the G0W0 level and show a notable reduction of PT band gap compared to that of the isolated chain.

Effects of variable attachment shapes and aligner material on aligner retention.

Science.gov (United States)

Dasy, Hiltrud; Dasy, Andreas; Asatrian, Greg; Rózsa, Noémi; Lee, Hao-Fu; Kwak, Jin Hee

2015-11-01

To evaluate the retention of four types of aligners on a dental arch with various attachments. For this study, three casts were manufactured, two of which contained attachments (ellipsoid and beveled), and one without any attachments to serve as a control. Four types of aligners were thermoformed: Clear-Aligner (CA)-soft, CA-medium, and CA-hard, with various thicknesses, and Essix ACE. Measurements of vertical displacement force during aligner removal were performed with the Gabo Qualimeter Eplexor. Means and standard deviations were next compared between different aligner thicknesses and attachment shapes. CA-soft, CA-medium, and CA-hard did not present a significant increase in retention, except when used in the presence of attachments. Additionally, CA-medium and CA-hard required significantly more force for removal. Essix ACE demonstrated a significant decrease in retention when used with ellipsoid attachments. The force value for Essix ACE removal from the cast with beveled attachments was comparable to that of CA-medium. Forces for aligner removal from the model without attachments showed a linear trend. Essix ACE did not show a continuous increase in retention for each model. Overall, ellipsoid attachments did not present a significant change in retention. In contrast, beveled attachments improved retention. Ellipsoid attachments had no significant influence on the force required for aligner removal and hence on aligner retention. Essix ACE showed significantly less retention than CA-hard on the models with attachments. Furthermore, beveled attachments were observed to increase retention significantly, compared with ellipsoid attachments and when using no attachments.

Feature of the energy gap in YBa2 Cu3 O7 from break junction measurements

International Nuclear Information System (INIS)

Ekino, T.; Minami, T.; Fujii, H.

1995-01-01

Superconducting energy gap in YBa 2 Cu 3 O 7 have been investigated using break junctions. The tunneling conductance, dI/dV, at T=4.2 K shows no leakage around zero bias, while the gap edge peaks are broadened compared to the simple BCS density of states. These features suggest the spatial distribution of the energy gap or the anisotropic s-wave pairing. The observed largest gap value, determined by the peak-to-peak (p-p) separation in dI/dV, is 140 meV, which corresponds to the 4 δ p-p of an SIS junction. The observed tunneling density of states is fairly well expressed by the probability distribution of the energy gap using the BCS density of states

How to measure the cooper pair mass using plasmons in low-dimensional superconductor structures

International Nuclear Information System (INIS)

Mishonov, T.M.

1990-06-01

The creation of the Cooper pair mass-spectroscopy is suggested. The plasmons in low-dimensional superconductor structures (layers or wires in dielectric background) are theoretically considered to that purpose. The Cooper pair mass m * can be determined by measurements of the Doppler shift of the plasmon frequency when a direct current is applied through the superconductor. The plasmons with frequency ω lower than the superconducting gap 2 Δ can be detected by the same fare-infrared (FIR) absorption technique and grating couplings used previously for investigation of two-dimension (2D) plasmons in semiconductor microstructures. (author). 17 refs, 2 figs

Pairing and low temperature properties of 2 D Fermi-systems with attraction between particles

International Nuclear Information System (INIS)

Gorbar, E.V.; Gusynin, V.P.; Loktev, V.M.

1992-01-01

Proceeding from microscopic model Hamiltonian for the system of Fermi-particles with attraction the effective Lagrangian, admitting the analysis of its superconducting properties at arbitrary fermion concentration, is obtained.Exact solution for gap and chemical potential makes it possible to trace from local pair situation to Cooper pairing. The crucial parameter discriminating between the regions of exotic and normal superconducting behaviour is show to be that of the energy of the bound fermion state, which, however, rapidly disappears with fermion density increasing. The solutions of the equations for the case of finite temperatures are analysed. (author). 42 refs

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

Science.gov (United States)

Richmond, Nicola J.; Abrams, Charlene A.; Wolohan, Philippa R. N.; Abrahamian, Edmond; Willett, Peter; Clark, Robert D.

2006-09-01

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.

Development and preliminary evaluation of a new anatomically based prosthetic alignment method for below-knee prosthesis.

Science.gov (United States)

Tafti, Nahid; Karimlou, Masoud; Mardani, Mohammad Ali; Jafarpisheh, Amir Salar; Aminian, Gholam Reza; Safari, Reza

2018-04-20

The objectives of current study were to a) assess similarities and relationships between anatomical landmark-based angles and distances of lower limbs in unilateral transtibial amputees and b) develop and evaluate a new anatomically based static prosthetic alignment method. First sub-study assessed the anthropometrical differences and relationships between the lower limbs in the photographs taken from amputees. Data were analysed via paired t-test and regression analysis. Results show no significant differences in frontal and transverse planes. In the sagittal plane, the anthropometric parameters of the amputated limb were significantly correlated to the corresponding variables of the sound limb. The results served as bases for the development of a new prosthetic alignment method. The method was evaluated on a single subject study. Prosthetic alignment carried out by an experienced prosthetist was compared with such alignment adjusted by an inexperienced prosthetist but with the use of the developed method. In sagittal and frontal planes, the socket angle was tuned with respect to the shin angle, and the position of the prosthetic foot was tuned in relation to the pelvic landmarks. Further study is needed to assess the proposed method on a larger sample of amputees and prosthetists.

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

Science.gov (United States)

Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

Mask alignment system for semiconductor processing

Science.gov (United States)

Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.; Grant, Christopher N.

2017-02-14

A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.

Type I band alignment in GaAs{sub 81}Sb{sub 19}/GaAs core-shell nanowires

Energy Technology Data Exchange (ETDEWEB)

Xu, T. [Institut d' Electronique, de Microélectronique et de Nanotechnologies (IEMN), CNRS, UMR 8520, Département ISEN, 41 bd Vauban, 59046 Lille Cedex (France); Key Laboratory of Advanced Display and System Application, Shanghai University, 149 Yanchang Road, Shanghai 200072 (China); Wei, M. J. [Key Laboratory of Advanced Display and System Application, Shanghai University, 149 Yanchang Road, Shanghai 200072 (China); Capiod, P.; Díaz Álvarez, A.; Han, X. L.; Troadec, D.; Nys, J. P.; Berthe, M.; Lefebvre, I.; Grandidier, B., E-mail: bruno.grandidier@isen.iemn.univ-lille1.fr [Institut d' Electronique, de Microélectronique et de Nanotechnologies (IEMN), CNRS, UMR 8520, Département ISEN, 41 bd Vauban, 59046 Lille Cedex (France); Patriarche, G. [CNRS-Laboratoire de Photonique et de Nanostructures (LPN), Route de Nozay, 91460 Marcoussis (France); Plissard, S. R. [Institut d' Electronique, de Microélectronique et de Nanotechnologies (IEMN), CNRS, UMR 8520, Département ISEN, 41 bd Vauban, 59046 Lille Cedex (France); CNRS-Laboratoire d' Analyse et d' Architecture des Systèmes (LAAS), Univ. de Toulouse, 7 Avenue du Colonel Roche, F-31400 Toulouse (France); Caroff, P. [Institut d' Electronique, de Microélectronique et de Nanotechnologies (IEMN), CNRS, UMR 8520, Département ISEN, 41 bd Vauban, 59046 Lille Cedex (France); Department of Electronic Materials Engineering, Research School of Physics and Engineering, The Australian National University, Canberra, Australian Capital Territory 0200 (Australia); and others

2015-09-14

The composition and band gap of the shell that formed during the growth of axial GaAs/GaAs{sub 81}Sb{sub 19}/ GaAs heterostructure nanowires have been investigated by transmission electron microscopy combined with energy dispersion spectroscopy, scanning tunneling spectroscopy, and density functional theory calculations. On the GaAs{sub 81}Sb{sub 19} intermediate segment, the shell is found to be free of Sb (pure GaAs shell) and transparent to the tunneling electrons, despite the (110) biaxial strain that affects its band gap. As a result, a direct measurement of the core band gap allows the quantitative determination of the band offset between the GaAs{sub 81}Sb{sub 19} core and the GaAs shell and identifies it as a type I band alignment.

Ab initio calculation of band alignment of epitaxial La2O3 on Si(111 substrate

Directory of Open Access Journals (Sweden)

Alberto Debernardi

2015-08-01

Full Text Available By means of plane wave pseudopotential method we have studied the electronic properties of the heterostructure formed by an high dielectric constant (k oxide, the hexagonal La2O3 epitaxially grown with (0001-orientation on Si (111 substrate. We found that for La2O3 both the dielectric constant along the growth direction and the band gap are larger in the epitaxial film than in the bulk. By super-cell techniques we have computed the band alignment of the junction finding a valence band offset and a conduction band offset of ~1.6 eV and ~1.7 eV respectively. We demonstrate that the band alignment can be engineered by δ-doping the interface: our simulations show that, by doping the interface with S or Se monolayer, the valence (conduction band offset increases (decreases of about 0.5 eV without the formation of spurious electronic states in the semiconductor band-gap. The simulation of the critical thickness of pseudomorphic Lanthana film complete the work. Our results are relevant for the realization of a new generation of devices based on ultra-scaled complementary metal oxides semiconductors (CMOS technology.

Ballistic phonon and thermal radiation transport across a minute vacuum gap in between aluminum and silicon thin films: Effect of laser repetitive pulses on transport characteristics

Science.gov (United States)

Yilbas, B. S.; Ali, H.

2016-08-01

Short-pulse laser heating of aluminum and silicon thin films pair with presence of a minute vacuum gap in between them is considered and energy transfer across the thin films pair is predicted. The frequency dependent Boltzmann equation is used to predict the phonon intensity distribution along the films pair for three cycles of the repetitive short-pulse laser irradiation on the aluminum film surface. Since the gap size considered is within the Casimir limit, thermal radiation and ballistic phonon contributions to energy transfer across the vacuum gap is incorporated. The laser irradiated field is formulated in line with the Lambert's Beer law and it is considered as the volumetric source in the governing equations of energy transport. In order to assess the phonon intensity distribution in the films pair, equivalent equilibrium temperature is introduced. It is demonstrated that thermal separation of electron and lattice sub-systems in the aluminum film, due to the short-pulse laser irradiation, takes place and electron temperature remains high in the aluminum film while equivalent equilibrium temperature for phonons decays sharply in the close region of the aluminum film interface. This behavior is attributed to the phonon boundary scattering at the interface and the ballistic phonon transfer to the silicon film across the vacuum gap. Energy transfer due to the ballistic phonon contribution is significantly higher than that of the thermal radiation across the vacuum gap.

Ballistic phonon and thermal radiation transport across a minute vacuum gap in between aluminum and silicon thin films: Effect of laser repetitive pulses on transport characteristics

Energy Technology Data Exchange (ETDEWEB)

Yilbas, B.S., E-mail: bsyilbas@kfupm.edu.sa; Ali, H.

