WorldWideScience

Sample records for accurate molecular alignment

  1. Parameters for accurate genome alignment

    Directory of Open Access Journals (Sweden)

    Hamada Michiaki

    2010-02-01

    Full Text Available Abstract Background Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters to use. Surprisingly, there has been no large-scale assessment of these choices using real genomic data. Moreover, rigorous procedures to control the rate of spurious alignment have not been employed. Results We have assessed 495 combinations of score parameters for alignment of animal, plant, and fungal genomes. As our gold-standard of accuracy, we used genome alignments implied by multiple alignments of proteins and of structural RNAs. We found the HOXD scoring schemes underlying alignments in the UCSC genome database to be far from optimal, and suggest better parameters. Higher values of the X-drop parameter are not always better. E-values accurately indicate the rate of spurious alignment, but only if tandem repeats are masked in a non-standard way. Finally, we show that γ-centroid (probabilistic alignment can find highly reliable subsets of aligned bases. Conclusions These results enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases. This study was made possible by our new software, LAST, which can align vertebrate genomes in a few hours http://last.cbrc.jp/.

  2. Faster and More Accurate Sequence Alignment with SNAP

    CERN Document Server

    Zaharia, Matei; Curtis, Kristal; Fox, Armando; Patterson, David; Shenker, Scott; Stoica, Ion; Karp, Richard M; Sittler, Taylor

    2011-01-01

    We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The result is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today's fast aligners ignore. We calculate that SNAP can align a dataset with 30x coverage of a human genome in le...

  3. Molecular alignment using circularly polarized laser pulses

    CERN Document Server

    Smeenk, C T L

    2013-01-01

    We show that circularly polarized femtosecond laser pulses produce field-free alignment in linear and planar molecules. We study the rotational wavepacket evolution of O$_2$ and benzene created by circularly polarized light. For benzene, we align the molecular plane to the plane of polarization. For O$_2$, we demonstrate that circular polarization yields a net alignment along the laser propagation axis at certain phases of the evolution. Circular polarization gives us the ability to control alignment of linear molecules outside the plane of polarization, providing new capabilities for molecular imaging.

  4. Split-alignment of genomes finds orthologies more accurately.

    Science.gov (United States)

    Frith, Martin C; Kawaguchi, Risa

    2015-01-01

    We present a new pair-wise genome alignment method, based on a simple concept of finding an optimal set of local alignments. It gains accuracy by not masking repeats, and by using a statistical model to quantify the (un)ambiguity of each alignment part. Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous. The previous methods suffer from an overly-strong assumption of long un-rearranged blocks. The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors. PMID:25994148

  5. BBMap: A Fast, Accurate, Splice-Aware Aligner

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian

    2014-03-17

    Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].

  6. Molecular focusing and alignment with plasmon fields.

    Science.gov (United States)

    Artamonov, Maxim; Seideman, Tamar

    2010-12-01

    We show the possibility of simultaneously aligning molecules and focusing their center-of-mass motion near a metal nanoparticle in the field intensity gradient created by the surface plasmon enhancement of incident light. The rotational motion is described quantum mechanically while the translation is treated classically. The effects of the nanoparticle shape on the alignment and focusing are explored. Our results carry interesting implications to the field of molecular nanoplasmonics and suggest several potential applications in nanochemistry.

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

    DEFF Research Database (Denmark)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan;

    2009-01-01

    MOTIVATION: 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...

  8. A fast and accurate initial alignment method for strapdown inertial navigation system on stationary base

    Institute of Scientific and Technical Information of China (English)

    Xinlong WANG; Gongxun SHEN

    2005-01-01

    In this work,a fast and accurate stationary alignment method for strapdown inertial navigation system (SINS) is proposed.It has been demonstrated that the stationary alignment of SINS can be improved by employing the multiposition technique,but the alignment time of the azimuth error is relatively longer.Over here,the two-position alignment principle is presented.On the basis of this SINS error model,a fast estimation algorithm of the azimuth error for the initial alignment of SINS on stationary base is derived fully from the horizontal velocity outputs and the output rates,and the novel azimuth error estimation algorithm is used for the two-position alignment.Consequently,the speed and accuracy of the SINS's initial alignment is enhanced greatly.The computer simulation results illustrate the efficiency of this alignment method.

  9. Accurate monitoring of large aligned objects with videometric techniques

    CERN Document Server

    Klumb, F; Grussenmeyer, P

    1999-01-01

    This paper describes a new videometric technique designed to monitor the deformations and misalignments of large vital components in the centre of a future particle detector. It relies on a geometrical principle called "reciprocal collimation" of two CCD cameras: the combination of the video devices in pair gives rise to a network of well located reference lines that surround the object to be surveyed. Each observed point, which in practice is a bright point-like light- source, is accurately located with respect to this network of neighbouring axes. Adjustment calculations provide the three- dimensional position of the object fitted with various light-sources. An experimental test-bench, equipped with four cameras, has corroborated the precision predicted by previous simulations of the system. (11 refs).

  10. Node Handprinting: A Scalable and Accurate Algorithm for Aligning Multiple Biological Networks.

    Science.gov (United States)

    Radu, Alex; Charleston, Michael

    2015-07-01

    Due to recent advancements in high-throughput sequencing technologies, progressively more protein-protein interactions have been identified for a growing number of species. Subsequently, the protein-protein interaction networks for these species have been further refined. The increase in the quality and availability of these networks has in turn brought a demand for efficient methods to analyze such networks. The pairwise alignment of these networks has been moderately investigated, with numerous algorithms available, but there is very little progress in the field of multiple network alignment. Multiple alignment of networks from different organisms is ideal at finding abnormally conserved or disparate subnetworks. We present a fast and accurate algorithmic approach, Node Handprinting (NH), based on our previous work with Node Fingerprinting, which enables quick and accurate alignment of multiple networks. We also propose two new metrics for the analysis of multiple alignments, as the current metrics are not as sophisticated as their pairwise alignment counterparts. To assess the performance of NH, we use previously aligned datasets as well as protein interaction networks generated from the public database BioGRID. Our results indicate that NH compares favorably with current methodologies and is the only algorithm capable of performing the more complex alignments. PMID:25695597

  11. A test facility of super-accurate alignment system for a linear collider

    International Nuclear Information System (INIS)

    To develop an alignment system for Japan Linear Collider (JLC), a test facility consisting of a laser interferometer and piezo tranducers has been constructed at KEK. The fundamental test using the sine wave disturbing vibration shows the distance between the interferometer head and the corner cube has been kept stable within an accuracy of 50 nm up to 20 Hz by the feedback technique, called active alignment method. The experiment with the random frequency disturbance suggests this system can be extended to the possible super-accurate alignment system

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

    NARCIS (Netherlands)

    Warris, S.; Yalcin, F.; Jackson, K.J.; Nap, J.P.H.

    2015-01-01

    Motivation 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 d

  13. 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.

  14. Molecular alignment and filamentation: comparison between weak and strong field models

    CERN Document Server

    Berti, N; Wolf, J -P; Faucher, O

    2014-01-01

    The impact of nonadiabatic laser-induced molecular alignment on filamentation is numerically studied. Weak and strong field model of impulsive molecular alignment are compared in the context of nonlinear pulse propagation. It is shown that the widely used weak field model describing the refractive index modification induced by impulsive molecular alignment accurately reproduces the propagation dynamics providing that only a single pulse is involved during the experiment. On the contrary, it fails at reproducing the nonlinear propagation experienced by an intense laser pulse traveling in the wake of a second strong laser pulse. The discrepancy depends on the relative delay between the two pulses and is maximal for delays corresponding to half the rotational period of the molecule.

  15. Role of rotational temperature in adiabatic molecular alignment

    DEFF Research Database (Denmark)

    Kumarappan, Vinod; Bisgaard, Christer Z; Viftrup, Simon;

    2006-01-01

    One-dimensional alignment of molecules in the adiabatic limit, where the pulse duration greatly exceeds the molecular rotational periods, is studied experimentally. Four different asymmetric top molecules (iodobenzene, p-diiodobenzene, 3,4-dibromothiophene, and 4,4(')-dibromobiphenyl), rotationally...... cooled through a high pressure supersonic pulsed valve, are aligned by a 9-ns-long pulse. Their orientations are measured through Coulomb explosion, induced by a 130-fs-long pulse, and by recording the direction of the recoiling ions. The paper focuses on the crucial role of the initial rotational...... temperature for the degree of alignment. In particular, we show that at molecular temperatures in the 1 K range very strong alignment is obtained already at intensities of a few times 10(11) W/cm(2) for all four molecules. At the highest intensities (similar to 10(12) W/cm(2)) the molecules can tolerate...

  16. Optimal molecular alignment and orientation through rotational ladder climbing

    OpenAIRE

    Salomon, Julien; Dion, Claude M.; Turinici, Gabriel

    2005-01-01

    We study the control by electromagnetic fields of molecular alignment and orientation, in a linear, rigid rotor model. With the help of a monotonically convergent algorithm, we find that the optimal field is in the microwave part of the spectrum and acts by resonantly exciting the rotation of the molecule progressively from the ground state, i.e., by rotational ladder climbing. This mechanism is present not only when maximizing orientation or alignment, but also when using prescribed target s...

  17. Optimal molecular alignment and orientation through rotational ladder climbing

    Science.gov (United States)

    Salomon, Julien; Dion, Claude M.; Turinici, Gabriel

    2005-10-01

    We study the control by electromagnetic fields of molecular alignment and orientation in a linear, rigid-rotor model. With the help of a monotonically convergent algorithm, we find that the optimal field is in the microwave part of the spectrum and acts by resonantly exciting the rotation of the molecule progressively from the ground state, i.e., by rotational ladder climbing. This mechanism is present not only when maximizing orientation or alignment, but also when using prescribed target states that simultaneously optimize the efficiency of orientation/alignment and its duration. The extension of the optimization method to consider a finite rotational temperature is also presented.

  18. Optimal molecular alignment and orientation through rotational ladder climbing

    CERN Document Server

    Salomon, J; Turinici, G; Salomon, Julien; Dion, Claude M.; Turinici, Gabriel

    2005-01-01

    We study the control by electromagnetic fields of molecular alignment and orientation, in a linear, rigid rotor model. With the help of a monotonically convergent algorithm, we find that the optimal field is in the microwave part of the spectrum and acts by resonantly exciting the rotation of the molecule progressively from the ground state, i.e., by rotational ladder climbing. This mechanism is present not only when maximizing orientation or alignment, but also when using prescribed target states that simultaneously optimize the efficiency of orientation/alignment and its duration.

  19. An Accurate Timing Alignment Method with Time-to-Digital Converter Linearity Calibration for High-Resolution TOF PET

    OpenAIRE

    Li, Hongdi; Wang, Chao; An, Shaohui; Lu, Xingyu; Dong, Yun; Liu, Shitao; Baghaei, Hossain; Zhang, Yuxuan; Ramirez, Rocio; Wong, Wai-Hoi

    2015-01-01

    Accurate PET system timing alignment minimizes the coincidence time window and therefore reduces random events and improves image quality. It is also critical for time-of-flight (TOF) image reconstruction. Here, we use a thin annular cylinder (shell) phantom filled with a radioactive source and located axially and centrally in a PET camera for the timing alignment of a TOF PET system. This timing alignment method involves measuring the time differences between the selected coincidence detecto...

  20. FAMSA: Fast and accurate multiple sequence alignment of huge protein families

    Science.gov (United States)

    Deorowicz, Sebastian; Debudaj-Grabysz, Agnieszka; Gudyś, Adam

    2016-01-01

    Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilization of the longest common subsequence measure for determining pairwise similarities, a novel method of evaluating gap costs, and a new iterative refinement scheme. What matters is that its implementation is highly optimized and parallelized to make the most of modern computer platforms. Thanks to the above, quality indicators, i.e. sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms, such as Clustal Omega or MAFFT for datasets exceeding a few thousand sequences. Quality does not compromise on time or memory requirements, which are an order of magnitude lower than those in the existing solutions. For example, a family of 415519 sequences was analyzed in less than two hours and required no more than 8 GB of RAM. FAMSA is available for free at http://sun.aei.polsl.pl/REFRESH/famsa. PMID:27670777

  1. Constrained-DFT method for accurate energy-level alignment of metal/molecule interfaces

    KAUST Repository

    Souza, A. M.

    2013-10-07

    We present a computational scheme for extracting the energy-level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on Li(100), allows us to evaluate charge-transfer energies, as well as the spatial distribution of the image charge induced on the metal surface. We systematically study the energies for charge transfer from the molecule to the substrate as function of the molecule-substrate distance, and investigate the effects arising from image-charge confinement and local charge neutrality violation. For benzene on Li(100) we find that the image-charge plane is located at about 1.8 Å above the Li surface, and that our calculated charge-transfer energies compare perfectly with those obtained with a classical electrostatic model having the image plane located at the same position. The methodology outlined here can be applied to study any metal/organic interface in the weak coupling limit at the computational cost of a total energy calculation. Most importantly, as the scheme is based on total energies and not on correcting the Kohn-Sham quasiparticle spectrum, accurate results can be obtained with local/semilocal exchange and correlation functionals. This enables a systematic approach to convergence.

  2. Alignment layer-free molecular ordering induced by masked photopolymerization with non-polarized light

    Science.gov (United States)

    Hisano, Kyohei; Kurata, Yosuke; Aizawa, Miho; Ishizu, Masaki; Sasaki, Takeo; Shishido, Atsushi

    2016-07-01

    Controlled and uniform molecular alignment can provide and enhance functionality in polymer films. We first report that masked photopolymerization with non-polarized light enables direct and precise control of molecular alignment without using a conventional molecular alignment layer. The photopolymerization of a mixture composed of an optically anisotropic acrylate monomer and an isotropic dimethacrylate crosslinker induces either unidirectional or complex molecular alignment, depending upon the shape of the photomask. Such molecular alignments are successfully achieved by shear stress arising from molecular diffusion, even when the photopolymerization is carried out at isotropic temperatures of both the monomer mixture and the obtained polymers.

  3. A robust and accurate formulation of molecular and colloidal electrostatics

    Science.gov (United States)

    Sun, Qiang; Klaseboer, Evert; Chan, Derek Y. C.

    2016-08-01

    This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics.

  4. Global Alignment of Molecular Sequences via Ancestral State Reconstruction

    CERN Document Server

    Andoni, Alexandr; Hassidim, Avinatan; Roch, Sebastien

    2009-01-01

    Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on substitution-only models of sequence evolution. In practice these methods are extended beyond this simplified setting with the use of heuristics that produce global alignments of the input sequences--an important problem which has no rigorous model-based solution. In this paper we consider a new version of the multiple sequence alignment in the context of stochastic indel models. More precisely, we introduce the following {\\em trace reconstruction problem on a tree} (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves of the tree. We give a recursive procedure for this problem with strong reconstruction guarantees at low mut...

  5. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization

    Directory of Open Access Journals (Sweden)

    Klau Gunnar W

    2007-07-01

    Full Text Available Abstract Background The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. Results We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP. We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. Conclusion The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

  6. Molecular superfluidity in helium clusters studied using impulsive alignment

    Energy Technology Data Exchange (ETDEWEB)

    Galinis, Gediminas; Mendoza Luna, Luis Guillermo; Watkins, Mark; Von Haeften, Klaus [Department of Physics and Astronomy, University of Leicester (United Kingdom); Kazak, Lev; Goede, Sebastian; Skruszewicz, Slawomir; Irsig, Robert; Tiggesbaeumker, Josef; Meiwes-Broer, Karl-Heinz [Institut fuer Physik, Universitaet Rostock (Germany); Minns, Russell [Department of Chemistry, University of Southampton (United Kingdom); Ellis, Andrew [Department of Chemistry, University of Leicester (United Kingdom); Turcu, Edmon; Cacho, Cephise; Springate, Emma [CLF, STFC, Rutherford Appleton Laboratories (United Kingdom)

    2013-07-01

    Superfluidity is an intriguing phenomenon commonly associated with frictionless flow. Although this macroscopic effect is well understood, our understanding of how superfluidity evolves on the nanoscale is less extensive.We apply new approach to study superfluidity as a function of the number of helium atoms involved. A femtosecond pump-probe laser setup is used to excite a rotational wavepacket and to follow its propagation in time. The periodically recurring molecular alignment is probed by analyzing the emission characteristics in delayed Coulomb explosion with a velocity map imaging (VMI) spectrometer. First results show CO attached to five helium atoms and rotational features of HCCH-He corresponding to a linear configuration. To maximize the molecular beam intensity and to cope with the associated high gas load we developed a unique, differentially pumped VMI spectrometer.

  7. Electro-optical systems to accurately align (boresight) laser designator, FLIR, and CCD on the ground before the mission

    Science.gov (United States)

    Cabib, Dario; Segal, Alon; Dolev, Jacob

    2008-10-01

    CI Systems has been involved in the development and production of in-flight boresight equipment since 19891,2, by pioneering the field with innovative laser-FLIR and laser-CCD alignment solutions. In addition, over the years we have developed a number of systems for use on the ground to align the various electro-optical instrumentation to a common Line of Sight (LOS) before the mission. This adjustment is very important for the success of the mission: the more accurate the alignment and its retention during the flight, the better the chance of a precise hit. In this paper we describe various systems developed and built at CI for use with EO pods mounted on aircraft, especially UAV's. The most important engineering tasks are design for small size and convenient mechano-optical interfaces for different pods allowing system compactness, low weight and easy operation. Some of the design considerations to meet these challenges will be given here.