2016-08-15

Short-pulse laser heating of aluminum and silicon thin films pair with presence of a minute vacuum gap in between them is considered and energy transfer across the thin films pair is predicted. The frequency dependent Boltzmann equation is used to predict the phonon intensity distribution along the films pair for three cycles of the repetitive short-pulse laser irradiation on the aluminum film surface. Since the gap size considered is within the Casimir limit, thermal radiation and ballistic phonon contributions to energy transfer across the vacuum gap is incorporated. The laser irradiated field is formulated in line with the Lambert's Beer law and it is considered as the volumetric source in the governing equations of energy transport. In order to assess the phonon intensity distribution in the films pair, equivalent equilibrium temperature is introduced. It is demonstrated that thermal separation of electron and lattice sub-systems in the aluminum film, due to the short-pulse laser irradiation, takes place and electron temperature remains high in the aluminum film while equivalent equilibrium temperature for phonons decays sharply in the close region of the aluminum film interface. This behavior is attributed to the phonon boundary scattering at the interface and the ballistic phonon transfer to the silicon film across the vacuum gap. Energy transfer due to the ballistic phonon contribution is significantly higher than that of the thermal radiation across the vacuum gap.

Ballistic phonon and thermal radiation transport across a minute vacuum gap in between aluminum and silicon thin films: Effect of laser repetitive pulses on transport characteristics

International Nuclear Information System (INIS)

Yilbas, B.S.; Ali, H.

2016-01-01

Short-pulse laser heating of aluminum and silicon thin films pair with presence of a minute vacuum gap in between them is considered and energy transfer across the thin films pair is predicted. The frequency dependent Boltzmann equation is used to predict the phonon intensity distribution along the films pair for three cycles of the repetitive short-pulse laser irradiation on the aluminum film surface. Since the gap size considered is within the Casimir limit, thermal radiation and ballistic phonon contributions to energy transfer across the vacuum gap is incorporated. The laser irradiated field is formulated in line with the Lambert's Beer law and it is considered as the volumetric source in the governing equations of energy transport. In order to assess the phonon intensity distribution in the films pair, equivalent equilibrium temperature is introduced. It is demonstrated that thermal separation of electron and lattice sub-systems in the aluminum film, due to the short-pulse laser irradiation, takes place and electron temperature remains high in the aluminum film while equivalent equilibrium temperature for phonons decays sharply in the close region of the aluminum film interface. This behavior is attributed to the phonon boundary scattering at the interface and the ballistic phonon transfer to the silicon film across the vacuum gap. Energy transfer due to the ballistic phonon contribution is significantly higher than that of the thermal radiation across the vacuum gap.

Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

Directory of Open Access Journals (Sweden)

Hartmann Stefanie

2008-03-01

Full Text Available Abstract Background While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood and studied ways to improve the accuracy of trees obtained from such datasets. Results We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion These results demonstrate that partial gene

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Science.gov (United States)

Hartmann, Stefanie; Vision, Todd J

2008-03-26

While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets. We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a

Shedding Light on the Dark Continent: A Historical Perspective for U.S. Army Regional Alignment

Science.gov (United States)

2013-12-10

importantly, to identify gaps in understanding, training, and doctrine. In the early stages of regional alignment, operational planners would benefit from a...average soldier could expect access to a steady diet of maize , meat, tea, beans, and rice. In fact, at various times, more Ugandans volunteered than...presence or limited use of paramilitary agencies which yields relative stability. Senegal is a prime example of both ideas given its history of an

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

Science.gov (United States)

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an

GraphCrunch 2: Software tool for network modeling, alignment and clustering

Directory of Open Access Journals (Sweden)

Hayes Wayne

2011-01-01

Full Text Available Abstract Background Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. Results We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL" for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other

MUON DETECTORS: ALIGNMENT

CERN Multimedia

M. Dallavalle

2013-01-01

A new Muon misalignment scenario for 2011 (7 TeV) Monte Carlo re-processing was re-leased. The scenario is based on running of standard track-based reference-target algorithm (exactly as in data) using single-muon simulated sample (with the transverse-momentum spectrum matching data). It used statistics similar to what was used for alignment with 2011 data, starting from an initially misaligned Muon geometry from uncertainties of hardware measurements and using the latest Tracker misalignment geometry. Validation of the scenario (with muons from Z decay and high-pT simulated muons) shows that it describes data well. The study of systematic uncertainties (dominant by now due to huge amount of data collected by CMS and used for muon alignment) is finalised. Realistic alignment position errors are being obtained from the estimated uncertainties and are expected to improve the muon reconstruction performance. Concerning the Hardware Alignment System, the upgrade of the Barrel Alignment is in progress. By now, d...

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

2011-01-01

A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

Science.gov (United States)

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

Science.gov (United States)

Lizotte, Todd E.

2011-10-01

Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview

Gap Structure and Gapless Structure in Fractional Quantum Hall Effect

Directory of Open Access Journals (Sweden)

Shosuke Sasaki

2012-01-01

Full Text Available Higher-order composite fermion states are correlated with many quasiparticles. The energy calculations are very complicated. We develop the theory of Tao and Thouless to explain them. The total Hamiltonian is (+, where includes Landau energies and classical Coulomb energies. We find the most uniform electron configuration in Landau states which has the minimum energy of . At =(2−1/(2, all the nearest electron pairs are forbidden to transfer to any empty states because of momentum conservation. Therefore, perturbation energies of the nearest electron pairs are zero in all order of perturbation. At =/(2−1, /(2+1, all the nearest electron (or hole pairs can transfer to all hole (or electron states. At =4/11, 4/13, 5/13, 5/17, 6/17, only the specific nearest hole pairs can transfer to all electron states. For example, the nearest-hole-pair energy at =4/11 is lower than the limiting energies from both sides (the left side =(4+1/(11+3 and the right side =(4−1/(11−3 for infinitely large . Thus, the nearest-hole-pair energy at specific is different from the limiting values from both sides. The property yields energy gap for the specific . Also gapless structure appears at other filling factors (e.g., at =1/2.

Tidal alignment of galaxies

Energy Technology Data Exchange (ETDEWEB)

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

2015-08-01

We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.

Spin dynamics in the pseudo-gap state of a high-temperature superconductor

Energy Technology Data Exchange (ETDEWEB)

Hinkov, V; Lin, C T; Chen, D P; Keimer, B [Max Planck Inst Solid State Res, D-70569 Stuttgart, (Germany); Bourges, P; Pailhes, S; Sidis, Y [CEA, CNRS, CE Saclay, Lab Leon Brillouin, F-91191 Gif Sur Yvette, (France); Ivanov, A [Inst Max Von Laue Paul Langevin, F-38042 Grenoble, (France); Frost, C D; Perring, T G [Rutherford Appleton Lab, ISIS Facil, Didcot OX11 0QX, Oxon, (United Kingdom)

2007-07-01

The pseudo-gap is one of the most pervasive phenomena of high-temperature superconductors. It is attributed either to incoherent Cooper pairing setting in above the superconducting transition temperature, Tc, or to a hidden order parameter competing with superconductivity. Here, we use inelastic neutron scattering from under-doped YBa{sub 2}Cu{sub 3}O{sub 6.6} to show that the dispersion relations of spin excitations in the superconducting and pseudo-gap states are qualitatively different. Specifically, the extensively studied 'hour glass' shape of the magnetic dispersions in the superconducting state is no longer discernible in the pseudo-gap state and we observe an unusual 'vertical' dispersion with pronounced in-plane anisotropy. The differences between superconducting and pseudo-gap states are thus more profound than generally believed, suggesting a competition between these two states. Whereas the high-energy excitations are common to both states and obey the symmetry of the copper oxide square lattice, the low-energy excitations in the pseudo-gap state may be indicative of collective fluctuations towards a state with broken orientational symmetry predicted in theoretical work. (authors)

Preparation of the spacer for narrow electrode gap configuration in ionization-based gas sensor

International Nuclear Information System (INIS)

Saheed, Mohamed Shuaib Mohamed; Mohamed, Norani Muti; Burhanudin, Zainal Arif

2012-01-01

Carbon nanotubes (CNTs) have started to be developed as the sensing element for ionization-based gas sensors due to the demand for improved sensitivity, selectivity, stability and other sensing properties beyond what can be offered by the conventional ones. Although these limitations have been overcome, the problems still remain with the conventional ionization-based gas sensors in that they are bulky and operating with large breakdown voltage and high temperature. Recent studies have shown that the breakdown voltage can be reduced by using nanostructured electrodes and narrow electrode gap. Nanostructured electrode in the form of aligned CNTs array with evenly distributed nanotips can enhance the linear electric field significantly. The later is attributed to the shorter conductivity path through narrow electrode gap. The paper presents the study on the design consideration in order to realize ionization based gas sensor using aligned carbon nanotubes array in an optimum sensor configuration with narrow electrode gap. Several deposition techniques were studied to deposit the spacer, the key component that can control the electrode gap. Plasma spray deposition, electron beam deposition and dry oxidation method were employed to obtain minimum film thickness around 32 μm. For plasma spray method, sand blasting process is required in order to produce rough surface for strong bonding of the deposited film onto the surface. Film thickness, typically about 39 μm can be obtained. For the electron beam deposition and dry oxidation, the film thickness is in the range of nanometers and thus unsuitable to produce the spacer. The deposited multilayer film consisting of copper, alumina and ferum on which CNTs array will be grown was found to be removed during the etching process. This is attributed to the high etching rate on the thin film which can be prevented by reducing the rate and having a thicker conductive copper film.

Preparation of the spacer for narrow electrode gap configuration in ionization-based gas sensor

Energy Technology Data Exchange (ETDEWEB)

Saheed, Mohamed Shuaib Mohamed; Mohamed, Norani Muti; Burhanudin, Zainal Arif [Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, Seri Iskandar, Tronoh, Perak. (Malaysia); Fundamental and Applied Science, Universiti Teknologi PETRONAS, Seri Iskandar, Tronoh, Perak. (Malaysia); Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, Seri Iskandar, Tronoh, Perak. (Malaysia)

2012-09-26

Carbon nanotubes (CNTs) have started to be developed as the sensing element for ionization-based gas sensors due to the demand for improved sensitivity, selectivity, stability and other sensing properties beyond what can be offered by the conventional ones. Although these limitations have been overcome, the problems still remain with the conventional ionization-based gas sensors in that they are bulky and operating with large breakdown voltage and high temperature. Recent studies have shown that the breakdown voltage can be reduced by using nanostructured electrodes and narrow electrode gap. Nanostructured electrode in the form of aligned CNTs array with evenly distributed nanotips can enhance the linear electric field significantly. The later is attributed to the shorter conductivity path through narrow electrode gap. The paper presents the study on the design consideration in order to realize ionization based gas sensor using aligned carbon nanotubes array in an optimum sensor configuration with narrow electrode gap. Several deposition techniques were studied to deposit the spacer, the key component that can control the electrode gap. Plasma spray deposition, electron beam deposition and dry oxidation method were employed to obtain minimum film thickness around 32 {mu}m. For plasma spray method, sand blasting process is required in order to produce rough surface for strong bonding of the deposited film onto the surface. Film thickness, typically about 39 {mu}m can be obtained. For the electron beam deposition and dry oxidation, the film thickness is in the range of nanometers and thus unsuitable to produce the spacer. The deposited multilayer film consisting of copper, alumina and ferum on which CNTs array will be grown was found to be removed during the etching process. This is attributed to the high etching rate on the thin film which can be prevented by reducing the rate and having a thicker conductive copper film.

ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

Directory of Open Access Journals (Sweden)

Kim Taeho

2010-09-01

Full Text Available Abstract Background There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC environment with a greatly extended data storage capacity. Results We designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA. The new editing option and the graphical user interface (GUI provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets. Conclusions ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1 the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2 Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3 Support for both single PC and distributed cluster systems.

CsI Calorimeter for a Compton-Pair Telescope

Science.gov (United States)

Grove, Eric J.

We propose to build and test a hodoscopic CsI(Tl) scintillating-crystal calorimeter for a medium-energy γ-ray Compton and pair telescope. The design and technical approach for this calorimeter relies deeply on heritage from the Fermi LAT CsI Calorimeter, but it dramatically improves the low-energy performance of that design by reading out the scintillation light with silicon photomultipliers (SiPMs), making the technology developed for Fermi applicable in the Compton regime. While such a hodoscopic calorimeter is useful for an entire class of medium-energy γ-ray telescope designs, we propose to build it explicitly to support beam tests and balloon flight of the Proto-ComPair telescope, the development and construction of which was funded in a four-year APRA program beginning in 2015 ("ComPair: Steps to a Medium Energy γ-ray Mission" with PI J. McEnery of GSFC). That award did not include funding for its CsI calorimeter subsystem, and this proposal is intended to cover that gap. ComPair is a MIDEX-class instrument concept to perform a high-sensitivity survey of the γ-ray sky from 0.5 MeV to 500 MeV. ComPair is designed to provide a dramatic increase in sensitivity relative to previous instruments in this energy range (predominantly INTEGRAL/SPI and Compton COMPTEL), with the same transformative sensitivity increase - and corresponding scientific return- that the Fermi Large Area Telescope provided relative to Compton EGRET. To enable transformative science over a broad range of MeV energies and with a wide field of view, ComPair is a combined Compton telescope and pair telescope employing a silicon-strip tracker (for Compton scattering and pair conversion and tracking) and a solid-state CdZnTe calorimeter (for Compton absorption) and CsI calorimeter (for pair calorimetry), surrounded by a plastic scintillator anti-coincidence detector. Under the current proposal, we will complete the detailed design, assembly, and test of the CsI calorimeter for the risk

Alignment of ICNP® 2.0 ontology and a proposed INCP® Brazilian ontology.

Science.gov (United States)

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; Nóbrega, Maria Miriam Lima da

2014-01-01

to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology. document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence, their names, and their sibling, parent, and child classes. there were 2,682 concepts present in the ICNP® 2.0 Ontology that were missing in the Brazilian Ontology; 717 concepts present in the Brazilian Ontology were missing in the ICNP® 2.0 Ontology; and there were 215 pairs of matching concepts. it is believed that the correspondences identified in this study might contribute to the interoperability between the representations of nursing practice elements in ICNP®, thus allowing the standardization of nursing records based on this classification system.

Deformation properties of osmium, platinum, mercury isotopes from self-consistent calculations: influence of the pairing treatment

International Nuclear Information System (INIS)

Sauvage-Letessier, J.; Quentin, P.; Flocard, H.

1981-01-01

The deformation properties of several isotopes of the elements Os, Pt and Hg have been computed by means of Hartree-Fock plus BCS calculations. The Hartree-Fock potential has been derived from the Skyrme interaction S III. Two approximations have been used for the treatment of pairing correlations: the constant (versus deformation) gap method and the constant (versus deformation) pairing matrix element method. A good agreement with experimental data is obtained for ground state deformation properties except for the exact location of the prolate-oblate transition as a function of the neutron number. For one nucleus 184 Hg, the pairing matrix elements have been calculated from the Gogny interaction D1, in order to study their single particle state- and deformation-dependence. From these results, the validity of the two approximations used for pairing correlations, is discussed

Pairing in the BCS and LN approximations using continuum single particle level density

International Nuclear Information System (INIS)

Id Betan, R.M.; Repetto, C.E.

2017-01-01

Understanding the properties of drip line nuclei requires to take into account the correlations with the continuum spectrum of energy of the system. This paper has the purpose to show that the continuum single particle level density is a convenient way to consider the pairing correlation in the continuum. Isospin mean-field and isospin pairing strength are used to find the Bardeen–Cooper–Schrieffer (BCS) and Lipkin–Nogami (LN) approximate solutions of the pairing Hamiltonian. Several physical properties of the whole chain of the Tin isotope, as gap parameter, Fermi level, binding energy, and one- and two-neutron separation energies, were calculated and compared with other methods and with experimental data when they exist. It is shown that the use of the continuum single particle level density is an economical way to include explicitly the correlations with the continuum spectrum of energy in large scale mass calculation. It is also shown that the computed properties are in good agreement with experimental data and with more sophisticated treatment of the pairing interaction.

Defective pairing and synaptonemal complex formation in a Sordaria mutant (spo44) with a translocated segment of the nucleolar organizer.

Science.gov (United States)

Zickler, D; de Lares, L; Moreau, P J; Leblon, G

1985-01-01

The recessive meiotic mutant spo44 of Sordaria macrospora, with 90% ascospore abortion, exhibits striking effects on recombination (67% decrease), irregular segregation of the almost unpaired homologues, and a decrease in chiasma frequency in the few cases where bivalents are formed. Three-dimensional reconstructions of ten prophase nuclei indicate that pairing, as judged by the absence of fully formed synaptonemal complexes (SC), is not achieved although lateral elements (LE) assemble. The pairing failure is attributable to defects in the alignment of homologous chromosomes. The leptotene alignment seen in the wild type before SC formation was not observed in the spo44 nuclei. Dense material, considered to be precursor of SC central elements, was found scattered among the LE in two nuclei. The behaviour of spo44 substantiates the hypothesis that chromosome matching and SC formation are separable events. - The total length of the LE in the mutant is the same as in the wild type, but due to variable numbers and length of the individual LE, homologues cannot be lined up. Light microscopic observations indicate that the irregular length and number of LE is due to extensive chromosome breakage. The wild-type function corresponding to spo44 is required for both LE integrity and chromosome matching. Reconstructions of heterozygous nuclei reveal the presence of a supernumerary nucleolar organizer in one arm of chromosome 7. It is suggested that rDNA has been inserted into a gene whose function is involved in pairing or into a controlling sequence that interacts with the pairing process.

Theory of superconductivity. II. Excited Cooper pairs. Why does sodium remain normal down to 0 K?

International Nuclear Information System (INIS)

Fujita, S.

1992-01-01

Based on a generalized BCS Hamiltonian in which the interaction strengths (V 11 , V 22 , V 12 ) among and between electron (12) and hole (2) Cooper pairs are differentiated, the thermodynamic properties of a type-I superconductor below the critical temperature T c are investigated. An expression for the ground-state energy, W - W 0 , relative to the unperturbed Block system is obtained. The usual BCS formulas are obtained in the limits: (all) V jl = V 0 , N 1 (0) = N 2 (0). Any excitations generated through the BCS interaction Hamiltonian containing V jl must involve Cooper pairs of antiparallel spins and nearly opposite momenta. The nonzero momentum or excited Cooper pairs below T c are shown to have an excitation energy band minimum lower than the quasi-electrons, which were regarded as the elementary excitations in the original BCS theory. The energy gap var-epsilon g (T) defined relative to excited and zero-momentum Copper pairs (when V jl > 0) decreases from var-epsilon g (0) to 0 as the temperature T is raised from 0 to T c . If electrons only are available as in a monovalent metal like sodium (V 12 = 0), the energy constant Δ 1 is finite but the energy gap vanishes identically for all T. In agreement with the BCS theory, the present theory predicts that a pure nonmagnetic metal in any dimensions should have a Cooper-pair ground state whose energy is lower than that of the Bloch ground state. Additionally it predicts that a monovalent metal should remain normal down to 0 K, and that there should be no strictly one-dimensional superconductor

Optical properties of (AlxGa1-x)(0.52)In0.48P at the crossover from a direct-gap to an indirect-gap semiconductor

DEFF Research Database (Denmark)

Dörr, U.; Schwarz, W.; Wörner, A.

1998-01-01

The optical properties and the dynamics of excitons and the electron-hole plasma have been studied in disordered (AlxGa1 – x)0.52In0.48P near to the direct-to-indirect band gap crossover. In particular we have investigated three epitaxial layers grown by solid-source molecular beam epitaxy...... recombination processes depends strongly on temperature, excitation intensity, and excitation pulse duration, the processes can be identified by changing these parameters. As a result, we can determine the relative alignment of the conduction band minima and the distribution of the electrons among them. At high...... with varying Al content x. Two of them have compositions in the immediate vicinity of the crossover point, the other is assigned to the indirect-gap regime. Both direct and indirect recombination processes contribute to the photon emission from the material. Since the relative importance of the different...

Alignment of time-resolved data from high throughput experiments.

Science.gov (United States)

Abidi, Nada; Franke, Raimo; Findeisen, Peter; Klawonn, Frank

2016-12-01

To better understand the dynamics of the underlying processes in cells, it is necessary to take measurements over a time course. Modern high-throughput technologies are often used for this purpose to measure the behavior of cell products like metabolites, peptides, proteins, [Formula: see text]RNA or mRNA at different points in time. Compared to classical time series, the number of time points is usually very limited and the measurements are taken at irregular time intervals. The main reasons for this are the costs of the experiments and the fact that the dynamic behavior usually shows a strong reaction and fast changes shortly after a stimulus and then slowly converges to a certain stable state. Another reason might simply be missing values. It is common to repeat the experiments and to have replicates in order to carry out a more reliable analysis. The ideal assumptions that the initial stimulus really started exactly at the same time for all replicates and that the replicates are perfectly synchronized are seldom satisfied. Therefore, there is a need to first adjust or align the time-resolved data before further analysis is carried out. Dynamic time warping (DTW) is considered as one of the common alignment techniques for time series data with equidistant time points. In this paper, we modified the DTW algorithm so that it can align sequences with measurements at different, non-equidistant time points with large gaps in between. This type of data is usually known as time-resolved data characterized by irregular time intervals between measurements as well as non-identical time points for different replicates. This new algorithm can be easily used to align time-resolved data from high-throughput experiments and to come across existing problems such as time scarcity and existing noise in the measurements. We propose a modified method of DTW to adapt requirements imposed by time-resolved data by use of monotone cubic interpolation splines. Our presented approach

Distinguishing spin-aligned and isotropic black hole populations with gravitational waves.