  8. Effect of rotational-state-dependent molecular alignment on the optical dipole force

    CERN Document Server

    Kim, Lee Yeong; Kim, Hye Ah; Kwak, Sang Kyu; Friedrich, Bretislav; Zhao, Bum Suk

    2016-01-01

    The properties of molecule-optical elements such as lenses or prisms based on the interaction of molecules with optical fields depend in a crucial way on the molecular quantum state and its alignment created by the optical field. However, in previous experimental studies, the effects of state-dependent alignment have never been included in estimates of the optical dipole force acting on the molecules while previous theoretical investigations took the state-dependent molecular alignment into account only implicitly. Herein, we consider the effects of molecular alignment explicitly and, to this end, introduce an effective polarizability which takes proper account of molecular alignment and is directly related to the alignment-dependent optical dipole force. We illustrate the significance of including molecular alignment in the optical dipole force by a trajectory study that compares previously used approximations with the present approach. The trajectory simulations were carried out for an ensemble of linear mo...

  9. Accurate alignment of functional EPI data to anatomical MRI using a physics-based distortion model.

    Science.gov (United States)

    Studholme, C; Constable, R T; Duncan, J S

    2000-11-01

    Mapping of functional magnetic resonance imaging (fMRI) to conventional anatomical MRI is a valuable step in the interpretation of fMRI activations. One of the main limits on the accuracy of this alignment arises from differences in the geometric distortion induced by magnetic field inhomogeneity. This paper describes an approach to the registration of echo planar image (EPI) data to conventional anatomical images which takes into account this difference in geometric distortion. We make use of an additional spin echo EPI image and use the known signal conservation in spin echo distortion to derive a specialized multimodality nonrigid registration algorithm. We also examine a plausible modification using log-intensity evaluation of the criterion to provide increased sensitivity in areas of low EPI signal. A phantom-based imaging experiment is used to evaluate the behavior of the different criteria, comparing nonrigid displacement estimates to those provided by a imagnetic field mapping acquisition. The algorithm is then applied to a range of nine brain imaging studies illustrating global and local improvement in the anatomical alignment and localization of fMRI activations.

  10. Accurate molecular classification of cancer using simple rules

    OpenAIRE

    Gotoh Osamu; Wang Xiaosheng

    2009-01-01

    Abstract Background One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often ...

  11. Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling

    Directory of Open Access Journals (Sweden)

    Rahmann Sven

    2011-02-01

    Full Text Available Abstract Background Molecular database search tools need statistical models to assess the significance for the resulting hits. In the classical approach one asks the question how probable a certain score is observed by pure chance. Asymptotic theories for such questions are available for two random i.i.d. sequences. Some effort had been made to include effects of finite sequence lengths and to account for specific compositions of the sequences. In many applications, such as a large-scale database homology search for transmembrane proteins, these models are not the most appropriate ones. Search sensitivity and specificity benefit from position-dependent scoring schemes or use of Hidden Markov Models. Additional, one may wish to go beyond the assumption that the sequences are i.i.d. Despite their practical importance, the statistical properties of these settings have not been well investigated yet. Results In this paper, we discuss an efficient and general method to compute the score distribution to any desired accuracy. The general approach may be applied to different sequence models and and various similarity measures that satisfy a few weak assumptions. We have access to the low-probability region ("tail" of the distribution where scores are larger than expected by pure chance and therefore relevant for practical applications. Our method uses recent ideas from rare-event simulations, combining Markov chain Monte Carlo simulations with importance sampling and generalized ensembles. We present results for the score statistics of fixed and random queries against random sequences. In a second step, we extend the approach to a model of transmembrane proteins, which can hardly be described as i.i.d. sequences. For this case, we compare the statistical properties of a fixed query model as well as a hidden Markov sequence model in connection with a position based scoring scheme against the classical approach. Conclusions The results illustrate that the

  12. Accurate molecular classification of cancer using simple rules

    Directory of Open Access Journals (Sweden)

    Gotoh Osamu

    2009-10-01

    Full Text Available Abstract Background One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often hampers the interpretability of the models. For a better understanding of the classification results, it is desirable to develop simpler rule-based models with as few marker genes as possible. Methods We screened a small number of informative single genes and gene pairs on the basis of their depended degrees proposed in rough sets. Applying the decision rules induced by the selected genes or gene pairs, we constructed cancer classifiers. We tested the efficacy of the classifiers by leave-one-out cross-validation (LOOCV of training sets and classification of independent test sets. Results We applied our methods to five cancerous gene expression datasets: leukemia (acute lymphoblastic leukemia [ALL] vs. acute myeloid leukemia [AML], lung cancer, prostate cancer, breast cancer, and leukemia (ALL vs. mixed-lineage leukemia [MLL] vs. AML. Accurate classification outcomes were obtained by utilizing just one or two genes. Some genes that correlated closely with the pathogenesis of relevant cancers were identified. In terms of both classification performance and algorithm simplicity, our approach outperformed or at least matched existing methods. Conclusion In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction.

  13. Role of highest occupied molecular orbitals in molecular field-free alignment by a femtosecond pulse

    Institute of Scientific and Technical Information of China (English)

    Chen De-Ying; Wang Yu-Quan; Xia Yuan-Qin; Fan Rong-Wei; Zhang Sheng

    2009-01-01

    This paper studies the molecular rotational excitation and field-free spatial alignment in a nonresonant intense laser field numerically and analytically by using the time-dependent Schrodinger equation. The broad rotational wave packets excited by the femtosecond pulse are defined in conjugate angle space,and their coefficients are obtained by solving a set of coupled linear equations. Both single molecule orientation angles and an ensemble of O2 and CO molecule angular distributions are calculated in detail. The numerical results show that,for single molecule highest occupied molecular orbital (HOMO) symmetry σ tends to have a molecular orientation along the laser polarization direction and the permanent dipole moment diminishes the mean of the orientation angles; for an ensemble of molecules,angular distributions provide more complex and additional information at times where there are no revivals in the single molecule plot. In particular,at the revival peak instant,with the increase of temperature of the molecular ensemble,the anisotropic angular distributions with respect to the laser polarization direction of the πg orbital gradually transform to the symmetrical distributions regarding the laser polarization vector and for two HOMO configurations angular distributions of all directions are confined within a smaller angle when the temperature of the molecular ensemble is higher.

  14. Focus conditioning effects on molecular field-free alignment observed with high-order harmonic generation

    Institute of Scientific and Technical Information of China (English)

    吴家骏; 尉鹏飞

    2012-01-01

    We investigate the focus conditioning effects on molecular field-free alignment observed with high-order harmonic generation (HHG) from CO2 molecules.We also experimentally demonstrate that both the spectral shape and alignment signal of HHG significantly vary with changing focus position.A maximal alignment signal is achieved at a given focus position because of the optimal intensity of the driving laser.This intensity is related to the ionization potential of the molecules.These results indicate that a unique focus position provides an optimal alignment signal for practical applications.

  15. Measurement of field-free molecular alignment by balanced weak field polarization technique

    Directory of Open Access Journals (Sweden)

    Peng Peng

    2015-12-01

    Full Text Available We demonstrate the measurement of field-free molecular alignment of air can be realized by combining the weak field polarization technique (WFPT with a balanced detection system. The measured signal is proportional to the alignment parameter. Periodic revival structures of the transient alignment and permanent alignment between revivals can be detected clearly by a single measurement with high sensitivity. Fourier transform spectrum of the measured signal agrees well with the calculation result and provides information of the populations of different J states in the rotational wave packet.

  16. Deconvoluting nonaxial recoil in Coulomb explosion measurements of molecular axis alignment

    Science.gov (United States)

    Christensen, Lauge; Christiansen, Lars; Shepperson, Benjamin; Stapelfeldt, Henrik

    2016-08-01

    We report a quantitative study of the effect of nonaxial recoil during Coulomb explosion of laser-aligned molecules and introduce a method to remove the blurring caused by nonaxial recoil in the fragment-ion angular distributions. Simulations show that nonaxial recoil affects correlations between the emission directions of fragment ions differently from the effect caused by imperfect molecular alignment. The method, based on analysis of the correlation between the emission directions of the fragment ions from Coulomb explosion, is used to deconvolute the effect of nonaxial recoil from experimental fragment angular distributions. The deconvolution method is then applied to a number of experimental data sets to correct the degree of alignment for nonaxial recoil, to select optimal Coulomb explosion channels for probing molecular alignment, and to estimate the highest degree of alignment that can be observed from selected Coulomb explosion channels.

  17. Effect of rotational-state-dependent molecular alignment on the optical dipole force

    Science.gov (United States)

    Kim, Lee Yeong; Lee, Ju Hyeon; Kim, Hye Ah; Kwak, Sang Kyu; Friedrich, Bretislav; Zhao, Bum Suk

    2016-07-01

    The properties of molecule-optical elements such as lenses or prisms based on the interaction of molecules with optical fields depend in a crucial way on the molecular quantum state and its alignment created by the optical field. Herein, we consider the effects of state-dependent alignment in estimating the optical dipole force acting on the molecules and, to this end, introduce an effective polarizability which takes proper account of molecular alignment and is directly related to the alignment-dependent optical dipole force. We illustrate the significance of including molecular alignment in the optical dipole force by a trajectory study that compares previously used approximations with the present approach. The trajectory simulations were carried out for an ensemble of linear molecules subject to either propagating or standing-wave optical fields for a range of temperatures and laser intensities. The results demonstrate that the alignment-dependent effective polarizability can serve to provide correct estimates of the optical dipole force, on which a state-selection method applicable to nonpolar molecules could be based. We note that an analogous analysis of the forces acting on polar molecules subject to an inhomogeneous static electric field reveals a similarly strong dependence on molecular orientation.

  18. Cavity-enhanced field-free molecular alignment at high repetition rate

    CERN Document Server

    Benko, Craig; Allison, Thomas K; Labaye, François; Ye, Jun

    2015-01-01

    Extreme ultraviolet frequency combs are a versatile tool with applications including precision measurement, strong-field physics, and solid-state physics. Here we report on an application of extreme ultraviolet frequency combs and their driving lasers to studying strong-field effects in molecular systems. We perform field-free molecular alignment and high-order hamonic generation with aligned molecules in a gas jet at 154 MHz repetition rate using a high-powered optical frequency comb inside a femtosecond enhancement cavity. The cavity-enhanced system provides means to reach suitable intensities to study field-free molecular alignment and enhance the observable effects of the molecule-field interaction. We observe modulations of the driving field, arising from the nature of impulsive stimulated Raman scattering responsible for coherent molecular rotations. We foresee impact of this work on the study of molecule-based strong-field physics, with improved precision and a more fundamental understanding of the int...

  19. Molecular Alignment and Orientation From Laser-Induced Mechanisms to Optimal Control

    CERN Document Server

    Atabek, O

    2002-01-01

    Genetic algorithms, as implemented in optimal control strategies, are currently successfully exploited in a wide range of problems in molecular physics. In this context, laser control of molecular alignment and orientation remains a very promising issue with challenging applications extending from chemical reactivity to nanoscale design. We emphasize the complementarity between basic quantum mechanisms monitoring alignment/orientation processes and optimal control scenarios. More explicitly, if on one hand we can help the optimal control scheme to take advantage of such mechanisms by appropriately building the targets and delineating the parameter sampling space, on the other hand we expect to learn, from optimal control results, some robust and physically sound dynamical mechanisms. We present basic mechanisms for alignment and orientation, such as pendular states accommodated by the molecule-plus-field effective potential and the "kick" mechanism obtained by a sudden excitation. Very interestingly, an optim...

  20. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Science.gov (United States)

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-01

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. PMID:27106060

  1. Preparation and detection of states with simultaneous spin alignment and molecular orientation in PbO

    CERN Document Server

    Bickman, S; Jiang, Y; DeMille, D

    2008-01-01

    We are pursuing an experiment to measure the electric dipole moment of the electron using the molecule PbO. This measurement requires the ability to prepare quantum states with orientation of the molecular axis and, simultaneously, alignment of the electron spin perpendicular to this axis. It also requires efficient detection of the evolution of the spin alignment direction within such a state. We describe a series of experiments that have achieved these goals, and the features and limitations of the techniques. We also discuss possible new approaches for improved efficiency in this and similar systems.

  2. Alignment of a Molecular Anion via a Shape Resonance in Near-Threshold Photodetachment

    Science.gov (United States)

    Lu, Zhou; Continetti, Robert E.

    2007-09-01

    One-color two-photon photodetachment of HOCO- at Ehν=1.60eV accompanied by a measurement of the photoelectron angular distribution (PAD) is used to illustrate a novel approach to the alignment of a molecular anion. A quantitative analysis of the PAD reveals this alignment process is associated with a temporary anion formed by a p-wave shape resonance and the PAD in the two-photon signal is a result of interfering s- and d-partial waves within the atomic approximation. The extracted intensity and phase shift of the partial waves are consistent with the Wigner threshold law for photodetachment.

  3. Compounding of hydroxyapatite crystals to molecularly aligned crab tendon chitosan: the effect of heat treatment

    Energy Technology Data Exchange (ETDEWEB)

    Matsuda, Atsushi [Creative Research Initiative ' Sousei' , Hokkaido University, Sapporo, Hokkaido 001-0021 (Japan) and Biomaterials Research Center, National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044 (Japan)]. E-mail: Matsuda.Atsushi@nims.go.jp; Kasahara, Mayumi [School of Science and Engineering, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo 169-0072 (Japan); Kobayashi, Hisatoshi [Biomaterials Research Center, National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044 (Japan)]. E-mail: Kobayashi.Hisatoshi@nims.go.jp; Ichinose, Noboru [School of Science and Engineering, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo 169-0072 (Japan); Tanaka, Junzo [Creative Research Initiative ' Sousei' , Hokkaido University, Sapporo, Hokkaido 001-0021 (Japan); Biomaterials Research Center, National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044 (Japan)

    2004-12-01

    The aim of this study was to demonstrate the effect of heat treatment on the formation of hydroxyapatite crystals in molecularly aligned chitosan. Molecularly aligned chitosan was prepared from crab (Macrocheira Kaempferi) tendons by treatment with ethanol and a 4 wt.% NaOH solution to remove proteins and calcium phosphate, subsequently performed was deacetyl treatment using a 50 wt.% NaOH solution at 100 deg. C. The tendon chitosan (t-chitosan) obtained was compounded with hydroxyapatite (HAp) before and after heat treatment by applying an alternate soaking method. The amount of compounded HAp to t-chitosan before heat treatment was larger than that after heat treatment as shown by thermogravimetric and differential thermal analysis (TG-DTA) analysis. The HAp compounded to t-chitosan before heat treatment was distributed on the whole area as shown by energy dispersive X-ray spectroscopy (EDS) analysis. On the other hand, the compound after heat treatment was distributed only on the surface of t-chitosan. The compounded HAp crystals to t-chitosan before heat treatment were aligned in the horizontal direction to t-chitosan molecules as shown by transmission electron microscopy (TEM) and electron diffraction technique. These results suggest the control of crystallographic orientation in HAp by aligned amino groups.

  4. Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

    Science.gov (United States)

    Yuwen, Tairan; Post, Carol Beth; Skrynnikov, Nikolai R

    2011-09-01

    Many proteins have modular design with multiple globular domains connected via flexible linkers. As a simple model of such system, we study a tandem construct consisting of two identical SH3 domains and a variable-length Gly/Ser linker. When the linker is short, this construct represents a dumbbell-shaped molecule with limited amount of domain-domain mobility. Due to its elongated shape, this molecule efficiently aligns in steric alignment media. As the length of the linker increases, the two domains become effectively uncoupled and begin to behave as independent entities. Consequently, their degree of alignment drops, approaching that found in the (near-spherical) isolated SH3 domains. To model the dependence of alignment parameters on the length of the interdomain linker, we have generated in silico a series of conformational ensembles representing SH3 tandems with different linker length. These ensembles were subsequently used as input for alignment prediction software PALES. The predicted alignment tensors were compared with the results of experimental measurements using a series of tandem-SH3 samples in PEG/hexanol alignment media. This comparison broadly confirmed the expected trends. At the same time, it has been found that the isolated SH3 domain aligns much stronger than expected. This finding can be attributed to complex morphology of the PEG/hexanol media and/or to weak site-specific interactions between the protein and the media. In the latter case, there are strong indications that electrostatic interactions may play a role. The fact that PEG/hexanol does not behave as a simple steric media should serve as a caution for studies that use PALES as a quantitative prediction tool (especially for disordered proteins). Further progress in this area depends on our ability to accurately model the anisotropic media and its site-specific interactions with protein molecules. Once this ability is improved, it should be possible to use the alignment parameters as a

  5. Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

    International Nuclear Information System (INIS)

    Many proteins have modular design with multiple globular domains connected via flexible linkers. As a simple model of such system, we study a tandem construct consisting of two identical SH3 domains and a variable-length Gly/Ser linker. When the linker is short, this construct represents a dumbbell-shaped molecule with limited amount of domain–domain mobility. Due to its elongated shape, this molecule efficiently aligns in steric alignment media. As the length of the linker increases, the two domains become effectively uncoupled and begin to behave as independent entities. Consequently, their degree of alignment drops, approaching that found in the (near-spherical) isolated SH3 domains. To model the dependence of alignment parameters on the length of the interdomain linker, we have generated in silico a series of conformational ensembles representing SH3 tandems with different linker length. These ensembles were subsequently used as input for alignment prediction software PALES. The predicted alignment tensors were compared with the results of experimental measurements using a series of tandem-SH3 samples in PEG/hexanol alignment media. This comparison broadly confirmed the expected trends. At the same time, it has been found that the isolated SH3 domain aligns much stronger than expected. This finding can be attributed to complex morphology of the PEG/hexanol media and/or to weak site-specific interactions between the protein and the media. In the latter case, there are strong indications that electrostatic interactions may play a role. The fact that PEG/hexanol does not behave as a simple steric media should serve as a caution for studies that use PALES as a quantitative prediction tool (especially for disordered proteins). Further progress in this area depends on our ability to accurately model the anisotropic media and its site-specific interactions with protein molecules. Once this ability is improved, it should be possible to use the alignment parameters as

  6. Ionization behavior of molecular hydrogen in intense laser fields: Influence of molecular vibration and alignment

    CERN Document Server

    Förster, Johann; Saenz, Alejandro

    2014-01-01

    The alignment- and internuclear-distance dependent ionization of H$_2$ exposed to intense, ultrashort laser fields is studied by solving the time-dependent two-electron Schr\\"odinger equation. In the regime of perturbative few-photon ionization, a strong dependence of the ionization yield on the internuclear distance is found. While this finding confirms a previously reported breakdown of the fixed-nuclei approximation for parallel alignment, a simpler explanation is provided and it is demonstrated that this breakdown is not due to vibrational dynamics during the laser pulse. The persistence of this effect even for randomly aligned molecules is demonstrated. Furthermore, the transition from the multiphoton to the quasi-static (tunneling) regime is investigated considering intense 800 nm laser pulses. While the obtained ionization yields differ significantly from the prediction of Ammosov-Delone-Krainov rates, we find a surprisingly good quantitative agreement after introducing a simple frequency-dependent cor...

  7. Immobilization of laminin peptide in molecularly aligned chitosan by covalent bonding.

    Science.gov (United States)

    Matsuda, Atsushi; Kobayashi, Hisatoshi; Itoh, Soichiro; Kataoka, Kazunori; Tanaka, Junzo

    2005-05-01

    We developed a new biomaterial effective for nerve regeneration consisting of molecularly aligned chitosan with laminin peptides bonded covalently. Molecularly aligned chitosan was prepared from crab (Macrocheira kaempferi) tendons by ethanol treatment and 4 wt%-NaOH aqueous solutions to remove proteins and calcium phosphate, followed by deacetyl treatment using a 50 wt%-NaOH aqueous solution at 100 degrees C. Molecularly aligned tendon chitosan was chemically thiolated by reacting 4-thiobutyrolactone with the chitosan amino group. The introduction of thiol groups and their distribution to tendon chitosan and chitosan cast film were confirmed using ATR FT-IR, (1)H-NMR, and EDS. The 1.24 micromol/g of thiol groups introduced on the surface of tendon chitosan and the chitosan cast film was confirmed using ultraviolet (UV) spectra. Thiol groups of cysteine located at the end of synthetic laminin peptides were then reacted chemically with thiolated chitosan to form chitosan-S-S-laminin peptide. YIGSR estimated at 0.92 micromol/g and IKVAV estimated at 0.28 micromol/g on thiolated tendon chitosan were confirmed using UV spectra. YIGSR was estimated at 0.85 micromol/g and IKVAV was estimated at 0.34 micromol/g on the thiolated chitosan cast film.

  8. Alignment of leading-edge and peak-picking time of arrival methods to obtain accurate source locations

    Energy Technology Data Exchange (ETDEWEB)

    Roussel-Dupre, R.; Symbalisty, E.; Fox, C.; and Vanderlinde, O.

    2009-08-01

    The location of a radiating source can be determined by time-tagging the arrival of the radiated signal at a network of spatially distributed sensors. The accuracy of this approach depends strongly on the particular time-tagging algorithm employed at each of the sensors. If different techniques are used across the network, then the time tags must be referenced to a common fiducial for maximum location accuracy. In this report we derive the time corrections needed to temporally align leading-edge, time-tagging techniques with peak-picking algorithms. We focus on broadband radio frequency (RF) sources, an ionospheric propagation channel, and narrowband receivers, but the final results can be generalized to apply to any source, propagation environment, and sensor. Our analytic results are checked against numerical simulations for a number of representative cases and agree with the specific leading-edge algorithm studied independently by Kim and Eng (1995) and Pongratz (2005 and 2007).

  9. DINAMO: a coupled sequence alignment editor/molecular graphics tool for interactive homology modeling of proteins.

    Science.gov (United States)

    Hansen, M; Bentz, J; Baucom, A; Gregoret, L

    1998-01-01

    Gaining functional information about a novel protein is a universal problem in biomedical research. With the explosive growth of the protein sequence and structural databases, it is becoming increasingly common for researchers to attempt to build a three-dimensional model of their protein of interest in order to gain information about its structure and interactions with other molecules. The two most reliable methods for predicting the structure of a protein are homology modeling, in which the novel sequence is modeled on the known three-dimensional structure of a related protein, and fold recognition (threading), where the sequence is scored against a library of fold models, and the highest scoring model is selected. The sequence alignment to a known structure can be ambiguous, and human intervention is often required to optimize the model. We describe an interactive model building and assessment tool in which a sequence alignment editor is dynamically coupled to a molecular graphics display. By means of a set of assessment tools, the user may optimize his or her alignment to satisfy the known heuristics of protein structure. Adjustments to the sequence alignment made by the user are reflected in the displayed model by color and other visual cues. For instance, residues are colored by hydrophobicity in both the three-dimensional model and in the sequence alignment. This aids the user in identifying undesirable buried polar residues. Several different evaluation metrics may be selected including residue conservation, residue properties, and visualization of predicted secondary structure. These characteristics may be mapped to the model both singly and in combination. DINAMO is a Java-based tool that may be run either over the web or installed locally. Its modular architecture also allows Java-literate users to add plug-ins of their own design.

  10. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    International Nuclear Information System (INIS)

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the 'holy grail' of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies

  11. Accurate studies on the full vibrational energy spectra and molecular dissociation energies for some electronic states of N2 molecule

    Institute of Scientific and Technical Information of China (English)

    REN; Weiyi; SUN; Weiguo; HOU; Shilin; FENG; Hao

    2005-01-01

    It is usually very difficult to directly obtain molecular dissociation energy De and all accurate high-lying vibrational energies for most diatomic electronic states using modern experimental techniques or quantum theories, and it is also very difficult to give accurate analytical expression for diatomic molecular dissociation energy. This study proposes a new analytical formula for obtaining accurate molecular dissociation energy based on the LeRoy and Bernstein's energy expression in dissociation limit. A set of full vibrational energy spectra for some electronic states of N2 molecule are studied using the algebraic method (AM) suggested recently, and the corresponding accurate molecular dissociation energies are evaluated using the proposed new formula and high-lying AM vibrational energies. The results show that the AM spectra and the new theoretical dissociation energies agree excellently with experimental data, and thereby providing a new physical approach to generating accurate dissociation energies for electronic states of diatomic molecules.

  12. Spectral modulation of third-harmonic generation by molecular alignment and preformed plasma

    Science.gov (United States)

    Li, Min; Li, An-Yuan; He, Bo-Qu; Yuan, Shuai; Zeng, He-Ping

    2016-08-01

    We demonstrate spectral modulation of third-harmonic generation from molecular alignment effects. The third harmonic spectrum is broadened or narrowed under different influences of cross-phase modulations originating from various molecular alignment revivals. Furthermore, the spectrum and spatial distribution of the generated third harmonic pulse change dramatically in the presence of a preformed plasma. Under the influence of a preformed plasma, a narrower third harmonic spectrum is observed, and the conical third-harmonic pulse increases while the axial part decreases. The investigation provides an effective method to modulate the spectral characteristic and spatial distribution of third-harmonic generation from intense femtosecond filament. Project supported by the National Key Scientific Instrument Project, China (Grant No. 2012YQ150092), the National Basic Research Program of China (Grant No. 2011CB808105), the National Natural Science Foundation of China (Grant No. 11434005), China Postdoctoral Science Foundation (Grant No. 2014M560348), the National Natural Science Foundation of China (Grant No. 11504237), and the Shanghai Municipal Science and Technology Commission, China (Grant No. 14JC1401600).

  13. Molecular alignment effect on the photoassociation process via a pump-dump scheme.

    Science.gov (United States)

    Wang, Bin-Bin; Han, Yong-Chang; Cong, Shu-Lin

    2015-09-01

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X(1)Σ(+)) is associated into the molecule in the bound states of the excited state (A(1)Σ(+)) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j〉 on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse. PMID:26342366

  14. Molecular alignment effect on the photoassociation process via a pump-dump scheme

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Bin-Bin; Han, Yong-Chang, E-mail: ychan@dlut.edu.cn; Cong, Shu-Lin [School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China)

    2015-09-07

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na{sub 2}) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X{sup 1}Σ{sup +}) is associated into the molecule in the bound states of the excited state (A{sup 1}Σ{sup +}) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j〉 on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.

  15. Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

    Science.gov (United States)

    Sellers, Michael; Lisal, Martin; Brennan, John

    2015-06-01

    Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

  16. A large catalog of accurate distances to molecular clouds from PS1 photometry

    Energy Technology Data Exchange (ETDEWEB)

    Schlafly, E. F.; Rix, H.-W.; Martin, N. F. [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Green, G.; Finkbeiner, D. P. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Bell, E. F. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Burgett, W. S.; Chambers, K. C.; Hodapp, K. W.; Kaiser, N.; Magnier, E. A.; Tonry, J. L. [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States); Draper, P. W.; Metcalfe, N. [Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Price, P. A. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States)

    2014-05-01

    Distance measurements to molecular clouds are important but are often made separately for each cloud of interest, employing very different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the systematic uncertainty stemming from the quality of our stellar models is about 10%. The resulting catalog is the largest catalog of accurate, directly measured distances to molecular clouds. Our distance estimates are generally consistent with available distance estimates from the literature, though in some cases the literature estimates are off by a factor of more than two.

  17. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    Science.gov (United States)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  18. Surface electron density models for accurate ab initio molecular dynamics with electronic friction

    Science.gov (United States)

    Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.

    2016-06-01

    Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.

  19. Molecular scale buckling mechanics in individual aligned single-wall carbon nanotubes on elastomeric substrates.

    Science.gov (United States)

    Khang, Dahl-Young; Xiao, Jianliang; Kocabas, Coskun; MacLaren, Scott; Banks, Tony; Jiang, Hanqing; Huang, Yonggang Y; Rogers, John A

    2008-01-01

    We have studied the scaling of controlled nonlinear buckling processes in materials with dimensions in the molecular range (i.e., approximately 1 nm) through experimental and theoretical studies of buckling in individual single-wall carbon nanotubes on substrates of poly(dimethylsiloxane). The results show not only the ability to create and manipulate patterns of buckling at these molecular scales, but also, that analytical continuum mechanics theory can explain, quantitatively, all measurable aspects of this system. Inverse calculation applied to measurements of diameter-dependent buckling wavelengths yields accurate values of the Young's moduli of individual SWNTs. As an example of the value of this system beyond its use in this type of molecular scale metrology, we implement parallel arrays of buckled SWNTs as a class of mechanically stretchable conductor.

  20. Transient molecular orientation and rheology in flow aligning thermotropic liquid crystalline polymers

    International Nuclear Information System (INIS)

    Quantitative measurements of molecular orientation and rheology are reported for various transient shear flows of a nematic semiflexible copolyether. Unlike the case of lyotropic liquid crystalline polymers (LCPs), whose structure and rheology in shear are dominated by director tumbling, this material exhibits flow aligning behavior. The observed behavior is quite similar to that seen in a copolyester that we have recently studied [Ugaz and Burghardt (1998)], suggesting that flow aligning dynamics may predominate in main-chain thermotropes that incorporate significant chain flexibility. Since the flow aligning regime has received little attention in previous attempts to model the rheology of textured, polydomain LCPs, we attempt to determine whether available models are capable of predicting the orientation and stress response of this class of LCP. We first examine the predictions of the polydomain Ericksen model, an adaptation of Ericksen's transversely isotropic fluid model which accounts for the polydomain distribution of director orientation while neglecting distortional elasticity. This simple model captures a number of qualitative and quantitative features associated with the evolution of orientation and stress during shear flow inception, but cannot cope with reversing flows. To consider the possible role of distortional elasticity in the re-orientation dynamics upon reversal, we evaluate the mesoscopically averaged domain theory of Larson and Doi [Larson and Doi (1991)], which incorporates a phenomenological description of distortional elastic effects. To date, their approach to account for polydomain structure has only been applied to describe tumbling LCPs. We find that it captures the qualitative transient orientation response to flow reversals, but is less successful in describing the evolution of stresses. This is linked to the decoupling approximation adopted during the model's development. Finally, a modified polydomain Ericksen model is introduced

  1. Warm gas in the rotating disk of the Red Rectangle: accurate models of molecular line emission

    CERN Document Server

    Bujarrabal, V

    2013-01-01

    We aim to study the excitation conditions of the molecular gas in the rotating disk of the Red Rectangle, the only post-Asymptotic-Giant-Branch object in which the existence of an equatorial rotating disk has been demonstrated. For this purpose, we developed a complex numerical code that accurately treats radiative transfer in 2-D, adapted to the study of molecular lines from rotating disks. We present far-infrared Herschel/HIFI observations of the 12CO and 13CO J=6-5, J=10-9, and J=16-15 transitions in the Red Rectangle. We also present our code in detail and discuss the accuracy of its predictions, from comparison with well-tested codes. Theoretical line profiles are compared with the empirical data to deduce the physical conditions in the disk by means of model fitting. We conclude that our code is very efficient and produces reliable results. The comparison of the theoretical predictions with our observations reveals that the temperature of the Red Rectangle disk is typically ~ 100-150 K, about twice as h...

  2. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  3. Alignment dependence of photoelectron momentum distributions of atomic and molecular targets probed by few-cycle circularly polarized laser pulses

    Science.gov (United States)

    Abu-samha, M.; Madsen, Lars Bojer

    2016-08-01

    We present theoretical photoelectron momentum distributions (PMDs) for ionization from Ar(3 p ) and H2+ (σg) orbitals by few-cycle, high-intensity, near-infrared laser fields circularly polarized in the x y plane. The three-dimensional time-dependent Schrödinger equation is solved numerically within the single-active-electron approximation for Ar and within the fixed nuclei approximation for H2+ . The PMDs are investigated for alignment of the probed target orbitals relative to the polarization plane of the laser field. In the atomic case, the PMDs in the polarization plane for aligned 3 p Ar orbitals are, up to an overall scaling factor, insensitive to alignment of the probed orbital, while the lateral PMDs show a signature of the orbital node when that node is sufficiently close to the polarization plane. For the molecular case of H2+ (σg), our results show a significant impact of alignment on the PMDs due to the anisotropic molecular potential and the alignment-dependent coupling between the ground state and excited states.

  4. A novel approach to multiple sequence alignment using hadoop data grids.

    Science.gov (United States)

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences. PMID:21224205

  5. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    Science.gov (United States)

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  6. Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

    Science.gov (United States)

    Padial, José M; Grant, Taran; Frost, Darrel R

    2014-01-01

    Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates

  7. A molecular design principle of lyotropic liquid-crystalline conjugated polymers with directed alignment capability for plastic electronics.

    Science.gov (United States)

    Kim, Bong-Gi; Jeong, Eun Jeong; Chung, Jong Won; Seo, Sungbaek; Koo, Bonwon; Kim, Jinsang

    2013-07-01

    Conjugated polymers with a one-dimensional p-orbital overlap exhibit optoelectronic anisotropy. Their unique anisotropic properties can be fully realized in device applications only when the conjugated chains are aligned. Here, we report a molecular design principle of conjugated polymers to achieve concentration-regulated chain planarization, self-assembly, liquid-crystal-like good mobility and non-interdigitated side chains. As a consequence of these intra- and intermolecular attributes, chain alignment along an applied flow field occurs. This liquid-crystalline conjugated polymer was realized by incorporating intramolecular sulphur-fluorine interactions and bulky side chains linked to a tetrahedral carbon having a large form factor. By optimizing the polymer concentration and the flow field, we could achieve a high dichroic ratio of 16.67 in emission from conducting conjugated polymer films. Two-dimensional grazing-incidence X-ray diffraction was performed to analyse a well-defined conjugated polymer alignment. Thin-film transistors built on highly aligned conjugated polymer films showed more than three orders of magnitude faster carrier mobility along the conjugated polymer alignment direction than the perpendicular direction.