Science.gov (United States)

Farr, Will M; Stevenson, Simon; Miller, M Coleman; Mandel, Ilya; Farr, Ben; Vecchio, Alberto

2017-08-23

The direct detection of gravitational waves from merging binary black holes opens up a window into the environments in which binary black holes form. One signature of such environments is the angular distribution of the black hole spins. Binary systems that formed through dynamical interactions between already-compact objects are expected to have isotropic spin orientations (that is, the spins of the black holes are randomly oriented with respect to the orbit of the binary system), whereas those that formed from pairs of stars born together are more likely to have spins that are preferentially aligned with the orbit. The best-measured combination of spin parameters for each of the four likely binary black hole detections GW150914, LVT151012, GW151226 and GW170104 is the 'effective' spin. Here we report that, if the magnitudes of the black hole spins are allowed to extend to high values, the effective spins for these systems indicate a 0.015 odds ratio against an aligned angular distribution compared to an isotropic one. When considering the effect of ten additional detections, this odds ratio decreases to 2.9 × 10 -7 against alignment. The existing preference for either an isotropic spin distribution or low spin magnitudes for the observed systems will be confirmed (or overturned) confidently in the near future.

The alignment of espoused values and organisational culture at a South African parastatal organisation

OpenAIRE

2012-01-01

M.Comm. The primary purpose of the present study was to identify whether the organisational culture of the Transmission Division of Eskom is aligned to its stated values. In seeking to reach this objective, it was necessary to assess the gap between espoused and practised organisational values. The study also sought to identify the Transmission Division’s organisational culture. A correlation between the stated values and identified organisational culture was calculated and this was used t...

GAP ANALYSIS OF TRAVELOKA.COM: HOTEL CONSUMERS’ EXPECTATIONS AND PERCEPTIONS OF THE WEBSITE

Directory of Open Access Journals (Sweden)

Fransisca Andreani

2018-03-01

Full Text Available Traveloka.com is one of the famous online travel agents to make hotel reservation in Indonesia. Consumers making online hotel reservation can sometimes find that the performance of the website does not meet their needs. This study is to analyze the gap between hotel consumer expectations and perceptions on the website dimensions of traveloka.com. It is a quantitative method with 150 respondents who made hotel re­ser­vations through traveloka.com. The analysis techniques used are mean test and paired t-test. The results show that there are significant gaps between consumer expectations and perceptions on the website dimensions of traveloka.com. The biggest gap is on the images displayed which are in accordance with the real conditions.

Clear aligners in orthodontic treatment.

Science.gov (United States)

Weir, T

2017-03-01

Since the introduction of the Tooth Positioner (TP Orthodontics) in 1944, removable appliances analogous to clear aligners have been employed for mild to moderate orthodontic tooth movements. Clear aligner therapy has been a part of orthodontic practice for decades, but has, particularly since the introduction of Invisalign appliances (Align Technology) in 1998, become an increasingly common addition to the orthodontic armamentarium. An internet search reveals at least 27 different clear aligner products currently on offer for orthodontic treatment. The present paper will highlight the increasing popularity of clear aligner appliances, as well as the clinical scope and the limitations of aligner therapy in general. Further, the paper will outline the differences between the various types of clear aligner products currently available. © 2017 Australian Dental Association.

Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

Science.gov (United States)

Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

2008-09-01

A method to functionally annotate structural genomics targets, based on a novel structural alignment scoring function, is proposed. In the proposed score, position-specific scoring matrices are used to weight structurally aligned residue pairs to highlight evolutionarily conserved motifs. The functional form of the score is first optimized for discriminating domains belonging to the same Pfam family from domains belonging to different families but the same CATH or SCOP superfamily. In the optimization stage, we consider four standard weighting functions as well as our own, the "maximum substitution probability," and combinations of these functions. The optimized score achieves an area of 0.87 under the receiver-operating characteristic curve with respect to identifying Pfam families within a sequence-unique benchmark set of domain pairs. Confidence measures are then derived from the benchmark distribution of true-positive scores. The alignment method is next applied to the task of functionally annotating 230 query proteins released to the public as part of the Protein 3000 structural genomics project in Japan. Of these queries, 78 were found to align to templates with the same Pfam family as the query or had sequence identities > or = 30%. Another 49 queries were found to match more distantly related templates. Within this group, the template predicted by our method to be the closest functional relative was often not the most structurally similar. Several nontrivial cases are discussed in detail. Finally, 103 queries matched templates at the fold level, but not the family or superfamily level, and remain functionally uncharacterized. 2008 Wiley-Liss, Inc.

Topological superfluids with finite-momentum pairing and Majorana fermions.

Science.gov (United States)

Qu, Chunlei; Zheng, Zhen; Gong, Ming; Xu, Yong; Mao, Li; Zou, Xubo; Guo, Guangcan; Zhang, Chuanwei

2013-01-01

Majorana fermions (MFs), quantum particles that are their own antiparticles, are not only of fundamental importance in elementary particle physics and dark matter, but also building blocks for fault-tolerant quantum computation. Recently MFs have been intensively studied in solid state and cold atomic systems. These studies are generally based on superconducting pairing with zero total momentum. On the other hand, finite total momentum Cooper pairings, known as Fulde-Ferrell (FF) Larkin-Ovchinnikov (LO) states, were widely studied in many branches of physics. However, whether FF and LO superconductors can support MFs has not been explored. Here we show that MFs can exist in certain types of gapped FF states, yielding a new quantum matter: topological FF superfluids/superconductors. We demonstrate the existence of such topological FF superfluids and the associated MFs using spin-orbit-coupled degenerate Fermi gases and derive their parameter regions. The implementation of topological FF superconductors in semiconductor/superconductor heterostructures is also discussed.

Close near-degeneracy in a pair of four-quasiparticle bands in 194Tl

International Nuclear Information System (INIS)

Masiteng, P.L.; Lawrie, E.A.; Ramashidzha, T.M.; Bark, R.A.; Carlsson, B.G.; Lawrie, J.J.; Lindsay, R.; Komati, F.; Kau, J.; Maine, P.; Maliage, S.M.; Matamba, I.; Mullins, S.M.; Murray, S.H.T.; Mutshena, K.P.; Pasternak, A.A.; Ragnarsson, I.

2013-01-01

A pair of rotational bands associated with the πh 9/2 ⊗νi 13/2 −1 configuration at lower spins and with the πh 9/2 ⊗νi 13/2 −3 configuration at higher spins is found in 194 Tl. The two 4-quasiparticle bands show exceptionally close near-degeneracy in the excitation energies. Furthermore close similarity is also found in their alignments and B(M1)/B(E2) reduced transition probability ratios. Such close near-degeneracy probably indicates chiral geometry in the angular momentum space

MUON DETECTORS: ALIGNMENT

CERN Multimedia

Gervasio Gomez

2012-01-01

  The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

2010-01-01

For the last three months, the Muon Alignment group has focussed on providing a new, improved set of alignment constants for the end-of-year data reprocessing. These constants were delivered on time and approved by the CMS physics validation team on November 17. The new alignment incorporates several improvements over the previous one from March for nearly all sub-systems. Motivated by the loss of information from a hardware failure in May (an entire MAB was lost), the optical barrel alignment has moved from a modular, super-plane reconstruction, to a full, single loop calculation of the entire geometry for all DTs in stations 1, 2 and 3. This makes better use of the system redundancy, mitigating the effect of the information loss. Station 4 is factorised and added afterwards to make the system smaller (and therefore faster to run), and also because the MAB calibration at the MB4 zone is less precise. This new alignment procedure was tested at 0 T against photogrammetry resulting in precisions of the order...

Non-separable pairing interaction kernels applied to superconducting cuprates

International Nuclear Information System (INIS)

Haley, Stephen B.; Fink, Herman J.

2014-01-01

Highlights: • Non-separable interaction kernels with weak interactions produces HTS. • A probabilistic approach is used in filling the electronic states in the unit cell. • A set of coupled equations is derived which describes the energy gap. • SC properties of separable with non-separable interactions are compared. • There is agreement with measured properties of the SC and normal states. - Abstract: A pairing Hamiltonian H(Γ) with a non-separable interaction kernel Γ produces HTS for relatively weak interactions. The doping and temperature dependence of Γ(x,T) and the chemical potential μ(x) is determined by a probabilistic filling of the electronic states in the cuprate unit cell. A diverse set of HTS and normal state properties is examined, including the SC phase transition boundary T C (x), SC gap Δ(x,T), entropy S(x,T), specific heat C(x,T), and spin susceptibility χ s (x,T). Detailed x,T agreement with cuprate experiment is obtained for all properties

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

Directory of Open Access Journals (Sweden)

von Reumont Björn M

2010-03-01

Full Text Available Abstract Background Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. Results ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Conclusions Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment

How accurate is anatomic limb alignment in predicting mechanical limb alignment after total knee arthroplasty?

Science.gov (United States)

Lee, Seung Ah; Choi, Sang-Hee; Chang, Moon Jong

2015-10-27

Anatomic limb alignment often differs from mechanical limb alignment after total knee arthroplasty (TKA). We sought to assess the accuracy, specificity, and sensitivity for each of three commonly used ranges for anatomic limb alignment (3-9°, 5-10° and 2-10°) in predicting an acceptable range (neutral ± 3°) for mechanical limb alignment after TKA. We also assessed whether the accuracy of anatomic limb alignment was affected by anatomic variation. This retrospective study included 314 primary TKAs. The alignment of the limb was measured with both anatomic and mechanical methods of measurement. We also measured anatomic variation, including the femoral bowing angle, tibial bowing angle, and neck-shaft angle of the femur. All angles were measured on the same full-length standing anteroposterior radiographs. The accuracy, specificity, and sensitivity for each range of anatomic limb alignment were calculated and compared using mechanical limb alignment as the reference standard. The associations between the accuracy of anatomic limb alignment and anatomic variation were also determined. The range of 2-10° for anatomic limb alignment showed the highest accuracy, but it was only 73 % (3-9°, 65 %; 5-10°, 67 %). The specificity of the 2-10° range was 81 %, which was higher than that of the other ranges (3-9°, 69 %; 5-10°, 67 %). However, the sensitivity of the 2-10° range to predict varus malalignment was only 16 % (3-9°, 35 %; 5-10°, 68 %). In addition, the sensitivity of the 2-10° range to predict valgus malalignment was only 43 % (3-9°, 71 %; 5-10°, 43 %). The accuracy of anatomical limb alignment was lower for knees with greater femoral (odds ratio = 1.2) and tibial (odds ratio = 1.2) bowing. Anatomic limb alignment did not accurately predict mechanical limb alignment after TKA, and its accuracy was affected by anatomic variation. Thus, alignment after TKA should be assessed by measuring mechanical alignment rather than anatomic

Proposal for the generation of photon pairs with nonzero orbital angular momentum in a ring fiber

Czech Academy of Sciences Publication Activity Database

Javůrek, D.; Svozilík, J.; Peřina ml., Jan

2014-01-01

Roč. 22, č. 19 (2014), s. 23743-23748 ISSN 1094-4087 R&D Projects: GA ČR GAP205/12/0382 Institutional support: RVO:68378271 Keywords : photon pairs * orbital-angular-momentum states * spontaneous parametric down-conversion Subject RIV: BH - Optics , Masers, Lasers Impact factor: 3.488, year: 2014

Strategic Alignment and New Product Development

DEFF Research Database (Denmark)

Acur, Nuran; Kandemir, Destan; Boer, Harry

2012-01-01

Strategic alignment is widely accepted as a prerequisite for a firm’s success, but insight into the role of alignment in, and its impact on, the new product evelopment (NPD) process and its performance is less well developed. Most publications on this topic either focus on one form of alignment...... of NPD performance indicators. Strategic planning and innovativeness appear to affect technological, market, and NPD-marketing alignment positively. Environmental munificence is negatively associated with NPD-marketing alignment, but has no effect on the two other forms of alignment. Technological change...... has a positive effect on technological alignment, a negative effect on NPD-marketing alignment, but no effect on market alignment. These findings suggest that internal capabilities are more likely to be associated with the development of strategic alignment than environmental factors are. Furthermore...

Evidence for phononic pairing in extremely overdoped ``pure'' d-wave superconductor Bi2212

Science.gov (United States)

He, Yu; Hishimoto, Makoto; Song, Dongjoon; Eisaki, Hiroshi; Shen, Zhi-Xun

2015-03-01

Recent advancement in High Tc cuprate superconductor research has elucidated strong interaction between superconductivity and competing orders. Therefore, the mechanism behind the 'pure' d-wave superconducting behavior becomes the next stepping stone to further the understanding. We have performed photoemission study on extremely overdoped Bi2212 single crystal synthesized via high pressure method. In this regime, we demonstrate the much reduced superconducting gap and the absence of pseudogap. Clear gap shifted bosonic mode coupling is observed throughout the entire Brillouin zone. Via full Eliashberg treatment, we find the electron-phonon coupling strength capable of producing a transition temperature very close to Tc. This strongly implies bosonic contribution to cuprate superconductivity's pairing glue.

Optical study of the band structure of wurtzite GaP nanowires

KAUST Repository

Assali, S.

2016-07-25

We investigated the optical properties of wurtzite (WZ) GaP nanowires by performing photoluminescence (PL) and time-resolved PL measurements in the temperature range from 4 K to 300 K, together with atom probe tomography to identify residual impurities in the nanowires. At low temperature, the WZ GaP luminescence shows donor-acceptor pair emission at 2.115 eV and 2.088 eV, and Burstein-Moss band-filling continuum between 2.180 and 2.253 eV, resulting in a direct band gap above 2.170 eV. Sharp exciton α-β-γ lines are observed at 2.140–2.164–2.252 eV, respectively, showing clear differences in lifetime, presence of phonon replicas, and temperature-dependence. The excitonic nature of those peaks is critically discussed, leading to a direct band gap of ∼2.190 eV and to a resonant state associated with the γ-line ∼80 meV above the Γ8C conduction band edge.

Optical study of the band structure of wurtzite GaP nanowires

KAUST Repository

Assali, S.; Greil, J.; Zardo, I.; Belabbes, Abderrezak; de Moor, M. W. A.; Koelling, S.; Koenraad, P. M.; Bechstedt, F.; Bakkers, E. P. A. M.; Haverkort, J. E. M.

2016-01-01

We investigated the optical properties of wurtzite (WZ) GaP nanowires by performing photoluminescence (PL) and time-resolved PL measurements in the temperature range from 4 K to 300 K, together with atom probe tomography to identify residual impurities in the nanowires. At low temperature, the WZ GaP luminescence shows donor-acceptor pair emission at 2.115 eV and 2.088 eV, and Burstein-Moss band-filling continuum between 2.180 and 2.253 eV, resulting in a direct band gap above 2.170 eV. Sharp exciton α-β-γ lines are observed at 2.140–2.164–2.252 eV, respectively, showing clear differences in lifetime, presence of phonon replicas, and temperature-dependence. The excitonic nature of those peaks is critically discussed, leading to a direct band gap of ∼2.190 eV and to a resonant state associated with the γ-line ∼80 meV above the Γ8C conduction band edge.

Individualized FAC on bottom tab subassemblies to minimize adhesive gap between emitter and optics

Science.gov (United States)

Sauer, Sebastian; Müller, Tobias; Haag, Sebastian; Beleke, Andreas; Zontar, Daniel; Baum, Christoph; Brecher, Christian

2017-02-01

High Power Diode Laser (HPDL) systems with short focal length fast-axis collimators (FAC) require submicron assembly precision. Conventional FAC-Lens assembly processes require adhesive gaps of 50 microns or more in order to compensate for component tolerances (e.g. deviation of back focal length) and previous assembly steps. In order to control volumetric shrinkage of fast-curing UV-adhesives shrinkage compensation is mandatory. The novel approach described in this paper aims to minimize the impact of volumetric shrinkage due to the adhesive gap between HPDL edge emitters and FAC-Lens. Firstly, the FAC is actively aligned to the edge emitter without adhesives or bottom tab. The relative position and orientation of FAC to emitter are measured and stored. Consecutively, an individual subassembly of FAC and bottom tab is assembled on Fraunhofer IPT's mounting station with a precision of +/-1 micron. Translational and lateral offsets can be compensated, so that a narrow and uniform glue gap for the consecutive bonding process of bottom tab to heatsink applies (Figure 4). Accordingly, FAC and bottom tab are mounted to the heatsink without major shrinkage compensation. Fraunhofer IPT's department assembly of optical systems and automation has made several publications regarding active alignment of FAC lenses [SPIE LASE 8241-12], volumetric shrinkage compensation [SPIE LASE 9730-28] and FAC on bottom tab assembly [SPIE LASE 9727-31] in automated production environments. The approach described in this paper combines these and is the logical continuation of that work towards higher quality of HPDLs.

Pair creation, motion, and annihilation of topological defects in two-dimensional nematic liquid crystals

Science.gov (United States)

Cortese, Dario; Eggers, Jens; Liverpool, Tanniemola B.

2018-02-01

We present a framework for the study of disclinations in two-dimensional active nematic liquid crystals and topological defects in general. The order tensor formalism is used to calculate exact multiparticle solutions of the linearized static equations inside a planar uniformly aligned state so that the total charge has to vanish. Topological charge conservation then requires that there is always an equal number of q =1 /2 and q =-1 /2 charges. Starting from a set of hydrodynamic equations, we derive a low-dimensional dynamical system for the parameters of the static solutions, which describes the motion of a half-disclination pair or of several pairs. Within this formalism, we model defect production and annihilation, as observed in experiments. Our dynamics also provide an estimate for the critical density at which production and annihilation rates are balanced.

ABS: Sequence alignment by scanning

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

ABS: Sequence alignment by scanning

KAUST Repository

Bonny, Mohamed Talal

2011-08-01

Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

Electron Band Alignment at Interfaces of Semiconductors with Insulating Oxides: An Internal Photoemission Study

Directory of Open Access Journals (Sweden)

Valeri V. Afanas'ev

2014-01-01

Full Text Available Evolution of the electron energy band alignment at interfaces between different semiconductors and wide-gap oxide insulators is examined using the internal photoemission spectroscopy, which is based on observations of optically-induced electron (or hole transitions across the semiconductor/insulator barrier. Interfaces of various semiconductors ranging from the conventional silicon to the high-mobility Ge-based (Ge, Si1-xGex, Ge1-xSnx and AIIIBV group (GaAs, InxGa1-xAs, InAs, GaP, InP, GaSb, InSb materials were studied revealing several general trends in the evolution of band offsets. It is found that in the oxides of metals with cation radii larger than ≈0.7 Å, the oxide valence band top remains nearly at the same energy (±0.2 eV irrespective of the cation sort. Using this result, it becomes possible to predict the interface band alignment between oxides and semiconductors as well as between dissimilar insulating oxides on the basis of the oxide bandgap width which are also affected by crystallization. By contrast, oxides of light elements, for example, Be, Mg, Al, Si, and Sc exhibit significant shifts of the valence band top. General trends in band lineup variations caused by a change in the composition of semiconductor photoemission material are also revealed.

Factors affecting femoral rotational angle based on the posterior condylar axis in gap-based navigation-assisted total knee arthroplasty for valgus knee.

Science.gov (United States)

Lee, Sung-Sahn; Lee, Yong-In; Kim, Dong-Uk; Lee, Dae-Hee; Moon, Young-Wan

2018-01-01

Achieving proper rotational alignment of the femoral component in total knee arthroplasty (TKA) for valgus knee is challenging because of lateral condylar hypoplasia and lateral cartilage erosion. Gap-based navigation-assisted TKA enables surgeons to determine the angle of femoral component rotation (FCR) based on the posterior condylar axis. This study evaluated the possible factors that affect the rotational alignment of the femoral component based on the posterior condylar axis. Between 2008 and 2016, 28 knees were enrolled. The dependent variable for this study was FCR based on the posterior condylar axis, which was obtained from the navigation system archives. Multiple regression analysis was conducted to identify factors that might predict FCR, including body mass index (BMI), Kellgren-Lawrence grade (K-L grade), lateral distal femoral angles obtained from the navigation system and radiographs (NaviLDFA, XrayLDFA), hip-knee-ankle (HKA) axis, lateral gap under varus stress (LGVS), medial gap under valgus stress (MGVS), and side-to-side difference (STSD, MGVS - LGVS). The mean FCR was 6.1° ± 2.0°. Of all the potentially predictive factors evaluated in this study, only NaviLDFA (β = -0.668) and XrayLDFA (β = -0.714) predicted significantly FCR. The LDFAs, as determined using radiographs and the navigation system, were both predictive of the rotational alignment of the femoral component based on the posterior condylar axis in gap-based TKA for valgus knee. A 1° increment with NaviLDFA led to a 0.668° decrement in FCR, and a 1° increment with XrayLDFA led to a 0.714° decrement. This suggests that symmetrical lateral condylar hypoplasia of the posterior and distal side occurs in lateral compartment end-stage osteoarthritis with valgus deformity.

Alignment for CSR

International Nuclear Information System (INIS)

Wang Shoujin; Man Kaidi; Guo Yizhen; Cai Guozhu; Guo Yuhui

2002-01-01

Cooled Storage Ring of Heavy Ion Research Facility in Lanzhou (HIRFL-CSR) belongs to China great scientific project in China. The alignment for it is very difficult because of very large area and very high accuracy. For the special case in HIRFL-CSR, some new methods and new instruments are used, including the construction of survey control network, the usage of laser tracker, and CSR alignment database system with applications developed to store and analyze data. The author describes the whole procedure of CSR alignment

Goldstone mode and pair-breaking excitations in atomic Fermi superfluids

Science.gov (United States)

Hoinka, Sascha; Dyke, Paul; Lingham, Marcus G.; Kinnunen, Jami J.; Bruun, Georg M.; Vale, Chris J.