  8. The director and molecular dynamics of the field-induced alignment of a Gay-Berne nematic phase: An isothermal-isobaric nonequilibrium molecular dynamics simulation study

    Science.gov (United States)

    Luckhurst, Geoffrey R.; Satoh, Katsuhiko

    2010-05-01

    Isothermal-isobaric molecular dynamics simulations have been performed for the generic Gay-Berne (GB) mesogen, GB(4.4, 20.0, 1, 1), to investigate director and molecular rotational motion during the field-induced alignment of a nematic. The alignment process for the director is discussed within the context of a hydrodynamic analysis based on the Ericksen-Leslie theory and this is found to predict the simulated behavior well. The dependence of the relaxation time for the alignment on the field strength is also in good accord with the theory. The rotational viscosity coefficient estimated from the simulation is smaller than that typically observed for real nematics and the possible reasons for this are discussed. However, the simulation results are found to follow not only the theory but also the experiments, at least qualitatively. No significant variation in the local and long-range structure of the nematic phase is found during the field-induced alignment process. In addition, we have explored the molecular dynamics in the nematic phase in the presence of the field using the first- and second-rank time autocorrelation functions. More importantly we are able to show that the director relaxation time is longer than that for molecular rotation. It is also possible to use the two orientational correlation times to explore the relationship between the rotational viscosity coefficient and the rotational diffusion constant. The diffusion constants determined from the orientational correlation times, based on the short-time expansion of the autocorrelation functions, are found to be significantly different. In consequence it is not possible to test, unambiguously, the relationship between the rotational viscosity coefficient and the rotational diffusion constant. However, it would seem that the second-rank rotational correlation time provides the most reliable route to the rotational viscosity coefficient.

  9. Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

    CERN Document Server

    Rupp, Matthias; Müller, Klaus-Robert; von Lilienfeld, O Anatole

    2011-01-01

    We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\\"odinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross-validation over more than seven thousand small organic molecules yields a mean absolute error of ~10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.

  10. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    Science.gov (United States)

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  11. Catalyst-free highly vertically aligned ZnO nanoneedle arrays grown by plasma-assisted molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J.S.; Chiu, K.C. [Chung Yuan Christian University, Department of Physics, Chung-Li (China); Chung Yuan Christian University, Center for Nano-Technology, Chung-Li (China); Yang, C.S. [Tatung University, Graduate Institute of Electro-Optical Engineering, Taipei (China); Chen, P.I.; Su, C.F.; Chen, W.J. [Chung Yuan Christian University, Department of Physics, Chung-Li (China); Chou, W.C. [National Chiao Tung University, Department of Electrophysics, Hsin-Chu (China)

    2009-11-15

    This work describes the growth of highly vertically aligned ZnO nanoneedle arrays on wafer-scale catalyst-free c-plane sapphire substrates by plasma-assisted molecular beam epitaxy under high Zn flux conditions. The photoluminescence spectrum of the as-grown samples reveals strong free exciton emissions and donor-bound exciton emissions with an excellent full width at half maximum (FWHM) of 1.4 meV. The field emission of highly vertically aligned ZnO nanoneedle arrays closely follows the Fowler-Nordheim theory. The turn-on electric field was about 5.9 V/{mu}m with a field enhancement factor {beta} of around 793. (orig.)

  12. Catalyst-free highly vertically aligned ZnO nanoneedle arrays grown by plasma-assisted molecular beam epitaxy

    Science.gov (United States)

    Wang, J. S.; Yang, C. S.; Chen, P. I.; Su, C. F.; Chen, W. J.; Chiu, K. C.; Chou, W. C.

    2009-11-01

    This work describes the growth of highly vertically aligned ZnO nanoneedle arrays on wafer-scale catalyst-free c-plane sapphire substrates by plasma-assisted molecular beam epitaxy under high Zn flux conditions. The photoluminescence spectrum of the as-grown samples reveals strong free exciton emissions and donor-bound exciton emissions with an excellent full width at half maximum (FWHM) of 1.4 meV. The field emission of highly vertically aligned ZnO nanoneedle arrays closely follows the Fowler-Nordheim theory. The turn-on electric field was about 5.9 V/µm with a field enhancement factor β of around 793.

  13. Radiation and chemical crosslinking promote strain hardening behavior and molecular alignment in ultra high molecular weight polyethylene during multi-axial loading conditions.

    Science.gov (United States)

    Kurtz, S M; Pruitt, L A; Jewett, C W; Foulds, J R; Edidin, A A

    1999-08-01

    The mechanical behavior and evolution of crystalline morphology during large deformation of eight types of virgin and crosslinked ultra high molecular weight polyethylene (UHMWPE) were studied using the small punch test and transmission electron microscopy (TEM). We investigated the hypothesis that both radiation and chemical crosslinking hinder molecular mobility at large deformations, and hence promote strain hardening and molecular alignment during the multiaxial loading of the small punch test. Chemical crosslinking of UHMWPE was performed using 0.25% dicumyl peroxide (GHR 8110, GUR 1020 and 1050), and radiation crosslinking was performed using 150 kGy of electron beam radiation (GUR 1150). Crosslinking increased the ultimate load at failure and decreased the ultimate displacement of the polyethylenes during the small punch test. Crosslinking also increased the near-ultimate hardening behavior of the polyethylenes. Transmission electron microscopy was used to characterize the crystalline morphology of the bulk material, undeformed regions of the small punch test specimens, and deformed regions of the specimens oriented perpendicular and parallel to the punch direction. In contrast with the virgin polyethylenes, which showed only subtle evidence of lamellar alignment, the crosslinked polyethylenes exhibited enhanced crystalline lamellae orientation after the small punch test, predominantly in the direction parallel to the punch direction or deformation axis. Thus, the results of this study support the hypothesis that crosslinking promotes strain hardening during multiaxial loading because of increased resistance to molecular mobility at large deformations effected by molecular alignment. The data also illustrate the sensitivity of large deformation mechanical behavior and crystalline morphology to the method of crosslinking and resin of polyethylene.

  14. A Large Catalog of Accurate Distances to Molecular Clouds from PS1 Photometry

    CERN Document Server

    Schlafly, E F; Finkbeiner, D P; Rix, H -W; Bell, E F; Burgett, W S; Chambers, K C; Draper, P W; Hodapp, K W; Kaiser, N; Magnier, E A; Martin, N F; Metcalfe, N; Price, P A; Tonry, J L

    2014-01-01

    Distance measurements to molecular clouds are important, but are often made separately for each cloud of interest, employing very different different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. (2014). We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. (1985) catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the sys...

  15. Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations.

    Science.gov (United States)

    Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

    2015-03-14

    Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online. PMID:25770527

  16. Observation of enhanced field-free molecular alignment by two laser pulses

    DEFF Research Database (Denmark)

    Bisgaard, Christer; Poulsen, Mikael Dahlerup; Peronne, Emmanuel;

    2004-01-01

    We show experimentally that field-free alignment of iodobenzene molecules, induced by a single, intense, linearly polarized 1.4-ps-long laser pulse, can be strongly enhanced by dividing the pulse into two optimally synchronized pulses of the same duration. For a given total energy of the two...

  17. Pair-eigenstates and mutual alignment of coupled molecular rotors in a magnetic field.

    Science.gov (United States)

    Sharma, Ketan; Friedrich, Bretislav

    2016-05-11

    We examine the rotational states of a pair of polar (2)Σ molecules subject to a uniform magnetic field. The electric dipole-dipole interaction between the molecules creates entangled pair-eigenstates of two types. In one type, the Zeeman interaction between the inherently paramagnetic molecules and the magnetic field destroys the entanglement of the pair-eigenstates, whereas in the other type it does not. The pair-eigenstates exhibit numerous intersections, which become avoided for pair-eigenstates comprised of individual states that meet the selection rules ΔJi = 0, ± 1, ΔNi = 2n (n = 0, ±1, ±2,…), and ΔMi = 0, ± 1 imposed by the electric dipole-dipole operator. Here Ji, Ni and Mi are the total, rotational and projection angular momentum quantum numbers of molecules i = 1, 2 in the absence of the electric dipole-dipole interaction. We evaluate the mutual alignment of the pair-eigenstates and find it to be independent of the magnetic field, except for states that undergo avoided crossings, in which case the alignment of the interacting states is interchanged at the magnetic field corresponding to the crossing point. We present an analytic model which provides ready estimates of the pairwise alignment cosine that characterises the mutual alignment of the pair of coupled rotors. PMID:27126576

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

    DEFF Research Database (Denmark)

    Stadler, Robert; Jacobsen, Karsten Wedel

    2006-01-01

    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...

  19. Reconstruction of two-dimensional molecular structure with laser-induced electron diffraction from laser-aligned polyatomic molecules

    International Nuclear Information System (INIS)

    Imaging the transient process of molecules has been a basic way to investigate photochemical reactions and dynamics. Based on laser-induced electron diffraction and partial one-dimensional molecular alignment, here we provide two effective methods for reconstructing two-dimensional structure of polyatomic molecules. We demonstrate that electron diffraction images in both scattering angles and broadband energy can be utilized to retrieve complementary structure information, including positions of light atoms. Lastly, with picometre spatial resolution and the inherent femtosecond temporal resolution of lasers, laser-induced electron diffraction method offers significant opportunities for probing atomic motion in a large molecule in a typical pump-probe measurement

  20. Imaging Molecular Structure through Femtosecond Photoelectron Diffraction on Aligned and Oriented Gas-Phase Molecules

    CERN Document Server

    Boll, R; Adolph, M; Anielski, D; Aquila, A; Bari, S; Bomme, C; Bostedt, C; Bozek, J D; Chapman, H N; Christensen, L; Coffee, R; Coppola, N; De, S; Decleva, P; Epp, S W; Erk, B; Filsinger, F; Foucar, L; Gorkhover, T; Gumprecht, L; Hoemke, A; Holmegaard, L; Johnsson, P; Kienitz, J S; Kierspel, T; Krasniqi, F; Kuehnel, K -U; Maurer, J; Messerschmidt, M; Moshammer, R; Mueller, Nele L M; Rudek, B; Savelyev, E; Schlichting, I; Schmidt, C; Scholz, F; Schorb, S; Schulz, J; Seltmann, J; Stener, M; Stern, S; Techert, S; Thogersen, J; Trippel, S; Viefhaus, J; Vrakking, M; Stapelfeldt, H; Kuepper, J; Ullrich, J; Rudenko, A; Rolles, D

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray Free-Electron Laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C8H5F) and dissociating, laseraligned 1,4-dibromobenzene (C6H4Br2) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  1. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations.

    Science.gov (United States)

    Hepburn, I; Chen, W; De Schutter, E

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification. PMID:27497550

  2. A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat

    Science.gov (United States)

    Liu, Jian; Li, Dezhang; Liu, Xinzijian

    2016-07-01

    We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

  3. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations

    Science.gov (United States)

    Hepburn, I.; Chen, W.; De Schutter, E.

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.

  4. A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat.

    Science.gov (United States)

    Liu, Jian; Li, Dezhang; Liu, Xinzijian

    2016-07-14

    We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

  5. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    Science.gov (United States)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  6. Identifying New Drug Targets for Potent Phospholipase D Inhibitors: Combining Sequence Alignment, Molecular Docking, and Enzyme Activity/Binding Assays.

    Science.gov (United States)

    Djakpa, Helene; Kulkarni, Aditya; Barrows-Murphy, Scheneque; Miller, Greg; Zhou, Weihong; Cho, Hyejin; Török, Béla; Stieglitz, Kimberly

    2016-05-01

    Phospholipase D enzymes cleave phospholipid substrates generating choline and phosphatidic acid. Phospholipase D from Streptomyces chromofuscus is a non-HKD (histidine, lysine, and aspartic acid) phospholipase D as the enzyme is more similar to members of the diverse family of metallo-phosphodiesterase/phosphatase enzymes than phospholipase D enzymes with active site HKD repeats. A highly efficient library of phospholipase D inhibitors based on 1,3-disubstituted-4-amino-pyrazolopyrimidine core structure was utilized to evaluate the inhibition of purified S. chromofuscus phospholipase D. The molecules exhibited inhibition of phospholipase D activity (IC50 ) in the nanomolar range with monomeric substrate diC4 PC and micromolar range with phospholipid micelles and vesicles. Binding studies with vesicle substrate and phospholipase D strongly indicate that these inhibitors directly block enzyme vesicle binding. Following these compelling results as a starting point, sequence searches and alignments with S. chromofuscus phospholipase D have identified potential new drug targets. Using AutoDock, inhibitors were docked into the enzymes selected from sequence searches and alignments (when 3D co-ordinates were available) and results analyzed to develop next-generation inhibitors for new targets. In vitro enzyme activity assays with several human phosphatases demonstrated that the predictive protocol was accurate. The strategy of combining sequence comparison, docking, and high-throughput screening assays has helped to identify new drug targets and provided some insight into how to make potential inhibitors more specific to desired targets. PMID:26691755

  7. Boundary conditions for fluids with internal orientational degrees of freedom: Apparent velocity slip associated with the molecular alignment

    International Nuclear Information System (INIS)

    Boundary effects are investigated for fluids with internal orientational degrees of freedom such as molecular liquids, thermotropic and lyotropic liquid crystals, and polymeric fluids. The orientational degrees of freedom are described by the second rank alignment tensor which is related to the birefringence. We use a standard model to describe the orientational dynamics in the presence of flow, the momentum balance equations, and a constitutive law for the pressure tensor to describe our system. In the spirit of irreversible thermodynamics, boundary conditions are formulated for the mechanical slip velocity and the flux of the alignment. They are set up such that the entropy production at the wall inferred from the entropy flux is positive definite. Even in the absence of a true mechanical slip, the coupling between orientation and flow leads to flow profiles with an apparent slip. This has consequences for the macroscopically measurable effective velocity. In analytical investigations, we consider the simplified case of an isotropic fluid in the Newtonian and stationary flow regime. For special geometries such as plane and cylindrical Couette flow, plane Poiseuille flow, and a flow down an inclined plane, we demonstrate explicitly how the boundary conditions lead to an apparent slip. Furthermore, we discuss the dependence of the effective viscosity and of the effective slip length on the model parameters

  8. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  9. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    Science.gov (United States)

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-01

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.

  10. Charge Transport in Molecular Junctions: A Study of Level-Alignment, Thermoelectric Properties, and Environmental Effects

    Science.gov (United States)

    Kotiuga, Michele

    Here, we use and develop first-principles methods based on density functional theory (DFT) and beyond to understand and predict charge transport phenomena in the novel class of nanostructured devices: molecular junctions. Molecular junctions, individual molecules contacted to two metallic leads, which can be systematically altered by modifying the chemistry of each component, serve as test beds for the study of transport at the nanoscale. To date, various experimental methods have been designed to reliably assemble and measure transport properties of molecular junctions. Furthermore, theoretical methods built on DFT designed to yield quantitative agreement with these experiments for certain classes of molecular junctions have been developed. In order to gain insight into a broader range of molecular junctions and environmental effects associated with the surrounding solution, this dissertation will employ, explore and extend first-principles DFT calculations coupled with approximate self-energy corrections known to yield quantitative agreement with experiments for certain classes of molecular junctions. To start we examine molecular junctions in which the molecule is strongly hybridized with the leads: a challenging limit for the existing methodology. Using a physically motivated tight-binding model, we find that the experimental trends observed for such molecules can be explained by the presence of a so-called "gateway" state associated with the chemical bond that bridges the molecule and the lead. We discuss the ingredients of a self-energy corrected DFT based approach to quantitatively predict conductance in the presence of these hybridization effects. We also develop and apply an approach to account for the surrounding environment on the conductance, which has been predominantly ignored in past transport calculations due to computational complexity. Many experiments are performed in a solution of non-conducting molecules; far from benign, this solution is known

  11. Pair-eigenstates and mutual alignment of coupled molecular rotors in a magnetic field

    CERN Document Server

    Sharma, Ketan

    2016-01-01

    We examine the rotational states of a pair of polar $^2\\Sigma$ molecules subject to a uniform magnetic field. The electric dipole-dipole interaction between the molecules creates entangled pair-eigenstates of two types. In one type, the Zeeman interaction between the inherently paramagnetic molecules and the magnetic field destroys the entanglement of the pair-eigenstates, whereas in the other type it does not. The pair-eigenstates exhibit numerous intersections, which become avoided for pair-eigenstates comprised of individual states that meet the selection rules $\\Delta J_{i}=0,\\pm 1$, $\\Delta N_{i}=0,\\pm 2$, and $\\Delta M_{i}=0,\\pm 1$ imposed by the electric dipole-dipole operator. Here $J_{i}$, $N_{i}$ and $M_{i}$ are the total, rotational and projection angular momentum quantum numbers of molecules $i=1,2$ in the absence of the electric dipole-dipole interaction. We evaluate the mutual alignment of the pair-eigenstates and find it to be independent of the magnetic field, except for states that undergo av...

  12. Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs

    Directory of Open Access Journals (Sweden)

    Fereshteh Shiri

    2016-03-01

    Full Text Available Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD and the enhanced replacement method (ERM were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND approach. After variable selection, GRIND were correlated with activity values (pIC50 by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q2 value of 0.77, an rpred2 of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.