2017-10-01

Spontaneous symmetry breaking is a central paradigm of elementary particle physics, magnetism, superfluidity and superconductivity. According to Goldstone's theorem, phase transitions that break continuous symmetries lead to the existence of gapless excitations in the long-wavelength limit. These Goldstone modes can become the dominant low-energy excitation, showing that symmetry breaking has a profound impact on the physical properties of matter. Here, we present a comprehensive study of the elementary excitations in a homogeneous strongly interacting Fermi gas through the crossover from a Bardeen-Cooper-Schrieffer (BCS) superfluid to a Bose-Einstein condensate (BEC) of molecules using two-photon Bragg spectroscopy. The spectra exhibit a discrete Goldstone mode, associated with the broken-symmetry superfluid phase, as well as pair-breaking single-particle excitations. Our techniques yield a direct determination of the superfluid pairing gap and speed of sound in close agreement with strong-coupling theories.

Limitations of the dual voltage clamp method in assaying conductance and kinetics of gap junction channels

OpenAIRE

Wilders, R.; Jongsma, H.J.

1992-01-01

The electrical properties of gap junctions in cell pairs are usually studied by means of the dual voltage clamp method. The voltage across the junctional channels, however, cannot be controlled adequately due to an artificial resistance and a natural resistance, both connected in series with the gap junction. The access resistances to the cell interior of the recording pipettes make up the artificial resistance. The natural resistance consists of the cytoplasmic access resistances to the tigh...

Pairwise Sequence Alignment Library

Energy Technology Data Exchange (ETDEWEB)

2015-05-20

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Belt Aligning Revisited

Directory of Open Access Journals (Sweden)

Yurchenko Vadim

2017-01-01

parts of the conveyor, the sides of the belt wear intensively. This results in reducing the life of the belt. The reasons for this phenomenon are well investigated, but the difficulty lies in the fact that they all act simultaneously. The belt misalignment prevention can be carried out in two ways: by minimizing the effect of causes and by aligning the belt. The construction of aligning devices and errors encountered in practice are considered in this paper. Self-aligning roller supports rotational in plan view are recommended as a means of combating the belt misalignment.

Antares beam-alignment-system performance

International Nuclear Information System (INIS)

Appert, Q.D.; Bender, S.C.

1983-01-01

The beam alignment system for the 24-beam-sector Antares CO 2 fusion laser automatically aligns more than 200 optical elements. A visible-wavelength alignment technique is employed which uses a telescope/TV system to view point-light sources appropriately located down the beamline. The centroids of the light spots are determined by a video tracker, which generates error signals used by the computer control system to move appropriate mirrors in a closed-loop system. Final touch-up alignment is accomplished by projecting a CO 2 alignment laser beam through the system and sensing its position at the target location. The techniques and control algorithms employed have resulted in alignment accuracies exceeding design requirements. By employing video processing to determine the centroids of diffraction images and by averaging over multiple TV frames, we achieve alignment accuracies better than 0.1 times system diffraction limits in the presence of air turbulence

A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

Energy Technology Data Exchange (ETDEWEB)

Hoang, Thiem [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Lazarian, A. [Department of Astronomy, University of Wisconsin-Madison (United States)

2016-11-10

The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model of RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.

Evaluation of alignment marks using ASML ATHENA alignment system in 90nm BEOL process

CERN Document Server

Tan Chin Boon; Koh Hui Peng; Koo Chee, Kiong; Siew Yong Kong; Yeo Swee Hock

2003-01-01

As the critical dimension (CD) in integrated circuit (IC) device reduces, the total overlay budget needs to be more stringent. Typically, the allowable overlay error is 1/3 of the CD in the IC device. In this case, robustness of alignment mark is critical, as accurate signal is required by the scanner's alignment system to precisely align a layer of pattern to the previous layer. Alignment issue is more severe in back-end process partly due to the influenced of Chemical Mechanical Polishing (CMP), which contribute to the asymmetric or total destruction of the alignment marks. Alignment marks on the wafer can be placed along the scribe-line of the IC pattern. ASML scanner allows such type of wafer alignment using phase grating mark, known as Scribe-line Primary Mark (SPM) which can be fit into a standard 80um scribe-line. In this paper, we have studied the feasibility of introducing Narrow SPM (NSPM) to enable a smaller scribe-line. The width of NSPM has been shrunk down to 70% of the SPM and the length remain...

Sordaria, a model system to uncover links between meiotic pairing and recombination.

Science.gov (United States)

Zickler, Denise; Espagne, Eric

2016-06-01

The mycelial fungus Sordaria macrospora was first used as experimental system for meiotic recombination. This review shows that it provides also a powerful cytological system for dissecting chromosome dynamics in wild-type and mutant meioses. Fundamental cytogenetic findings include: (1) the identification of presynaptic alignment as a key step in pairing of homologous chromosomes. (2) The discovery that biochemical complexes that mediate recombination at the DNA level concomitantly mediate pairing of homologs. (3) This pairing process involves not only resolution but also avoidance of chromosomal entanglements and the resolution system includes dissolution of constraining DNA recombination interactions, achieved by a unique role of Mlh1. (4) Discovery that the central components of the synaptonemal complex directly mediate the re-localization of the recombination proteins from on-axis to in-between homologue axis positions. (5) Identification of putative STUbL protein Hei10 as a structure-based signal transduction molecule that coordinates progression and differentiation of recombinational interactions at multiple stages. (6) Discovery that a single interference process mediates both nucleation of the SC and designation of crossover sites, thereby ensuring even spacing of both features. (7) Discovery of local modulation of sister-chromatid cohesion at sites of crossover recombination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features.

Science.gov (United States)

Iwata, Hiroaki; Gotoh, Osamu

2012-11-01

Spliced alignment plays a central role in the precise identification of eukaryotic gene structures. Even though many spliced alignment programs have been developed, recent rapid progress in DNA sequencing technologies demands further improvements in software tools. Benchmarking algorithms under various conditions is an indispensable task for the development of better software; however, there is a dire lack of appropriate datasets usable for benchmarking spliced alignment programs. In this study, we have constructed two types of datasets: simulated sequence datasets and actual cross-species datasets. The datasets are designed to correspond to various real situations, i.e. divergent eukaryotic species, different types of reference sequences, and the wide divergence between query and target sequences. In addition, we have developed an extended version of our program Spaln, which incorporates two additional features to the scoring scheme of the original version, and examined this extended version, Spaln2, together with the original Spaln and other representative aligners based on our benchmark datasets. Although the effects of the modifications are not individually striking, Spaln2 is consistently most accurate and reasonably fast in most practical cases, especially for plants and fungi and for increasingly divergent pairs of target and query sequences.

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

Science.gov (United States)

Gao, Song; Sung, Wing-Kin; Nagarajan, Niranjan

2011-11-01

Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ ).

Ultrasonic welding for fast bonding of self-aligned structures in lab-on-a-chip systems

DEFF Research Database (Denmark)

Kistrup, Kasper; Poulsen, Carl Esben; Hansen, Mikkel Fougt

2015-01-01

Ultrasonic welding is a rapid, promising bonding method for the bonding of polymer chips; yet its use is still limited. We present two lab-on-a-chip applications where ultrasonic welding can be preferably applied: (1) Self-aligned gapless bonding of a two-part chip with a tolerance of 50 um; (2...... solutions offered here can significantly help bridge the gap between academia and industry, where the differences in production methods and materials pose a challenge when transferring technology....

In-gap corner states in core-shell polygonal quantum rings.

Science.gov (United States)

Sitek, Anna; Ţolea, Mugurel; Niţă, Marian; Serra, Llorenç; Gudmundsson, Vidar; Manolescu, Andrei

2017-01-10

We study Coulomb interacting electrons confined in polygonal quantum rings. We focus on the interplay of localization at the polygon corners and Coulomb repulsion. Remarkably, the Coulomb repulsion allows the formation of in-gap states, i.e., corner-localized states of electron pairs or clusters shifted to energies that were forbidden for non-interacting electrons, but below the energies of corner-side-localized states. We specify conditions allowing optical excitation to those states.

In-gap corner states in core-shell polygonal quantum rings

Science.gov (United States)

Sitek, Anna; Ţolea, Mugurel; Niţă, Marian; Serra, Llorenç; Gudmundsson, Vidar; Manolescu, Andrei

2017-01-01

We study Coulomb interacting electrons confined in polygonal quantum rings. We focus on the interplay of localization at the polygon corners and Coulomb repulsion. Remarkably, the Coulomb repulsion allows the formation of in-gap states, i.e., corner-localized states of electron pairs or clusters shifted to energies that were forbidden for non-interacting electrons, but below the energies of corner-side-localized states. We specify conditions allowing optical excitation to those states.

Galaxy Alignments: Theory, Modelling & Simulations

Science.gov (United States)

Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

2015-11-01

The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

The CMS Muon System Alignment

CERN Document Server

Martinez Ruiz-Del-Arbol, P

2009-01-01

The alignment of the muon system of CMS is performed using different techniques: photogrammetry measurements, optical alignment and alignment with tracks. For track-based alignment, several methods are employed, ranging from a hit and impact point (HIP) algorithm and a procedure exploiting chamber overlaps to a global fit method based on the Millepede approach. For start-up alignment as long as available integrated luminosity is still significantly limiting the size of the muon sample from collisions, cosmic muon and beam halo signatures play a very strong role. During the last commissioning runs in 2008 the first aligned geometries have been produced and validated with data. The CMS offline computing infrastructure has been used in order to perform improved reconstructions. We present the computational aspects related to the calculation of alignment constants at the CERN Analysis Facility (CAF), the production and population of databases and the validation and performance in the official reconstruction. Also...

Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

Directory of Open Access Journals (Sweden)

Inês Soares

2012-01-01

Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

Gap Analysis between Students' Perceptions and Expectations of Quality

Directory of Open Access Journals (Sweden)

Maryam Abbasian

2013-07-01

Full Text Available Backgrounds and Objectives: Assessing the educational services provided for students and determining the gap between the current status and the expected status can pave the way for developing programs to promote the quality of educational services. This study was performed aiming at determining the quality of educational services in Shahroud University of Medical Sciences in 2010.Methods: In this cross-sectional study, 274 students of Shahroud University of Medical Sciences were selected by random sampling method. The data were collected using SERVQUAL standard questionnaire. The 27-question questionnaire included two sections of demographic data and five-dimension educational services quality, which was completed as self-administered. The data were analyzed through independent samples t-test, paired samples t-test, and one-way ANOVA.Results: There were quality gaps in all dimensions of educational services quality and the statements to assess them. The biggest quality gap was in the responsiveness dimension (-1.45, and the lowest gap was in the reliability dimension (-1.14. The mean gap scores in female students were higher than male students in all five dimensions of educational services quality, and this difference were statistically significant (p<0.001.Conclusion: The results of this study showed that the students’ expectations are not fulfilled in all service dimensions. Therefore, responsiveness, customer-orientation, improvement of work processes and physical spaces, and paying attention to other dimensions could play a key role in promoting the quality of educational services.