  13. Ultrahigh density array of vertically aligned small-molecular organic nanowires on arbitrary substrates.

    Science.gov (United States)

    Starko-Bowes, Ryan; Pramanik, Sandipan

    2013-01-01

    In recent years π-conjugated organic semiconductors have emerged as the active material in a number of diverse applications including large-area, low-cost displays, photovoltaics, printable and flexible electronics and organic spin valves. Organics allow (a) low-cost, low-temperature processing and (b) molecular-level design of electronic, optical and spin transport characteristics. Such features are not readily available for mainstream inorganic semiconductors, which have enabled organics to carve a niche in the silicon-dominated electronics market. The first generation of organic-based devices has focused on thin film geometries, grown by physical vapor deposition or solution processing. However, it has been realized that organic nanostructures can be used to enhance performance of above-mentioned applications and significant effort has been invested in exploring methods for organic nanostructure fabrication. A particularly interesting class of organic nanostructures is the one in which vertically oriented organic nanowires, nanorods or nanotubes are organized in a well-regimented, high-density array. Such structures are highly versatile and are ideal morphological architectures for various applications such as chemical sensors, split-dipole nanoantennas, photovoltaic devices with radially heterostructured "core-shell" nanowires, and memory devices with a cross-point geometry. Such architecture is generally realized by a template-directed approach. In the past this method has been used to grow metal and inorganic semiconductor nanowire arrays. More recently π-conjugated polymer nanowires have been grown within nanoporous templates. However, these approaches have had limited success in growing nanowires of technologically important π-conjugated small molecular weight organics, such as tris-8-hydroxyquinoline aluminum (Alq3), rubrene and methanofullerenes, which are commonly used in diverse areas including organic displays, photovoltaics, thin film transistors

  14. An accurate metalloprotein-specific scoring function and molecular docking program devised by a dynamic sampling and iteration optimization strategy.

    Science.gov (United States)

    Bai, Fang; Liao, Sha; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin

    2015-04-27

    Metalloproteins, particularly zinc metalloproteins, are promising therapeutic targets, and recent efforts have focused on the identification of potent and selective inhibitors of these proteins. However, the ability of current drug discovery and design technologies, such as molecular docking and molecular dynamics simulations, to probe metal-ligand interactions remains limited because of their complicated coordination geometries and rough treatment in current force fields. Herein we introduce a robust, multiobjective optimization algorithm-driven metalloprotein-specific docking program named MpSDock, which runs on a scheme similar to consensus scoring consisting of a force-field-based scoring function and a knowledge-based scoring function. For this purpose, in this study, an effective knowledge-based zinc metalloprotein-specific scoring function based on the inverse Boltzmann law was designed and optimized using a dynamic sampling and iteration optimization strategy. This optimization strategy can dynamically sample and regenerate decoy poses used in each iteration step of refining the scoring function, thus dramatically improving both the effectiveness of the exploration of the binding conformational space and the sensitivity of the ranking of the native binding poses. To validate the zinc metalloprotein-specific scoring function and its special built-in docking program, denoted MpSDockZn, an extensive comparison was performed against six universal, popular docking programs: Glide XP mode, Glide SP mode, Gold, AutoDock, AutoDock4Zn, and EADock DSS. The zinc metalloprotein-specific knowledge-based scoring function exhibited prominent performance in accurately describing the geometries and interactions of the coordination bonds between the zinc ions and chelating agents of the ligands. In addition, MpSDockZn had a competitive ability to sample and identify native binding poses with a higher success rate than the other six docking programs.

  15. Nonlinear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes.

    Science.gov (United States)

    Timr, Štěpán; Brabec, Jiří; Bondar, Alexey; Ryba, Tomáš; Železný, Miloš; Lazar, Josef; Jungwirth, Pavel

    2015-07-30

    Several methods based on single- and two-photon fluorescence detected linear dichroism have recently been used to determine the orientational distributions of fluorescent dyes in lipid membranes. However, these determinations relied on simplified descriptions of nonlinear anisotropic properties of the dye molecules, using a transition dipole-moment-like vector instead of an absorptivity tensor. To investigate the validity of the vector approximation, we have now carried out a combination of computer simulations and polarization microscopy experiments on two representative fluorescent dyes (DiI and F2N12S) embedded in aqueous phosphatidylcholine bilayers. Our results indicate that a simplified vector-like treatment of the two-photon transition tensor is applicable for molecular geometries sampled in the membrane at ambient conditions. Furthermore, our results allow evaluation of several distinct polarization microscopy techniques. In combination, our results point to a robust and accurate experimental and computational treatment of orientational distributions of DiI, F2N12S, and related dyes (including Cy3, Cy5, and others), with implications to monitoring physiologically relevant processes in cellular membranes in a novel way. PMID:26146848

  16. Dynamical image-charge effect in molecular tunnel junctions: Beyond energy level alignment

    Science.gov (United States)

    Jin, Chengjun; Thygesen, Kristian S.

    2014-01-01

    When an electron tunnels between two metal contacts it temporarily induces an image charge (IC) in the electrodes which acts back on the tunneling electron. It is usually assumed that the IC forms instantaneously such that a static model for the image potential applies. Here we investigate how the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z2, where Z is the quasiparticle renormalization factor, compared to the static IC approximation. We show that Z can be expressed either in terms of the plasma frequency of the electrode or as the overlap between electrode wave functions corresponding to an empty and filled level, respectively. First-principles GW calculations for benzene-diamine connected to gold electrodes show that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels.

  17. 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

    The conductance of π-conjugated molecular wires bonded to gold electrodes at zero bias is studied using density functional theory combined with nonequilibrium Green’s function method. For all systems considered, we find that the conductance length dependence follows the simple exponential law...... characteristic of tunneling through a barrier, G = Gc exp(−βL). For thiophene, pyrrole, and phenyl wires with thiol end-groups, we calculate decay constants (β) of 0.211, 0.257, and 0.264 Å−1, respectively, and contact conductances (Gc) of 1.25, 2.90, and 1.22G0, where G0 = 2e2/h is the conductance quantum....... In comparison, the corresponding values for amine-terminated thiophene are calculated to be β = 0.160 Å−1 and Gc = 0.038G0. These results show that (1) the contact resistance is mainly determined by the anchoring group and (2) the decay constant, which determines the conductance in the long wire limit...

  18. Orientation and morphology of chloroaluminum phthalocyanine films grown by vapor deposition: Electrical field-induced molecular alignment

    Energy Technology Data Exchange (ETDEWEB)

    Basova, Tamara V., E-mail: basova@niic.nsc.ru [Nikolaev Institute of Inorganic Chemistry, 3 Lavrentiev Ave., Novosibirsk 630090 (Russian Federation); Kiselev, Vitaly G., E-mail: vitaly.kiselev@kinetics.nsc.ru [Institute of Chemical Kinetics and Combustion, 3 Institutskaya Str., Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090 (Russian Federation); Plyashkevich, Vladimir A. [Nikolaev Institute of Inorganic Chemistry, 3 Lavrentiev Ave., Novosibirsk 630090 (Russian Federation); Cheblakov, Pavel B. [Institute of Chemical Kinetics and Combustion, 3 Institutskaya Str., Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090 (Russian Federation); Latteyer, Florian; Peisert, Heiko; Chasse, Thomas [Institute of Physical and Theoretical Chemistry, University of Tuebingen, D-72074 Tubingen (Germany)

    2011-02-28

    Graphical abstract: The external electric field applied during the physical vapor deposition process of thin chloroaluminum(III) phthalocyanine films modified noticeably the molecular orientation and the surface morphology of the films. These effects were studied by combining both experimental (polarized Raman spectroscopy and atomic force microscopy) and theoretical (quantum chemical calculations) techniques. Research highlights: {yields} The electric field was applied during the PVD of thin AlClPc films. {yields} The electric field of 1.4 kV mm{sup -1} modified the film structure noticeably. {yields} Tilt angles of the molecules were measured using polarised Raman spectroscopy. {yields} Assignments in vibrational spectra were performed using DFT computations. - Abstract: The electric field influence on the molecular orientation and the surface morphology of the chloroaluminum(III) phthalocyanine (AlClPc) films has been studied using polarization dependent Raman spectroscopy and atomic force microscopy. The experimental studies were supported by DFT quantum chemical computations of the AlClPc vibrational spectra and {sup 15}N isotopic shifts. The electric field of 1.4 kV mm{sup -1} applied parallel to the substrate plane during the physical vapour deposition modified the film structure noticeable. The AlClPc molecules were aligned nearly perpendicular to the substrate surface (the mean tilt angle increased to {approx}80 deg. from {approx}20 deg. in the films grown without the electric field). The AFM images of the AlClPc films grown in the absence of electric field revealed a predominant amount of crystallites of polyhedron shape, whereas in the case of the applied electric field the surface was more ordered and consisted of the crystallites of a smoother shape.

  19. Orientation and morphology of chloroaluminum phthalocyanine films grown by vapor deposition: Electrical field-induced molecular alignment

    International Nuclear Information System (INIS)

    Graphical abstract: The external electric field applied during the physical vapor deposition process of thin chloroaluminum(III) phthalocyanine films modified noticeably the molecular orientation and the surface morphology of the films. These effects were studied by combining both experimental (polarized Raman spectroscopy and atomic force microscopy) and theoretical (quantum chemical calculations) techniques. Research highlights: → The electric field was applied during the PVD of thin AlClPc films. → The electric field of 1.4 kV mm-1 modified the film structure noticeably. → Tilt angles of the molecules were measured using polarised Raman spectroscopy. → Assignments in vibrational spectra were performed using DFT computations. - Abstract: The electric field influence on the molecular orientation and the surface morphology of the chloroaluminum(III) phthalocyanine (AlClPc) films has been studied using polarization dependent Raman spectroscopy and atomic force microscopy. The experimental studies were supported by DFT quantum chemical computations of the AlClPc vibrational spectra and 15N isotopic shifts. The electric field of 1.4 kV mm-1 applied parallel to the substrate plane during the physical vapour deposition modified the film structure noticeable. The AlClPc molecules were aligned nearly perpendicular to the substrate surface (the mean tilt angle increased to ∼80 deg. from ∼20 deg. in the films grown without the electric field). The AFM images of the AlClPc films grown in the absence of electric field revealed a predominant amount of crystallites of polyhedron shape, whereas in the case of the applied electric field the surface was more ordered and consisted of the crystallites of a smoother shape.

  20. Twist viscosities and flow alignment of biaxial nematic liquid crystal phases of a soft ellipsoid-string fluid studied by molecular dynamics simulation.

    Science.gov (United States)

    Sarman, Sten; Laaksonen, Aatto

    2012-09-14

    We have calculated the twist viscosity and the alignment angle between the director and the stream lines in shear flow of a liquid crystal model system, which forms biaxial nematic liquid crystals, as functions of the density, from the Green-Kubo relations by equilibrium molecular dynamics simulation and by a nonequilibrium molecular dynamics algorithm, where a torque conjugate to the director angular velocity is applied to rotate the director. The model system consists of a soft ellipsoid-string fluid where the ellipsoids interact according a repulsive version of the Gay-Berne potential. Four different length-to-width-to-breadth ratios have been studied. On compression, this system forms discotic or calamitic uniaxial nematic phases depending on the dimensions of the molecules, and on further compression a biaxial nematic phase is formed. In the uniaxial nematic phase there is one twist viscosity and one alignment angle. In the biaxial nematic phase there are three twist viscosities and three alignment angles corresponding to the rotation around the various directors and the different alignments of the directors relative to the stream lines, respectively. It is found that the smallest twist viscosity arises by rotation around the director formed by the long axes, the second smallest one arises by rotation around the director formed by the normals of the broadsides, and the largest one by rotation around the remaining director. The first twist viscosity is rather independent of the density whereas the last two ones increase strongly with density. One finds that there is one stable director alignment relative to the streamlines, namely where the director formed by the long axes is almost parallel to the stream lines and where the director formed by the normals of the broadsides is almost parallel to the shear plane. The relative magnitudes of the components of the twist viscosities span a fairly wide interval so this model should be useful for parameterisation

  1. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, R.C.

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  2. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, R.C.

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese's group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  3. Change of Magnetic Field$-$Gas Alignment at Gravity-Driven Alfv\\'enic Transition in Molecular Clouds: Implications for Dust Polarization Observations

    CERN Document Server

    Chen, Che-Yu; Li, Zhi-Yun

    2016-01-01

    Diffuse striations in molecular clouds are preferentially aligned with local magnetic fields whereas dense filaments tend to be perpendicular to them. When and why this transition occurs remain uncertain. To explore the physics behind this transition, we compute the histogram of relative orientation (HRO) between the density gradient and the magnetic field in 3D MHD simulations of prestellar core formation in shock-compressed regions within GMCs. We find that, in the magnetically-dominated (sub-Alfv\\'enic) post-shock region, the gas structure is preferentially aligned with the local magnetic field. For overdense sub-regions with super-Alfv\\'enic gas, their elongation becomes preferentially perpendicular to the local magnetic field instead. The transition occurs when self-gravitating gas gains enough kinetic energy from the gravitational acceleration to overcome the magnetic support against the cross-field contraction, which results in a power-law increase of the field strength with density. Similar results ca...

  4. Fragment oriented molecular shapes.

    Science.gov (United States)

    Hain, Ethan; Camacho, Carlos J; Koes, David Ryan

    2016-05-01

    Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search. PMID:27085751

  5. Accurate and Scalable O(N) Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Osei-Kuffuor, Daniel [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fattebert, Jean-Luc [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-01-01

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10-4 Ha/Bohr.

  6. Development of an accurate molecular mechanics model for buckling behavior of multi-walled carbon nanotubes under axial compression.

    Science.gov (United States)

    Safaei, B; Naseradinmousavi, P; Rahmani, A

    2016-04-01

    In the present paper, an analytical solution based on a molecular mechanics model is developed to evaluate the elastic critical axial buckling strain of chiral multi-walled carbon nanotubes (MWCNTs). To this end, the total potential energy of the system is calculated with the consideration of the both bond stretching and bond angular variations. Density functional theory (DFT) in the form of generalized gradient approximation (GGA) is implemented to evaluate force constants used in the molecular mechanics model. After that, based on the principle of molecular mechanics, explicit expressions are proposed to obtain elastic surface Young's modulus and Poisson's ratio of the single-walled carbon nanotubes corresponding to different types of chirality. Selected numerical results are presented to indicate the influence of the type of chirality, tube diameter, and number of tube walls in detailed. An excellent agreement is found between the present numerical results and those found in the literature which confirms the validity as well as the accuracy of the present closed-form solution. It is found that the value of critical axial buckling strain exhibit significant dependency on the type of chirality and number of tube walls.

  7. Detecting the limits of regulatory element conservation anddivergence estimation using pairwise and multiple alignments

    Energy Technology Data Exchange (ETDEWEB)

    Pollard, Daniel A.; Moses, Alan M.; Iyer, Venky N.; Eisen,Michael B.

    2006-08-14

    Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background noncoding andtranscription factor binding site evolution, and use simulated alignmentsto systematically examine multiple alignment accuracy and its impact ontwo key molecular evolutionary inferences: transcription factor bindingsite conservation and divergence estimation. We find that the accuracy ofmultiple alignments is determined almost exclusively by the pairwisedivergence distance of the two most diverged species and that additionalspecies have a negligible influence on alignment accuracy. Conservedtranscription factor binding sites align better than surroundingnoncoding DNA yet are often found to be misaligned at relatively shortdivergence distances, such that studies of binding site gain and losscould easily be confounded by alignment error. Divergence estimates frommultiple alignments tend to be overestimated at short divergencedistances but reach a tool specific divergence at which they cease toincrease, leading to underestimation at long divergences. Our moststriking finding was that overall alignment accuracy, binding sitealignment accuracy and divergence estimation accuracy vary greatly acrossbranches in a tree and are most accurate for terminal branches connectingsister taxa and least accurate for internal branches connectingsub-alignments. Conclusions: Our results suggest that variation inalignment accuracy can lead to errors in molecular evolutionaryinferences that could be construed as biological variation. Thesefindings have implications for which species to choose for analyses, whatkind of errors would be expected for a given set of species and howmultiple alignment tools and

  8. Aligned Molecular Clouds towards SS433 and L=348.5 degrees; Possible Evidence for Galactic "Vapor Trail" Created by Relativistic Jet

    CERN Document Server

    Yamamoto, Hiroaki; Ishigami, Shinji; Fujishita, Motosuji; Kawase, Tokuichi; Kawamura, Akiko; Mizuno, Norikazu; Onishi, Toshikazu; Mizuno, Akira; McClure-Griffiths, Naomi M; Fukui, Yasuo

    2008-01-01

    We have carried out a detailed analysis of the NANTEN 12CO(J=1-0) dataset in two large areas of ~25 square degrees towards SS433 (l~40 degree) and of ~18 square degrees towards l~348.5 degree, respectively. We have discovered two groups of remarkably aligned molecular clouds at |b|~1--5 degree in the two regions. In SS433, we have detected 10 clouds in total, which are well aligned nearly along the axis of the X-ray jet emanating from SS433. These clouds have similar line-of-sight velocities of 42--56 km s^-1 and the total projected length of the feature is ~300 pc, three times larger than that of the X-ray jet, at a distance of 3 kpc. Towards l~348.5 degree, we have detected four clouds named as MJG348.5 at line-of-sight velocities of -80 -- -95 km s^-1 in V_LSR, which also show alignment nearly perpendicular to the Galactic plane. The total length of the feature is ~400 pc at a kinematic distance of 6 kpc. In the both cases, the CO clouds are distributed at high galactic latitudes where such clouds are very...

  9. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    Science.gov (United States)

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  10. An accurate and scalable O(N) algorithm for First-Principles Molecular Dynamics computations on petascale computers and beyond

    Science.gov (United States)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-03-01

    We present a truly scalable First-Principles Molecular Dynamics algorithm with O(N) complexity and fully controllable accuracy, capable of simulating systems of sizes that were previously impossible with this degree of accuracy. By avoiding global communication, we have extended W. Kohn's condensed matter ``nearsightedness'' principle to a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wavefunctions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 100,000 atoms on 100,000 processors, with a wall-clock time of the order of one minute per molecular dynamics time step. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  11. MECHANICAL PERTURBATION INDUCED MOLECULAR ALIGNMENTS IN A SIDE-CHAIN LIQUID CRYSTALLINE POLYACETYLENE, POLY{10-[4-(4'-METHOXYPHENOXYCARBONYL)PHENOXYCARBONYL]-1-DECYNE}

    Institute of Scientific and Technical Information of China (English)

    Ben-zhong Tang; Xiang-xing Kong; Xin-de Feng

    1999-01-01

    A new liquid crystalline polyacetylene containing a phenyl benzoate mesogen (5) is synthesized,whose mesomorphic properties are found to be easily "tunable" by simple mechanical perturbation. The polymerization of 10-[4-(4'-methoxyphenoxycarbonyl)phenoxycarbonyl]-1-decyne (4) initiated by the WCl6-Ph4Sn/dioxane complex yields polymer 5 with a Mw of 28400. The molecular structure of 5 is characterized by NMR, IR, and UV spectroscopy and its liquid crystalline behavior is investigated by DSC,POM, and XRD analysis. Upon mechanical perturbation, 5 exhibits unusual agitation-induced high-strength disclinations, shear-induced inversion walls, and solidification-induced banded textures. Such phenomena have been observed in the main-chain liquid crystalline polymers with rigid backbones, but have seldom been reported for the side-chain liquid crystalline polymers with flexible backbones, suggesting that the rigid polyacetylene backbone of 5 plays a constructive role in inducing the novel molecular alignments.

  12. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, T; Manz, TA; Sholl, DS

    2011-03-24

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO(2) adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIE-8, ZIE-90, and Zn(nicotinate)(2). The resulting CO(2) adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry's constant (109 mmol/g.bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)(2), which makes it a potentially attractive mateiial for CO(2) adsorption applications.

  13. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Taku [Georgia Inst. of Technology, Atlanta, GA (United States); Manz, Thomas A. [Georgia Inst. of Technology, Atlanta, GA (United States); Sholl, David S. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2011-02-28

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO2 adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIF-8, ZIF-90, and Zn(nicotinate)2. The resulting CO2 adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry’s constant (109 mmol/g·bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)2, which makes it a potentially attractive material for CO2 adsorption applications.

  14. Ultrafast electron diffraction from aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Centurion, Martin [Univ. of Nebraska, Lincoln, NE (United States)

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  15. Topology of surfaces for molecular Stark energy, alignment, and orientation generated by combined permanent and induced electric dipole interactions

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Burkhard, E-mail: burkhard.schmidt@fu-berlin.de [Institute for Mathematics, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin (Germany); Friedrich, Bretislav, E-mail: brich@fhi-berlin.mpg.de [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany)

    2014-02-14

    We show that combined permanent and induced electric dipole interactions of linear polar and polarizable molecules with collinear electric fields lead to a sui generis topology of the corresponding Stark energy surfaces and of other observables – such as alignment and orientation cosines – in the plane spanned by the permanent and induced dipole interaction parameters. We find that the loci of the intersections of the surfaces can be traced analytically and that the eigenstates as well as the number of their intersections can be characterized by a single integer index. The value of the index, distinctive for a particular ratio of the interaction parameters, brings out a close kinship with the eigenproperties obtained previously for a class of Stark states via the apparatus of supersymmetric quantum mechanics.

  16. Hardware Accelerated Sequence Alignment with Traceback

    OpenAIRE

    Scott Lloyd; Snell, Quinn O

    2009-01-01

    Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is pres...

  17. Conditional alignment random fields for multiple motion sequence alignment.

    Science.gov (United States)

    Kim, Minyoung

    2013-11-01

    We consider the multiple time-series alignment problem, typically focusing on the task of synchronizing multiple motion videos of the same kind of human activity. Finding an optimal global alignment of multiple sequences is infeasible, while there have been several approximate solutions, including iterative pairwise warping algorithms and variants of hidden Markov models. In this paper, we propose a novel probabilistic model that represents the conditional densities of the latent target sequences which are aligned with the given observed sequences through the hidden alignment variables. By imposing certain constraints on the target sequences at the learning stage, we have a sensible model for multiple alignments that can be learned very efficiently by the EM algorithm. Compared to existing methods, our approach yields more accurate alignment while being more robust to local optima and initial configurations. We demonstrate its efficacy on both synthetic and real-world motion videos including facial emotions and human activities. PMID:24051737

  18. Beyond Alignment

    DEFF Research Database (Denmark)

    Beyond Alignment: Applying Systems Thinking to Architecting Enterprises is a comprehensive reader about how enterprises can apply systems thinking in their enterprise architecture practice, for business transformation and for strategic execution. The book's contributors find that systems thinking...

  19. Change of Magnetic Field-gas Alignment at the Gravity-driven Alfvénic Transition in Molecular Clouds: Implications for Dust Polarization Observations

    Science.gov (United States)

    Chen, Che-Yu; King, Patrick K.; Li, Zhi-Yun

    2016-10-01

    Diffuse striations in molecular clouds are preferentially aligned with local magnetic fields, whereas dense filaments tend to be perpendicular to them. When and why this transition occurs remain uncertain. To explore the physics behind this transition, we compute the histogram of relative orientation (HRO) between the density gradient and the magnetic field in three-dimensional magnetohydrodynamic (MHD) simulations of prestellar core formation in shock-compressed regions within giant molecular clouds. We find that, in the magnetically dominated (sub-Alfvénic) post-shock region, the gas structure is preferentially aligned with the local magnetic field. For overdense sub-regions with super-Alfvénic gas, their elongation becomes preferentially perpendicular to the local magnetic field. The transition occurs when self-gravitating gas gains enough kinetic energy from the gravitational acceleration to overcome the magnetic support against the cross-field contraction, which results in a power-law increase of the field strength with density. Similar results can be drawn from HROs in projected two-dimensional maps with integrated column densities and synthetic polarized dust emission. We quantitatively analyze our simulated polarization properties, and interpret the reduced polarization fraction at high column densities as the result of increased distortion of magnetic field directions in trans- or super-Alfvénic gas. Furthermore, we introduce measures of the inclination and tangledness of the magnetic field along the line of sight as the controlling factors of the polarization fraction. Observations of the polarization fraction and angle dispersion can therefore be utilized in studying local magnetic field morphology in star-forming regions.

  20. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    International Nuclear Information System (INIS)

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures

  1. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    Science.gov (United States)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2015-09-01

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  2. Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

    Science.gov (United States)

    Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

    2016-03-01

    Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

  3. pH-Triggered Molecular Alignment for Reproducible SERS Detection via an AuNP/Nanocellulose Platform

    Science.gov (United States)

    Wei, Haoran; Vikesland, Peter J.

    2015-12-01

    The low affinity of neutral and hydrophobic molecules towards noble metal surfaces hinders their detection by surface-enhanced Raman spectroscopy (SERS). Herein, we present a method to enhance gold nanoparticle (AuNP) surface affinity by lowering the suspension pH below the analyte pKa. We developed an AuNP/bacterial cellulose (BC) nanocomposite platform and applied it to two common pollutants, carbamazepine (CBZ) and atrazine (ATZ) with pKa values of 2.3 and 1.7, respectively. Simple mixing of the analytes with AuNP/BC at pH pKa resulted in consistent electrostatic alignment of the CBZ and ATZ molecules across the nanocomposite and highly reproducible SERS spectra. Limits of detection of 3 nM and 11 nM for CBZ and ATZ, respectively, were attained. Tests with additional analytes (melamine, 2,4-dichloroaniline, 4-chloroaniline, 3-bromoaniline, and 3-nitroaniline) further illustrate that the AuNP/BC platform provides reproducible analyte detection and quantification while avoiding the uncontrolled aggregation and flocculation of AuNPs that often hinder low pH detection.

  4. pH-Triggered Molecular Alignment for Reproducible SERS Detection via an AuNP/Nanocellulose Platform

    Science.gov (United States)

    Wei, Haoran; Vikesland, Peter J.

    2015-12-01

    The low affinity of neutral and hydrophobic molecules towards noble metal surfaces hinders their detection by surface-enhanced Raman spectroscopy (SERS). Herein, we present a method to enhance gold nanoparticle (AuNP) surface affinity by lowering the suspension pH below the analyte pKa. We developed an AuNP/bacterial cellulose (BC) nanocomposite platform and applied it to two common pollutants, carbamazepine (CBZ) and atrazine (ATZ) with pKa values of 2.3 and 1.7, respectively. Simple mixing of the analytes with AuNP/BC at pH < pKa resulted in consistent electrostatic alignment of the CBZ and ATZ molecules across the nanocomposite and highly reproducible SERS spectra. Limits of detection of 3 nM and 11 nM for CBZ and ATZ, respectively, were attained. Tests with additional analytes (melamine, 2,4-dichloroaniline, 4-chloroaniline, 3-bromoaniline, and 3-nitroaniline) further illustrate that the AuNP/BC platform provides reproducible analyte detection and quantification while avoiding the uncontrolled aggregation and flocculation of AuNPs that often hinder low pH detection.

  5. CO(1-0) survey of high-z radio galaxies: alignment of molecular halo gas with distant radio sources

    CERN Document Server

    Emonts, B H C; Feain, I; Mao, M Y; Ekers, R D; Miley, G; Seymour, N; Roettgering, H J A; Villar-Martin, M; Sadler, E M; Carilli, C L; Mahony, E K; de Breuck, C; Stroe, A; Pentericci, L; van Moorsel, G A; Drouart, G; Ivison, R J; Greve, T R; Humphrey, A; Wylezalek, D; Tadhunter, C N

    2013-01-01

    We present a CO(1-0) survey for cold molecular gas in a representative sample of 13 high-z radio galaxies (HzRGs) at 1.4molecular gas mass derived for these two systems is M$_{\\rm H2} \\sim 6 \\times 10^{10}\\, {\\rm M}_{\\odot}$ (M$_{\\rm H2}$/$L'_{\\rm CO}$=0.8). For the remaining three CO-detected sources, the CO(1-0) emission is located in the halo (~50-kpc) environment. These three HzRGs are among the fainter far-IR emitters in our sample, suggesting that similar reservoirs of cold molecular halo gas may have been missed in earlier studies d...

  6. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    OpenAIRE

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of protein or DNA sequences. An accurate alignment can provide valuable information for experimentation on the newly found sequences. It is indispensable in basic research as well as in practical applic...

  7. Inferring comprehensible business/ICT alignment rules.

    OpenAIRE

    Cumps, Bjorn; Martens, David; De Backer, Manu; Haesen, Raf; Viaene, Stijn; Dedene, Guido; Baesens, Bart; Snoeck, Monique

    2009-01-01

    We inferred business rules for business/ICT alignment by applying a novel rule induction algorithm on a data set containing rich alignment information polled from 641 organisations in 7 European countries. The alignment rule set was created using AntMiner+, a rule induction technique with a reputation of inducing accurate, comprehensible, and intuitive predictive models from data. Our data set consisted of 18 alignment practices distilled from an analysis of relevant publications and validate...

  8. Magnetically aligned supramolecular hydrogels.

    Science.gov (United States)

    Wallace, Matthew; Cardoso, Andre Zamith; Frith, William J; Iggo, Jonathan A; Adams, Dave J

    2014-12-01

    The magnetic-field-induced alignment of the fibrillar structures present in an aqueous solution of a dipeptide gelator, and the subsequent retention of this alignment upon transformation to a hydrogel upon the addition of CaCl2 or upon a reduction in solution pH is reported. Utilising the switchable nature of the magnetic field coupled with the slow diffusion of CaCl2 , it is possible to precisely control the extent of anisotropy across a hydrogel, something that is generally very difficult to do using alternative methods. The approach is readily extended to other compounds that form viscous solutions at high pH. It is expected that this work will greatly expand the utility of such low-molecular-weight gelators (LMWG) in areas where alignment is key. PMID:25345918

  9. Alignment fixture

    Science.gov (United States)

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

    A part alignment fixture is provided which may be used for precise variable lateral and tilt alignment relative to the fixture base of various shaped parts. The fixture may be used as a part holder for machining or inspection of parts or alignment of parts during assembly and the like. The fixture includes a precisely machined diameter disc-shaped hub adapted to receive the part to be aligned. The hub is nested in a guide plate which is adapted to carry two oppositely disposed pairs of positioning wedges so that the wedges may be reciprocatively positioned by means of respective micrometer screws. The sloping faces of the wedges contact the hub at respective quadrants of the hub periphery. The lateral position of the hub relative to the guide plate is adjusted by positioning the wedges with the associated micrometer screws. The tilt of the part is adjusted relative to a base plate, to which the guide plate is pivotally connected by means of a holding plate. Two pairs of oppositely disposed wedges are mounted for reciprocative lateral positioning by means of separate micrometer screws between flanges of the guide plate and the base plate. Once the wedges are positioned to achieve the proper tilt of the part or hub on which the part is mounted relative to the base plate, the fixture may be bolted to a machining, inspection, or assembly device.

  10. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    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.

  11. Ring polymer molecular dynamics fast computation of rate coefficients on accurate potential energy surfaces in local configuration space: Application to the abstraction of hydrogen from methane

    Science.gov (United States)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2016-04-01

    To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.

  12. Direct characterization of the energy level alignments and molecular components in an organic hetero-junction by integrated photoemission spectroscopy and reflection electron energy loss spectroscopy analysis

    Science.gov (United States)

    Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon

    2016-08-01

    A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum.

  13. Direct characterization of the energy level alignments and molecular components in an organic hetero-junction by integrated photoemission spectroscopy and reflection electron energy loss spectroscopy analysis.

    Science.gov (United States)

    Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon

    2016-08-26

    A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum. PMID:27420635

  14. Accurate structural correlations from maximum likelihood superpositions.

    Directory of Open Access Journals (Sweden)

    Douglas L Theobald

    2008-02-01

    Full Text Available The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method ("PCA plots" for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology.

  15. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  16. Beam alignment system

    International Nuclear Information System (INIS)

    A patent is claimed for the invention of a beam alignment system. The aim of the invention is the obtention of an accurate monitoring of the beam position and direction. It is of great interest in the nuclear industry. The invention can be applied in an infrared laser beam for welding operations. An auxiliar radiation source is incorporated to the device. The system's configuration allows a simultaneous and separated utilisation of two beams. The description and the design of the proposed system are provided

  17. Magnetic alignment and the Poisson alignment reference system

    Science.gov (United States)

    Griffith, L. V.; Schenz, R. F.; Sommargren, G. E.

    1990-08-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This article begins with a review of the motivation for developing an alignment system that will assure better than 100-μm accuracy in the alignment of the magnetic axis throughout an FEL. The 100-μm accuracy is an error circle about an ideal axis for 300 m or more. The article describes techniques for identifying the magnetic axes of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development of a straight-line reference based on the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. The Poisson alignment reference system should be accurate to 25 μm over 300 m, which is believed to be a factor-of-4 improvement over earlier techniques. An error budget shows that only 25% of the total budgeted tolerance is used for the alignment reference system, so the remaining tolerances should fall within the allowable range for FEL alignment.

  18. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

    The first full-scale tests of the ATLAS Muon Spectrometer are about to begin in Prévessin. The set-up includes several layers of Monitored Drift Tubes Chambers (MDTs) and will allow tests of the performance of the detectors and of their highly accurate alignment system.   Monitored Drift Chambers in Building 887 in Prévessin, where they are just about to be tested. Muon chambers are keeping the ATLAS Muon Spectrometer team quite busy this summer. Now that most people go on holiday, the beam and alignment tests for these chambers are just starting. These chambers will measure with high accuracy the momentum of high-energy muons, and this implies very demanding requirements for their alignment. The MDT chambers consist of drift tubes, which are gas-filled metal tubes, 3 cm in diameter, with wires running down their axes. With high voltage between the wire and the tube wall, the ionisation due to traversing muons is detected as electrical pulses. With careful timing of the pulses, the position of the muon t...