Organic semiconductor density of states controls the energy level alignment at electrode interfaces

Science.gov (United States)

Oehzelt, Martin; Koch, Norbert; Heimel, Georg

2014-01-01

Minimizing charge carrier injection barriers and extraction losses at interfaces between organic semiconductors and metallic electrodes is critical for optimizing the performance of organic (opto-) electronic devices. Here, we implement a detailed electrostatic model, capable of reproducing the alignment between the electrode Fermi energy and the transport states in the organic semiconductor both qualitatively and quantitatively. Covering the full phenomenological range of interfacial energy level alignment regimes within a single, consistent framework and continuously connecting the limiting cases described by previously proposed models allows us to resolve conflicting views in the literature. Our results highlight the density of states in the organic semiconductor as a key factor. Its shape and, in particular, the energy distribution of electronic states tailing into the fundamental gap is found to determine both the minimum value of practically achievable injection barriers as well as their spatial profile, ranging from abrupt interface dipoles to extended band-bending regions. PMID:24938867

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez

Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

Science.gov (United States)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

Controllable growth and characterization of highly aligned ZnO nanocolumnar thin films

Energy Technology Data Exchange (ETDEWEB)

Onuk, Zuhal [Department of Physics, Recep Tayyip Erdogan University, Rize, 53100 (Turkey); Department of Materials Science and Engineering, University of Delaware, Newark, DE, 19716 (United States); Rujisamphan, Nopporn [Nanoscience and Nanotechnology Graduate Program, Faculty of Science, King Mongkut’s University of Technology Thonburi, 10140, Bangkok (Thailand); Theoretical and Computational Science Center (TaCS), Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140 (Thailand); Murray, Roy [Department of Physics and Astronomy, University of Delaware, Newark, DE, 19716 (United States); Bah, Mohamed [Department of Materials Science and Engineering, University of Delaware, Newark, DE, 19716 (United States); Tomakin, Murat [Department of Physics, Recep Tayyip Erdogan University, Rize, 53100 (Turkey); Shah, S.Ismat, E-mail: ismat@udel.edu [Department of Materials Science and Engineering, University of Delaware, Newark, DE, 19716 (United States); Department of Physics and Astronomy, University of Delaware, Newark, DE, 19716 (United States)

2017-02-28

Graphical abstract: Scanning electron micrographs of the top view surfaces (left column) and cross sections of sputtered ZnO thin films prepared at various Ar:O{sub 2} ratios: (a) and (b) 10:0, (c) and (d) 7.5:2.5, (e) and (f) 5:5, (g) and (h) 2.5:7.5. - Highlights: • Nanocolumnar ZnO films were prepared by controlling the argon-oxygen sputtering gas ratio. • Oxygen partial pressure affects the band gap alignment of the ZnO films. • Optical transmission spectroscopy and XPS were used to study band gap shifts. - Abstract: We investigated the effects of growth conditions during magnetron sputtering on the structural, morphological, and optical properties of nanostructured ZnO thin films. Undoped ZnO thin films are deposited onto p-type Si (100) and corning 7059 glass substrates by RF magnetron sputtering using a ZnO target in combination with various Ar-O{sub 2} sputtering gas mixtures at room temperature. The effect of the partial pressure of oxygen on the morphology of ZnO thin film structure and band alignment were investigated. Thickness, and therefore the growth rate of the samples measured from the cross-sectional SEM micrographs, is found to be strongly correlated with the oxygen partial pressure in the sputtering chamber. The optical transmittance spectrometry results show that the absorption edge shifts towards the longer wavelength at higher oxygen partial pressure. X-ray photoelectron spectroscopy (XPS) used for determining the surface chemical structure and valence band offsets show that conduction band can be controlled by changing the sputtering atmosphere.

Energy band structure tailoring of vertically aligned InAs/GaAsSb quantum dot structure for intermediate-band solar cell application by thermal annealing process.

Science.gov (United States)

Liu, Wei-Sheng; Chu, Ting-Fu; Huang, Tien-Hao

2014-12-15

This study presents an band-alignment tailoring of a vertically aligned InAs/GaAs(Sb) quantum dot (QD) structure and the extension of the carrier lifetime therein by rapid thermal annealing (RTA). Arrhenius analysis indicates a larger activation energy and thermal stability that results from the suppression of In-Ga intermixing and preservation of the QD heterostructure in an annealed vertically aligned InAs/GaAsSb QD structure. Power-dependent and time-resolved photoluminescence were utilized to demonstrate the extended carrier lifetime from 4.7 to 9.4 ns and elucidate the mechanisms of the antimony aggregation resulting in a band-alignment tailoring from straddling to staggered gap after the RTA process. The significant extension in the carrier lifetime of the columnar InAs/GaAsSb dot structure make the great potential in improving QD intermediate-band solar cell application.

Convection and field-aligned currents, related to polar cap arcs, during strongly northward IMF (11 January 1983)

International Nuclear Information System (INIS)

Israelevich, P.L.; Podgorny, I.M.; Kuzmin, A.K.; Nikolaeva, N.S.; Dubinin, E.M.

1988-01-01

Electric and magnetic fields and auroral emissions have been measured by the Intercosmos-Bulgaria-1300 satellite on 10-11 January 1983. The measured distributions of the plasma drift velocity show that viscous convection is diminished in the evening sector under IMF B y y > 0. A number of sun-aligned polar cap arcs were observed at the beginning of the period of strongly northward IMF and after a few hours a θ-aurora appeared. The intensity of ionized oxygen emission increased significantly reaching up to several kilo-Rayleighs in the polar cap arc. A complicated pattern of convection and field-aligned currents existed in the nightside polar cap which differed from the four-cell model of convection and NBZ field-aligned current system. This pattern was observed during 12 h and could be interpreted as six large scale field-aligned current sheets and three convective vortices inside the polar cap. Sun-aligned polar cap arcs may be located in regions both of sunward and anti-sunward convection. Structures of smaller spatial scale-correspond to the boundaries of hot plasma regions related to polar cap arcs. Obviously these structures are due to S-shaped distributions of electric potential. Parallel electric fields in these S-structures provide electron acceleration up to 1 keV at the boundaries of polar cap arcs. The pairs of field-aligned currents correspond to those S-structures: a downward current at the external side of the boundary and an upward current at the internal side of it. (author)

Magnetosphere and ionosphere response to a positive-negative pulse pair of solar wind dynamic pressure

Science.gov (United States)

Tian, A.; Degeling, A. W.

2017-12-01

Simulations and observations had shown that single positive/negative solar wind dynamic pressure pulse would excite geomagnetic impulsive events along with ionosphere and/or magnetosphere vortices which are connected by field aligned currents(FACs). In this work, a large scale ( 9min) magnetic hole event in solar wind provided us with the opportunity to study the effects of positive-negative pulse pair (△p/p 1) on the magnetosphere and ionosphere. During the magnetic hole event, two traveling convection vortices (TCVs, anti-sunward) first in anticlockwise then in clockwise rotation were detected by geomagnetic stations located along the 10:30MLT meridian. At the same time, another pair of ionospheric vortices azimuthally seen up to 3 MLT first in clockwise then in counter-clockwise rotation were also appeared in the afternoon sector( 14MLT) and centered at 75 MLAT without obvious tailward propagation feature. The duskside vortices were also confirmed in SuperDARN radar data. We simulated the process of magnetosphere struck by a positive-negative pulse pair and it shows that a pair of reversed flow vortices in the magnetosphere equatorial plane appeared which may provide FACs for the vortices observed in ionosphere. Dawn dusk asymmetry of the vortices as well as the global geomagnetism perturbation characteristics were also discussed.

Nova laser alignment control system

International Nuclear Information System (INIS)

Van Arsdall, P.J.; Holloway, F.W.; McGuigan, D.L.; Shelton, R.T.

1984-01-01

Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system

Majorana surface modes of nodal topological pairings in spin-3/2 semimetals

Science.gov (United States)

Yang, Wang; Xiang, Tao; Wu, Congjun

2017-10-01

When solid state systems possess active orbital-band structures subject to spin-orbit coupling, their multicomponent electronic structures are often described in terms of effective large-spin fermion models. Their topological structures of superconductivity are beyond the framework of spin singlet and triplet Cooper pairings for spin-1/2 systems. Examples include the half-Heusler compound series of RPtBi, where R stands for a rare-earth element. Their spin-orbit coupled electronic structures are described by the Luttinger-Kohn model with effective spin-3/2 fermions and are characterized by band inversion. Recent experiments provide evidence to unconventional superconductivity in the YPtBi material with nodal spin-septet pairing. We systematically study topological pairing structures in spin-3/2 systems with the cubic group symmetries and calculate the surface Majorana spectra, which exhibit zero energy flat bands, or, cubic dispersion depending on the specific symmetry of the superconducting gap functions. The signatures of these surface states in the quasiparticle interference patterns of tunneling spectroscopy are studied, which can be tested in future experiments.

BAND ALIGNMENT OF ULTRATHIN GIZO/SiO2/Si HETEROSTRUCTURE DETERMINED BY ELECTRON SPECTROSCOPY

Directory of Open Access Journals (Sweden)

Hee Jae Kang2

2011-11-01

Full Text Available Amorphous GaInZnO (GIZO thin films are grown on SiO2/Si substrate by the RF magnetron sputtering method. By thecombination of measured band gaps from reflection energy loss spectroscopy (REELS spectra and valence band fromX-ray photo-electron spectroscopy (XPS spectra, we have demonstrated the energy band alignment of GIZO thin films.The band gap values are 3.2 eV, 3.2 eV, 3.4eV and 3.6eV for the concentration ratios of Ga: In: Zn in GIZO thin filmsare 1:1:1, 2:2:1, 3:2:1 and 4:2:1, respectively. These are attributed to the larger band gap energy of Ga2O3 comparedwith In2O3 and ZnO. The valence band offsets (ΔEv decrease from 2.18 to 1.68 eV with increasing amount of Ga inGIZO thin films for GIZO1 to GIZO4, respectively. These experimental values of band gap and valence band offsetwill provide the further understanding in the fundamental properties of GIZO/SiO2/Si heterostructure, which will beuseful in the design, modeling and analysis of the performance devices applications.