  19. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.;

    1999-01-01

    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  20. Alignment method for solar collector arrays

    Science.gov (United States)

    Driver, Jr., Richard B

    2012-10-23

    The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

  1. Multiscale peak alignment for chromatographic datasets.

    Science.gov (United States)

    Zhang, Zhi-Min; Liang, Yi-Zeng; Lu, Hong-Mei; Tan, Bin-Bin; Xu, Xiao-Na; Ferro, Miguel

    2012-02-01

    Chromatography has been extensively applied in many fields, such as metabolomics and quality control of herbal medicines. Preprocessing, especially peak alignment, is a time-consuming task prior to the extraction of useful information from the datasets by chemometrics and statistics. To accurately and rapidly align shift peaks among one-dimensional chromatograms, multiscale peak alignment (MSPA) is presented in this research. Peaks of each chromatogram were detected based on continuous wavelet transform (CWT) and aligned against a reference chromatogram from large to small scale gradually, and the aligning procedure is accelerated by fast Fourier transform cross correlation. The presented method was compared with two widely used alignment methods on chromatographic dataset, which demonstrates that MSPA can preserve the shapes of peaks and has an excellent speed during alignment. Furthermore, MSPA method is robust and not sensitive to noise and baseline. MSPA was implemented and is available at http://code.google.com/p/mspa. PMID:22222564

  2. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations

    NARCIS (Netherlands)

    Fang, Changming; Li, Wun Fan; Koster, Rik S.; Klimeš, Jiří; Van Blaaderen, Alfons; Van Huis, Marijn A.

    2015-01-01

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initi

  3. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    Science.gov (United States)

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  4. Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

    Directory of Open Access Journals (Sweden)

    Hazelhurst Scott

    2010-03-01

    Full Text Available Abstract Background Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution. Results A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution, which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions. Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the

  5. Shuttle onboard IMU alignment methods

    Science.gov (United States)

    Henderson, D. M.

    1976-01-01

    The current approach to the shuttle IMU alignment is based solely on the Apollo Deterministic Method. This method is simple, fast, reliable and provides an accurate estimate for the present cluster to mean of 1,950 transformation matrix. If four or more star sightings are available, the application of least squares analysis can be utilized. The least squares method offers the next level of sophistication to the IMU alignment solution. The least squares method studied shows that a more accurate estimate for the misalignment angles is computed, and the IMU drift rates are a free by-product of the analysis. Core storage requirements are considerably more; estimated 20 to 30 times the core required for the Apollo Deterministic Method. The least squares method offers an intermediate solution utilizing as much data that is available without a complete statistical analysis as in Kalman filtering.

  6. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    Energy Technology Data Exchange (ETDEWEB)

    Kapil, V.; Ceriotti, M., E-mail: michele.ceriotti@epfl.ch [Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland); VandeVondele, J., E-mail: joost.vandevondele@mat.ethz.ch [Department of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich (Switzerland)

    2016-02-07

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  7. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    International Nuclear Information System (INIS)

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats

  8. Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.

    Science.gov (United States)

    Fukuda, Ikuo; Kamiya, Narutoshi; Yonezawa, Yasushige; Nakamura, Haruki

    2012-08-01

    The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we

  9. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    Science.gov (United States)

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-12-01

    Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy.

  10. Fiber optics welder having movable aligning mirror

    Science.gov (United States)

    Higgins, Robert W.; Robichaud, Roger E.

    1981-01-01

    A system for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45.degree. angle to the optical axis of a stereomicroscope mounted for viewing the junction of the ends provides two orthogonal views of the interface during the alignment operation.

  11. 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...

  12. Effects of aligning pulse duration on the degree and the slope of nitrogen field-free alignment

    Institute of Scientific and Technical Information of China (English)

    Wang Fei; Jiang Hong-Bing; Gong Qi-Huang

    2012-01-01

    Through theoretical analysis,we show how aligning pulse durations affect the degree and the time-rate slope of nitrogen field-free alignment at a fixed pulse intensity.It is found that both the degree and the slope first increase,then saturate,and finally decrease with the increasing pump duration.The optimal durations for the maximum degree and the maximum slope of the alignment are found to be different.Additionally,they are found to mainly depend on the molecular rotational period,and are affected by the temperature and the aligning pump intensities.The mechanism of molecular alignment is also discussed.

  13. Elastic collisions between Si and D atoms at low temperatures and accurate analytic potential energy function and molecular constants of the SiD(X2∏) radical

    Institute of Scientific and Technical Information of China (English)

    Shi De-Heng; Zhang Jin-Ping; Sun Jin-Feng; Zhu Zun-Lue

    2009-01-01

    Interaction potential of the SiD(X2∏) radical is constructed by using the CCSD(T) theory in combination with the largest correlation-consistent quintuple basis set augmented with the diffuse functions in the valence range. Using the interaction potential, the spectroscopic parameters are accurately determined. The present D0, De, Re, ωe, αe and Be values are of 3.0956 eV, 3.1863 eV, 0.15223 nm, 1472.894 cm-1, 0.07799 cm-1 and 3.8717 cm-1, respectively,which are in excellent agreement with the measurements. A total of 26 vibrational states is predicted when J = 0 by solving the radial Schr(o)dinger equation of nuclear motion. The complete vibrational levels, classical turning points,initial rotation and centrifugal distortion constants when J = 0 are reported for the first time, which are in good accord with the available experiments. The total and various partial-wave cross sections are calculated for the elastic collisions between Si and D atoms in their ground states at 1.0×10-11-1.0×10-3 a.u. when the two atoms approach each other along the SiD(X2∏) potential energy curve. Four shape resonances are found in the total elastic cross sections, and their resonant energies are of 1.73×10-5, 4.0×10-5, 6.45×10-5 and 5.5×10-4 a.u., respectively. Each shape resonance in the total elastic cross sections is carefully investigated. The results show that the shape of the total elastic cross sections is mainly dominated by the s partial wave at very low temperatures. Because of the weakness of the shape resonances coming from the higher partial waves, most of them are passed into oblivion by the strong s partial-wave elastic cross sections.

  14. 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 ...

  15. Fast statistical alignment.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2009-05-01

    Full Text Available We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/.

  16. Fast statistical alignment.

    Science.gov (United States)

    Bradley, Robert K; Roberts, Adam; Smoot, Michael; Juvekar, Sudeep; Do, Jaeyoung; Dewey, Colin; Holmes, Ian; Pachter, Lior

    2009-05-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/. PMID:19478997

  17. Novel, Precise, Accurate Ion-Pairing Method to Determine the Related Substances of the Fondaparinux Sodium Drug Substance: Low-Molecular-Weight Heparin.

    Science.gov (United States)

    Deshpande, Amol A; Madhavan, P; Deshpande, Girish R; Chandel, Ravi Kumar; Yarbagi, Kaviraj M; Joshi, Alok R; Moses Babu, J; Murali Krishna, R; Rao, I M

    2016-01-01

    Fondaparinux sodium is a synthetic low-molecular-weight heparin (LMWH). This medication is an anticoagulant or a blood thinner, prescribed for the treatment of pulmonary embolism and prevention and treatment of deep vein thrombosis. Its determination in the presence of related impurities was studied and validated by a novel ion-pair HPLC method. The separation of the drug and its degradation products was achieved with the polymer-based PLRPs column (250 mm × 4.6 mm; 5 μm) in gradient elution mode. The mixture of 100 mM n-hexylamine and 100 mM acetic acid in water was used as buffer solution. Mobile phase A and mobile phase B were prepared by mixing the buffer and acetonitrile in the ratio of 90:10 (v/v) and 20:80 (v/v), respectively. Mobile phases were delivered in isocratic mode (2% B for 0-5 min) followed by gradient mode (2-85% B in 5-60 min). An Evaporative Light Scattering Detector (ELSD) was connected to the LC system to detect the responses of chromatographic separation. Further, the drug was subjected to stress studies for acidic, basic, oxidative, photolytic, and thermal degradations as per ICH guidelines and the drug was found to be labile in acid, base hydrolysis, and oxidation, while stable in neutral, thermal, and photolytic degradation conditions. The method provided linear responses over the concentration range of the LOQ to 0.30% for each impurity with respect to the analyte concentration of 12.5 mg/mL, and regression analysis showed a correlation coefficient value (r(2)) of more than 0.99 for all the impurities. The LOD and LOQ were found to be 1.4 µg/mL and 4.1 µg/mL, respectively, for fondaparinux. The developed ion-pair method was validated as per ICH guidelines with respect to accuracy, selectivity, precision, linearity, and robustness. PMID:27110496

  18. Ultra-large alignments using phylogeny-aware profiles.

    Science.gov (United States)

    Nguyen, Nam-Phuong D; Mirarab, Siavash; Kumar, Keerthana; Warnow, Tandy

    2015-01-01

    Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, a multiple sequence alignment method that uses a new machine learning technique, the ensemble of hidden Markov models, which we propose here. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences. UPP is available at https://github.com/smirarab/sepp . PMID:26076734

  19. On comparing two structured RNA multiple alignments.

    Science.gov (United States)

    Patel, Vandanaben; Wang, Jason T L; Setia, Shefali; Verma, Anurag; Warden, Charles D; Zhang, Kaizhong

    2010-12-01

    We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. PMID:21121021

  20. Implementation of a parallel protein structure alignment service on cloud.

    Science.gov (United States)

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  1. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

  2. DNA-Assisted β-phase Nucleation and Alignment of Molecular Dipoles in PVDF Film: A Realization of Self-Poled Bioinspired Flexible Polymer Nanogenerator for Portable Electronic Devices.

    Science.gov (United States)

    Tamang, Abiral; Ghosh, Sujoy Kumar; Garain, Samiran; Alam, Md Mehebub; Haeberle, Jörg; Henkel, Karsten; Schmeisser, Dieter; Mandal, Dipankar

    2015-08-01

    A flexible nanogenerator (NG) is fabricated with a poly(vinylidene fluoride) (PVDF) film, where deoxyribonucleic acid (DNA) is the agent for the electroactive β-phase nucleation. Denatured DNA is co-operating to align the molecular -CH2/-CF2 dipoles of PVDF causing piezoelectricity without electrical poling. The NG is capable of harvesting energy from a variety of easily accessible mechanical stress such as human touch, machine vibration, football juggling, and walking. The NG exhibits high piezoelectric energy conversion efficiency facilitating the instant turn-on of several green or blue light-emitting diodes. The generated energy can be used to charge capacitors providing a wide scope for the design of self-powered portable devices. PMID:26189605

  3. 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, ...

  4. 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.

  5. Shod wear and foot alignment in clinical gait analysis.

    Science.gov (United States)

    Louey, Melissa Gar Yee; Sangeux, Morgan

    2016-09-01

    Sagittal plane alignment of the foot presents challenges when the subject wears shoes during gait analysis. Typically, visual alignment is performed by positioning two markers, the heel and toe markers, aligned with the foot within the shoe. Alternatively, software alignment is possible when the sole of the shoe lies parallel to the ground, and the change in the shoe's sole thickness is measured and entered as a parameter. The aim of this technical note was to evaluate the accuracy of visual and software foot alignment during shod gait analysis. We calculated the static standing ankle angles of 8 participants (mean age: 8.7 years, SD: 2.9 years) wearing bilateral solid ankle foot orthoses (BSAFOs) with and without shoes using the visual and software alignment methods. All participants were able to stand with flat feet in both static trials and the ankle angles obtained in BSAFOs without shoes was considered the reference. We showed that the current implementation of software alignment introduces a bias towards more ankle dorsiflexion, mean=3°, SD=3.4°, p=0.006, and proposed an adjusted software alignment method. We found no statistical differences using visual alignment and adjusted software alignment between the shoe and shoeless conditions, p=0.19 for both. Visual alignment or adjusted software alignment are advised to represent foot alignment accurately.

  6. Communication: Rate coefficients of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Qingyong, E-mail: mengqingyong@dicp.ac.cn; Chen, Jun, E-mail: chenjun@dicp.ac.cn; Zhang, Dong H., E-mail: zhangdh@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, 116023 Dalian (China)

    2015-09-14

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  7. Using local alignments for relation recognition

    NARCIS (Netherlands)

    S. Katrenko; P. Adriaans; M. van Someren

    2010-01-01

    This paper discusses the problem of marrying structural similarity with semantic relatedness for Information Extraction from text. Aiming at accurate recognition of relations, we introduce local alignment kernels and explore various possibilities of using them for this task. We give a definition of

  8. Anatomically Plausible Surface Alignment and Reconstruction

    DEFF Research Database (Denmark)

    Paulsen, Rasmus R.; Larsen, Rasmus

    2010-01-01

    With the increasing clinical use of 3D surface scanners, there is a need for accurate and reliable algorithms that can produce anatomically plausible surfaces. In this paper, a combined method for surface alignment and reconstruction is proposed. It is based on an implicit surface representation...

  9. Laser alignment of rotating equipment at PNL

    International Nuclear Information System (INIS)

    Lateral vibration in direct-drive equipment is usually caused by misalignment. Over the years, because of the need to improve on techniques and ways of working more efficiently, various types of alignment methods have evolved. In the beginning, craftsmen used a straight-edge scale across the coupling with a feeler gauge measuring the misalignment error. This is still preferred today for aligning small couplings. The industry has since decided that alignment of large direct-drive equipment needed a more accurate type of instrumentation. Rim and face is another of the first alignment methods and is used on all sizes of equipment. A disadvantage of the rim and face method is that in most cases the coupling has to be disassembled. This can cause alignment problems when the coupling is reassembled. Also, the rim and face method is not fast enough to work satisfactorily on alignment of thermally hot equipment. Another concern is that the coupling has to be manufactured accurately for correct rim and face readings. Reverse dial alignment is an improvement over the rim and face method, and depending on the operator's experience, this method can be very accurate. A good training program along with field experience will bring the operator to a proper level of proficiency for a successful program. A hand-held computer with reverse dial calculations in memory is a must for job efficiency. An advantage over the rim and face method is that the coupling is not disassembled and remains locked together. Reverse dial instrumentation measures from both shaft center lines, rather than the coupling surface so the machining of the coupling during manufacture is not a major concern

  10. Accurate Molecular Dimensions from Stearic Acid Monolayers.

    Science.gov (United States)

    Lane, Charles A.; And Others

    1984-01-01

    Discusses modifications in the fatty acid monolayer experiment to reduce the inaccurate moleculary data students usually obtain. Copies of the experimental procedure used and a Pascal computer program to work up the data are available from the authors. (JN)

  11. Face Alignment via Regressing Local Binary Features.

    Science.gov (United States)

    Ren, Shaoqing; Cao, Xudong; Wei, Yichen; Sun, Jian

    2016-03-01

    This paper presents a highly efficient and accurate regression approach for face alignment. Our approach has two novel components: 1) a set of local binary features and 2) a locality principle for learning those features. The locality principle guides us to learn a set of highly discriminative local binary features for each facial landmark independently. The obtained local binary features are used to jointly learn a linear regression for the final output. This approach achieves the state-of-the-art results when tested on the most challenging benchmarks to date. Furthermore, because extracting and regressing local binary features are computationally very cheap, our system is much faster than previous methods. It achieves over 3000 frames per second (FPS) on a desktop or 300 FPS on a mobile phone for locating a few dozens of landmarks. We also study a key issue that is important but has received little attention in the previous research, which is the face detector used to initialize alignment. We investigate several face detectors and perform quantitative evaluation on how they affect alignment accuracy. We find that an alignment friendly detector can further greatly boost the accuracy of our alignment method, reducing the error up to 16% relatively. To facilitate practical usage of face detection/alignment methods, we also propose a convenient metric to measure how good a detector is for alignment initialization.

  12. Fast Statistical Alignment

    OpenAIRE

    Bradley, Robert K.; Adam Roberts; Michael Smoot; Sudeep Juvekar; Jaeyoung Do; Colin Dewey; Ian Holmes; Lior Pachter

    2009-01-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multi...

  13. Horizontal carbon nanotube alignment.

    Science.gov (United States)

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies. PMID:27546174

  14. 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...

  15. Orthodontics and Aligners

    Science.gov (United States)

    ... Repairing Chipped Teeth Teeth Whitening Tooth-Colored Fillings Orthodontics and Aligners Straighten teeth for a healthier smile. Orthodontics When consumers think about orthodontics, braces are the ...

  16. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

    Science.gov (United States)

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

    2015-05-01

    We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

  17. Backup Alignment Devices on Shuttle: Heads-Up Display or Crew Optical Alignment Sight

    Science.gov (United States)

    Chavez, Melissa A.

    2011-01-01

    NASA s Space Shuttle was built to withstand multiple failures while still keeping the crew and vehicle safe. Although the design of the Space Shuttle had a great deal of redundancy built into each system, there were often additional ways to keep systems in the best configuration if a failure were to occur. One such method was to use select pieces of hardware in a way for which they were not primarily intended. The primary function of the Heads-Up Display (HUD) was to provide the crew with a display of flight critical information during the entry phase. The primary function of the Crew Optical Alignment Sight (COAS) was to provide the crew an optical alignment capability for rendezvous and docking phases. An alignment device was required to keep the Inertial Measurement Units (IMUs) well aligned for a safe Entry; nominally this alignment device would be the two on-board Star Trackers. However, in the event of a Star Tracker failure, the HUD or COAS could also be used as a backup alignment device, but only if the device had been calibrated beforehand. Once the HUD or COAS was calibrated and verified then it was considered an adequate backup to the Star Trackers for entry IMU alignment. There were procedures in place and the astronauts were trained on how to accurately calibrate the HUD or COAS and how to use them as an alignment device. The calibration procedure for the HUD and COAS had been performed on many Shuttle missions. Many of the first calibrations performed were for data gathering purposes to determine which device was more accurate as a backup alignment device, HUD or COAS. Once this was determined, the following missions would frequently calibrate the HUD in order to be one step closer to having the device ready in case it was needed as a backup alignment device.