Effect of single interstitial impurity in iron-based superconductors with sign-changed s-wave pairing symmetry

Energy Technology Data Exchange (ETDEWEB)

Yu, Xiang-Long, E-mail: xlyu@theory.issp.ac.cn [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, P. O. Box 1129, Hefei 230031 (China); Liu, Da-Yong; Quan, Ya-Min; Zheng, Xiao-Jun [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, P. O. Box 1129, Hefei 230031 (China); Zou, Liang-Jian, E-mail: zou@theory.issp.ac.cn [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, P. O. Box 1129, Hefei 230031 (China); Department of Physics, University of Science and Technology of China, Hefei 230026 (China)

2015-12-15

Highlights: • Effects of single interstitial impurity are studied in iron-based superconductors. • Bound states within the superconducting gap can be induced. • The interstitial impurity can induce a π phase shift of pairing order parameter. • For strong magnetic scattering the bound-state peak can appear at the Fermi level. - Abstract: We employ the self-consistent Bogoliubov-de Gennes (BdG) formulation to investigate the effect of single interstitial nonmagnetic/magnetic impurity in iron-based superconductors with s ± -wave pairing symmetry. We find that both the nonmagnetic and magnetic impurities can induce bound states within the superconducting (SC) gap and a π phase shift of SC order parameter at the impurity site. However, different from the interstitial-nonmagnetic-impurity case characterized by two symmetric peaks with respect to zero energy, the interstitial magnetic one only induces single bound-state peak. In the strong scattering regime this peak can appear at the Fermi level, which has been observed in the recent scanning tunneling microscope (STM) experiment of Fe(Te,Se) superconductor with interstitial Fe impurities (Yin et al. 2015 [44]). This novel single in-gap peak feature also distinguishes the interstitial case from the substitutional one with two peaks. These results provide important information for comparing the different impurity effects in the iron-based superconductors.

Stakeholders' perceptions of 10years of the Global Action Plan for Influenza Vaccines (GAP) - Results from a survey.

Science.gov (United States)

Nannei, Claudia; Goldin, Shoshanna; Torelli, Guido; Fatima, Hiba; Kumar, Kaveri; Bubb-Humfryes, Oliver; Stenson, Bo; Sparrow, Erin

2016-10-26

Ten years after the launch of the Global Action Plan for Influenza Vaccines (GAP), the World Health Organization (WHO) surveyed stakeholders to understand their perceptions of what the programme had achieved. This article provides a summary of the findings; the full report will be available on-line on the GAP website in November 2016 (http://www.who.int/influenza_vaccines_plan/en/). Seventy-seven responses were received from stakeholders including medical doctors, national influenza center officials, country immunization programme teams, surveillance and disease centers, policy-makers, researchers, vaccine manufacturers, and non-governmental organizations from 28 countries, representing all six WHO regions. Respondents cited GAP's biggest successes as capacity building in developing countries; raising international awareness of global needs in the event of a pandemic; and collaborative alignment of influenza stakeholders. The most commonly reported challenges were the limited progress in development of a broadly protective or universal vaccine and the perceived absence of a major increase in seasonal demand. These findings aligned with the perception that less global progress had been made under the third GAP objective, focused on research and development of better vaccines, than on increasing seasonal vaccine use (objective 1) and pandemic vaccine production capacity (objective 2). Respondents explained what they saw as the major challenges to development of better vaccines, including to development of a universal influenza vaccine. The majority of respondents agreed that the goal chosen at the GAP II consultation is still relevant. Results highlighted the importance of promoting research and development of better vaccines, both for facilitating uptake of seasonal vaccines and for ensuring timely vaccine availability in the event of a pandemic. As the GAP concludes its mandate this year, these findings will contribute to discussions on the impact of programme

Band alignment of ZnO/multilayer MoS{sub 2} interface determined by x-ray photoelectron spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Liu, Xinke, E-mail: xkliu@szu.edu.cn, E-mail: liuwj@szu.edu.cn; He, Jiazhu; Chen, Le; Li, Kuilong; Jia, Fang; Zeng, Yuxiang; Lu, Youming; Zhu, Deliang; Liu, Wenjun, E-mail: xkliu@szu.edu.cn, E-mail: liuwj@szu.edu.cn [College of Materials Science and Engineering, Nanshan District Key Lab for Biopolymer and Safety Evaluation, Shenzhen University, 3688 Nanhai Ave, Shenzhen 518060 (China); Zhang, Yuan [School of Physics and Electronic Information, Hua Bei Normal University, 100 Dongshan Road, Huai Bei 235000 (China); Liu, Qiang; Yu, Wenjie [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, CAS, 865 Chang Ning Road, Shanghai 200050 (China); Wu, Jing [Institute of Materials research and Engineering (IMRE), 2 Fusionopolis Way, Innovis, #08-03, 138634 Singapore (Singapore); He, Zhubing [Department of Materials Science and Engineering, South University of Science and Technology of China, 1088 Xueyuan Road, Shenzhen 518055 (China); Ang, Kah-Wee [Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore (Singapore)

2016-08-15

The energy band alignment between ZnO and multilayer (ML)-MoS{sub 2} was characterized using high-resolution x-ray photoelectron spectroscopy. The ZnO film was deposited using an atomic layer deposition tool, and ML-MoS{sub 2} was grown by chemical vapor deposition. A valence band offset (VBO) of 3.32 eV and a conduction band offset (CBO) of 1.12 eV were obtained for the ZnO/ML-MoS{sub 2} interface without any treatment. With CHF{sub 3} plasma treatment, a VBO and a CBO across the ZnO/ML-MoS{sub 2} interface were found to be 3.54 eV and 1.34 eV, respectively. With the CHF{sub 3} plasma treatment, the band alignment of the ZnO/ML-MoS{sub 2} interface has been changed from type II or staggered band alignment to type III or misaligned one, which favors the electron-hole pair separation. The band alignment difference is believed to be dominated by the down-shift in the core level of Zn 2p or the interface dipoles, which is caused by the interfacial layer rich in F.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

Science.gov (United States)

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Aligned Layers of Silver Nano-Fibers

Directory of Open Access Journals (Sweden)

Andrii B. Golovin

2012-02-01

Full Text Available We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

Analysis of trafficking, stability and function of human connexin 26 gap junction channels with deafness-causing mutations in the fourth transmembrane helix.

Directory of Open Access Journals (Sweden)

Cinzia Ambrosi

Full Text Available Human Connexin26 gene mutations cause hearing loss. These hereditary mutations are the leading cause of childhood deafness worldwide. Mutations in gap junction proteins (connexins can impair intercellular communication by eliminating protein synthesis, mis-trafficking, or inducing channels that fail to dock or have aberrant function. We previously identified a new class of mutants that form non-functional gap junction channels and hemichannels (connexons by disrupting packing and inter-helix interactions. Here we analyzed fourteen point mutations in the fourth transmembrane helix of connexin26 (Cx26 that cause non-syndromic hearing loss. Eight mutations caused mis-trafficking (K188R, F191L, V198M, S199F, G200R, I203K, L205P, T208P. Of the remaining six that formed gap junctions in mammalian cells, M195T and A197S formed stable hemichannels after isolation with a baculovirus/Sf9 protein purification system, while C202F, I203T, L205V and N206S formed hemichannels with varying degrees of instability. The function of all six gap junction-forming mutants was further assessed through measurement of dye coupling in mammalian cells and junctional conductance in paired Xenopus oocytes. Dye coupling between cell pairs was reduced by varying degrees for all six mutants. In homotypic oocyte pairings, only A197S induced measurable conductance. In heterotypic pairings with wild-type Cx26, five of the six mutants formed functional gap junction channels, albeit with reduced efficiency. None of the mutants displayed significant alterations in sensitivity to transjunctional voltage or induced conductive hemichannels in single oocytes. Intra-hemichannel interactions between mutant and wild-type proteins were assessed in rescue experiments using baculovirus expression in Sf9 insect cells. Of the four unstable mutations (C202F, I203T, L205V, N206S only C202F and N206S formed stable hemichannels when co-expressed with wild-type Cx26. Stable M195T hemichannels

Tunable Band Gap and Conductivity Type of ZnSe/Si Core-Shell Nanowire Heterostructures

Directory of Open Access Journals (Sweden)

Yijie Zeng

2014-10-01

Full Text Available The electronic properties of zincblende ZnSe/Si core-shell nanowires (NWs with a diameter of 1.1–2.8 nm are calculated by means of the first principle calculation. Band gaps of both ZnSe-core/Si-shell and Si-core/ZnSe-shell NWs are much smaller than those of pure ZnSe or Si NWs. Band alignment analysis reveals that the small band gaps of ZnSe/Si core-shell NWs are caused by the interface state. Fixing the ZnSe core size and enlarging the Si shell would turn the NWs from intrinsic to p-type, then to metallic. However, Fixing the Si core and enlarging the ZnSe shell would not change the band gap significantly. The partial charge distribution diagram shows that the conduction band maximum (CBM is confined in Si, while the valence band maximum (VBM is mainly distributed around the interface. Our findings also show that the band gap and conductivity type of ZnSe/Si core-shell NWs can be tuned by the concentration and diameter of the core-shell material, respectively.

Studies on top quark pair production in pp collisions at the Large Hadron Collider with the ATLAS experiment

International Nuclear Information System (INIS)

Pataraia, Sophio

2009-01-01

We studied the performance of the track based alignment software of the ATLAS Inner Detector. To improve the final alignment additional vertex and beam constraints on the track reconstruction were investigated. We also investigated the b-tagging performance at an early stage of the detector operation. The dependence of the performance on the jet reconstruction algorithm, and on the Inner Detector misalignment were studied. A Top quark pair-production cross section measurement with and without b-tagging using the simulated ATLAS data corresponding to the luminosity of 200 pb -1 was carried out. We applied a simple and robust cut and count method suitable for the early phase of the detector operation. We investigated the systematic uncertainties on the cross section measurements due to Monte Carlo modeling of the precesses, for various scenarios of the alignment of the inner detector, for several jet reconstruction algorithms and for variations of the absolute jet energy scale. It yields an early cross-section measurement with a systematic error of less than 30%. (orig.)

Studies on top quark pair production in pp collisions at the Large Hadron Collider with the ATLAS experiment

Energy Technology Data Exchange (ETDEWEB)

Pataraia, Sophio

2009-12-15

We studied the performance of the track based alignment software of the ATLAS Inner Detector. To improve the final alignment additional vertex and beam constraints on the track reconstruction were investigated. We also investigated the b-tagging performance at an early stage of the detector operation. The dependence of the performance on the jet reconstruction algorithm, and on the Inner Detector misalignment were studied. A Top quark pair-production cross section measurement with and without b-tagging using the simulated ATLAS data corresponding to the luminosity of 200 pb{sup -1} was carried out. We applied a simple and robust cut and count method suitable for the early phase of the detector operation. We investigated the systematic uncertainties on the cross section measurements due to Monte Carlo modeling of the precesses, for various scenarios of the alignment of the inner detector, for several jet reconstruction algorithms and for variations of the absolute jet energy scale. It yields an early cross-section measurement with a systematic error of less than 30%. (orig.)