  18. Tracing magnetic fields with aligned grains

    Energy Technology Data Exchange (ETDEWEB)

    Lazarian, A. [Astronomy Department, University of Wisconsin-Madison, 475 N. Charter St., Madison, WI 53706 (United States)]. E-mail: lazarian@astro.wisc.edu

    2007-07-15

    Magnetic fields play a crucial role in various astrophysical processes, including star formation, accretion of matter, transport processes (e.g., transport of heat), and cosmic rays. One of the easiest ways to determine the magnetic field direction is via polarization of radiation resulting from extinction or/and emission by aligned dust grains. Reliability of interpretation of the polarization maps in terms of magnetic fields depends on how well we understand the grain-alignment theory. Explaining what makes grains aligned has been one of the big issues of the modern astronomy. Numerous exciting physical effects have been discovered in the course of research undertaken in this field. As both the theory and observations matured, it became clear that the grain-alignment phenomenon is inherent not only in diffuse interstellar medium or molecular clouds but also is a generic property of the dust in circumstellar regions, interplanetary space and cometary comae. Currently the grain-alignment theory is a predictive one, and its results nicely match observations. Among its predictions is a subtle phenomenon of radiative torques. This phenomenon, after having stayed in oblivion for many years after its discovery, is currently viewed as the most powerful means of alignment. In this article, I shall review the basic physical processes involved in grain alignment, and the currently known mechanisms of alignment. I shall also discuss possible niches for different alignment mechanisms. I shall dwell on the importance of the concept of grain helicity for understanding of many properties of grain alignment, and shall demonstrate that rather arbitrarily shaped grains exhibit helicity when they interact with gaseous and radiative flows.

  19. 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 ...

  20. 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...

  1. 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...

  2. Real Interference Alignment

    CERN Document Server

    Motahari, Abolfazl Seyed; Maddah-Ali, Mohammad-Ali; Khandani, Amir Keyvan

    2010-01-01

    In this paper, we show that the total Degrees-Of-Freedoms (DOF) of the $K$-user Gaussian Interference Channel (GIC) can be achieved by incorporating a new alignment technique known as \\emph{real interference alignment}. This technique compared to its ancestor \\emph{vector interference alignment} performs on a single real line and exploits the properties of real numbers to provide optimal signaling. The real interference alignment relies on a new coding scheme in which several data streams having fractional multiplexing gains are sent by transmitters and interfering streams are aligned at receivers. The coding scheme is backed up by a recent result in the field of Diophantine approximation, which states that the convergence part of the Khintchine-Groshev theorem holds for points on non-degenerate manifolds.

  3. 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...

  4. Alignment for CSR

    International Nuclear Information System (INIS)

    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

  5. Galaxy Alignments: An Overview

    Science.gov (United States)

    Joachimi, Benjamin; Cacciato, Marcello; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Hoekstra, Henk; Kiessling, Alina; Kirk, Donnacha; Rassat, Anais

    2015-11-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  6. Galaxy alignments: An overview

    CERN Document Server

    Joachimi, Benjamin; Kitching, Thomas D; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Hoekstra, Henk; Kiessling, Alina; Kirk, Donnacha; Rassat, Anais

    2015-01-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  7. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.

    2009-01-01

    The alignment of shape data to a common mean before its subsequent processing is an ubiquitous step within the area shape analysis. Current approaches to shape analysis or, as more specifically considered in this work, shape classification perform the alignment in a fully unsupervised way......, not taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two...

  8. Control rod housing alignment and repair method

    International Nuclear Information System (INIS)

    This patent describes a method for underwater welding of a control rod drive housing inserted through a stub tube to maintain requisite alignment and elevation of the top of the control rod drive housing to an overlying and corresponding aperture in a core plate as measured by an alignment device which determines the relative elevation and angularity with respect to the aperture. It comprises providing a welding cylinder dependent from the alignment device such that the elevation of the top of the welding cylinder is in a fixed relationship to the alignment device and is gas-proof; pressurizing the welding cylinder with inert welding gas sufficient to maintain the interior of the welding cylinder dry; lowering the welding cylinder through the aperture in the core plate by depending the cylinder with respect to the alignment device, the lowering including lowering through and adjusting the elevation relationship of the welding cylinder to the alignment device such that when the alignment device is in position to measure the elevation and angularity of the new control rod drive housing, the lower distal end of the welding cylinder extends below the upper periphery of the stub where welding is to occur; inserting a new control rod drive housing through the stub tube and positioning the control rod drive housing to a predetermined relationship to the anticipated final position of the control rod drive housing; providing welding implements transversely rotatably mounted interior of the welding cylinder relative to the alignment device such that the welding implements may be accurately positioned for dispensing weldment around the periphery of the top of the stub tube and at the side of the control rod drive housing; measuring the elevation and angularity of the control rod drive housing; and dispensing weldment along the top of the stub tube and at the side of the control rod drive housing

  9. Tidal alignment of galaxies

    CERN Document Server

    Blazek, Jonathan; Seljak, Uroš

    2015-01-01

    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 ...

  10. 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...

  11. Isotope-selective ionization using four-pulse alignment

    International Nuclear Information System (INIS)

    We have proposed a laser isotope separation method utilizing molecular alignment and non-resonant multiphoton ionization, and demonstrated isotope-selective ionization of 14N2 and 15N2 isotopomers, using one-pulse alignment. In the present work, we used a train of four identical pulses, instead of one pulse, to obtain the higher selectivity. (author)

  12. 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...

  13. 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...

  14. Incremental Alignment Manifold Learning

    Institute of Scientific and Technical Information of China (English)

    Zhi Han; De-Yu Meng; Zong-Sen Xu; Nan-Nan Gu

    2011-01-01

    A new manifold learning method, called incremental alignment method (IAM), is proposed for nonlinear dimensionality reduction of high dimensional data with intrinsic low dimensionality. The main idea is to incrementally align low-dimensional coordinates of input data patch-by-patch to iteratively generate the representation of the entire dataset. The method consists of two major steps, the incremental step and the alignment step. The incremental step incrementally searches neighborhood patch to be aligned in the next step, and the alignment step iteratively aligns the low-dimensional coordinates of the neighborhood patch searched to generate the embeddings of the entire dataset. Compared with the existing manifold learning methods, the proposed method dominates in several aspects: high efficiency, easy out-of-sample extension, well metric-preserving, and averting of the local minima issue. All these properties are supported by a series of experiments performed on the synthetic and real-life datasets. In addition, the computational complexity of the proposed method is analyzed, and its efficiency is theoretically argued and experimentally demonstrated.

  15. Using structure to explore the sequence alignment space of remote homologs.

    Directory of Open Access Journals (Sweden)

    Andrew Kuziemko

    2011-10-01

    Full Text Available Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  16. HAMSA: Highly Accelerated Multiple Sequence Aligner

    Directory of Open Access Journals (Sweden)

    Naglaa M. Reda

    2016-06-01

    Full Text Available For biologists, the existence of an efficient tool for multiple sequence alignment is essential. This work presents a new parallel aligner called HAMSA. HAMSA is a bioinformatics application designed for highly accelerated alignment of multiple sequences of proteins and DNA/RNA on a multi-core cluster system. The design of HAMSA is based on a combination of our new optimized algorithms proposed recently of vectorization, partitioning, and scheduling. It mainly operates on a distance vector instead of a distance matrix. It accomplishes similarity computations and generates the guide tree in a highly accelerated and accurate manner. HAMSA outperforms MSAProbs with 21.9- fold speedup, and ClustalW-MPI of 11-fold speedup. It can be considered as an essential tool for structure prediction, protein classification, motive finding and drug design studies.

  17. Scintillation counter: photomultiplier tube alignment

    International Nuclear Information System (INIS)

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into the sample receiving zone. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (auth)

  18. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    Science.gov (United States)

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  19. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

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

    2007-01-01

    BACKGROUND: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. RESULTS: MaxAlign is a program that optimizes...... the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical...... analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign...

  20. Parameter Identification Method for SINS Initial Alignment under Inertial Frame

    Directory of Open Access Journals (Sweden)

    Haijian Xue

    2016-01-01

    Full Text Available The performance of a strapdown inertial navigation system (SINS largely depends on the accuracy and rapidness of the initial alignment. The conventional alignment method with parameter identification has been already applied widely, but it needs to calculate the gyroscope drifts through two-position method; then the time of initial alignment is greatly prolonged. For this issue, a novel self-alignment algorithm by parameter identification method under inertial frame for SINS is proposed in this paper. Firstly, this coarse alignment method using the gravity in the inertial frame as a reference is discussed to overcome the limit of dynamic disturbance on a rocking base and fulfill the requirement for the fine alignment. Secondly, the fine alignment method by parameter identification under inertial frame is formulated. The theoretical analysis results show that the fine alignment model is fully self-aligned with no external reference information and the gyrodrifts can be estimated in real time. The simulation results demonstrate that the proposed method can achieve rapid and highly accurate initial alignment for SINS.

  1. A New Analytic Alignment Method for a SINS

    Directory of Open Access Journals (Sweden)

    Caiming Tan

    2015-11-01

    Full Text Available Analytic alignment is a type of self-alignment for a Strapdown inertial navigation system (SINS that is based solely on two non-collinear vectors, which are the gravity and rotational velocity vectors of the Earth at a stationary base on the ground. The attitude of the SINS with respect to the Earth can be obtained directly using the TRIAD algorithm given two vector measurements. For a traditional analytic coarse alignment, all six outputs from the inertial measurement unit (IMU are used to compute the attitude. In this study, a novel analytic alignment method called selective alignment is presented. This method uses only three outputs of the IMU and a few properties from the remaining outputs such as the sign and the approximate value to calculate the attitude. Simulations and experimental results demonstrate the validity of this method, and the precision of yaw is improved using the selective alignment method compared to the traditional analytic coarse alignment method in the vehicle experiment. The selective alignment principle provides an accurate relationship between the outputs and the attitude of the SINS relative to the Earth for a stationary base, and it is an extension of the TRIAD algorithm. The selective alignment approach has potential uses in applications such as self-alignment, fault detection, and self-calibration.

  2. Conformational fluctuations affect protein alignment in dilute liquid crystal media

    DEFF Research Database (Denmark)

    Louhivuori, M.; Otten, R.; Lindorff-Larsen, Kresten;

    2006-01-01

    The discovery of dilute liquid crystalline media to align biological macromolecules has opened many new possibilities to study protein and nucleic acid structures by NMR spectroscopy. We inspect the basic alignment phenomenon for an ensemble of protein conformations to deduce relative contributions...... of each member to the residual dipolar coupling signals. We find that molecular fluctuations can affect the alignment and discover a resulting emphasis of certain conformations. However, the internal fluctuations are largely uncorrelated with those of the alignment, implying that proteins have liquidlike...

  3. Ergodic Secret Alignment

    CERN Document Server

    Bassily, Raef

    2010-01-01

    In this paper, we introduce two new achievable schemes for the fading multiple access wiretap channel (MAC-WT). In the model that we consider, we assume that perfect knowledge of the state of all channels is available at all the nodes in a causal fashion. Our schemes use this knowledge together with the time varying nature of the channel model to align the interference from different users at the eavesdropper perfectly in a one-dimensional space while creating a higher dimensionality space for the interfering signals at the legitimate receiver hence allowing for better chance of recovery. While we achieve this alignment through signal scaling at the transmitters in our first scheme (scaling based alignment (SBA)), we let nature provide this alignment through the ergodicity of the channel coefficients in the second scheme (ergodic secret alignment (ESA)). For each scheme, we obtain the resulting achievable secrecy rate region. We show that the secrecy rates achieved by both schemes scale with SNR as 1/2log(SNR...

  4. 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...

  5. 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...

  6. 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...

  7. Efficient alignment-free DNA barcode analytics

    OpenAIRE

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient ...

  8. Speaking Fluently And Accurately

    Institute of Scientific and Technical Information of China (English)

    JosephDeVeto

    2004-01-01

    Even after many years of study,students make frequent mistakes in English. In addition, many students still need a long time to think of what they want to say. For some reason, in spite of all the studying, students are still not quite fluent.When I teach, I use one technique that helps students not only speak more accurately, but also more fluently. That technique is dictations.

  9. Accurate Finite Difference Algorithms

    Science.gov (United States)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  10. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...

  11. Accuracy of structure-based sequence alignment of automatic methods

    Directory of Open Access Journals (Sweden)

    Lee Byungkook

    2007-09-01

    Full Text Available Abstract Background Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved than sequence, structure alignments have been used to guide sequence alignments and are commonly used as the gold standard for sequence alignment evaluation. Nonetheless, as far as we know, there is no report of a systematic evaluation of pairwise structure alignment programs in terms of the sequence alignment accuracy. Results In this study, we evaluate CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA and VAST in terms of the accuracy of the sequence alignments they produce, using sequence alignments from NCBI's human-curated Conserved Domain Database (CDD as the standard of truth. We find that 4 to 9% of the residues on average are either not aligned or aligned with more than 8 residues of shift error and that an additional 6 to 14% of residues on average are misaligned by 1–8 residues, depending on the program and the data set used. The fraction of correctly aligned residues generally decreases as the sequence similarity decreases or as the RMSD between the Cα positions of the two structures increases. It varies significantly across CDD superfamilies whether shift error is allowed or not. Also, alignments with different shift errors occur between proteins within the same CDD superfamily, leading to inconsistent alignments between superfamily members. In general, residue pairs that are more than 3.0 Å apart in the reference alignment are heavily (>= 25% on average misaligned in the test alignments. In addition, each method shows a different pattern of relative weaknesses for different SCOP classes. CE gives relatively poor results for β-sheet-containing structures (all-β, α/β, and α+β classes, DaliLite for "others" class where all but the major four classes are combined, and LOCK2 and VAST for all-β and "others" classes. Conclusion When the sequence

  12. Strategic Alignment of Business Intelligence

    OpenAIRE

    Cederberg, Niclas

    2010-01-01

    This thesis is about the concept of strategic alignment of business intelligence. It is based on a theoretical foundation that is used to define and explain business intelligence, data warehousing and strategic alignment. By combining a number of different methods for strategic alignment a framework for alignment of business intelligence is suggested. This framework addresses all different aspects of business intelligence identified as relevant for strategic alignment of business intelligence...

  13. Orientation and Alignment Echoes

    CERN Document Server

    Karras, G; Billard, F; Lavorel, B; Hartmann, J -M; Faucher, O; Gershnabel, E; Prior, Y; Averbukh, I Sh

    2015-01-01

    We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses.

  14. Aligning Mental Representations

    DEFF Research Database (Denmark)

    Kano Glückstad, Fumiko

    2013-01-01

    This work introduces a framework that implements asymmetric communication theory proposed by Sperber and Wilson [1]. The framework applies a generalization model known as the Bayesian model of generalization (BMG) [2] for aligning knowledge possessed by two communicating parties. The work focuses...... on the application of the BMG to publicly available datasets, the Leuven natural concept database [3] representing semantic structures of domain knowledge possessed by individual subjects [3]. Results indicate that the BMG is potentially a model applicable to simulating the alignment of domain knowledge from...

  15. PILOT optical alignment

    Science.gov (United States)

    Longval, Y.; Mot, B.; Ade, P.; André, Y.; Aumont, J.; Baustista, L.; Bernard, J.-Ph.; Bray, N.; de Bernardis, P.; Boulade, O.; Bousquet, F.; Bouzit, M.; Buttice, V.; Caillat, A.; Charra, M.; Chaigneau, M.; Crane, B.; Crussaire, J.-P.; Douchin, F.; Doumayrou, E.; Dubois, J.-P.; Engel, C.; Etcheto, P.; Gélot, P.; Griffin, M.; Foenard, G.; Grabarnik, S.; Hargrave, P..; Hughes, A.; Laureijs, R.; Lepennec, Y.; Leriche, B.; Maestre, S.; Maffei, B.; Martignac, J.; Marty, C.; Marty, W.; Masi, S.; Mirc, F.; Misawa, R.; Montel, J.; Montier, L.; Narbonne, J.; Nicot, J.-M.; Pajot, F.; Parot, G.; Pérot, E.; Pimentao, J.; Pisano, G.; Ponthieu, N.; Ristorcelli, I.; Rodriguez, L.; Roudil, G.; Salatino, M.; Savini, G.; Simonella, O.; Saccoccio, M.; Tapie, P.; Tauber, J.; Torre, J.-P.; Tucker, C.

    2016-07-01

    PILOT is a balloon-borne astronomy experiment designed to study the polarization of dust emission in the diffuse interstellar medium in our Galaxy at wavelengths 240 μm with an angular resolution about two arcminutes. Pilot optics is composed an off-axis Gregorian type telescope and a refractive re-imager system. All optical elements, except the primary mirror, are in a cryostat cooled to 3K. We combined the optical, 3D dimensional measurement methods and thermo-elastic modeling to perform the optical alignment. The talk describes the system analysis, the alignment procedure, and finally the performances obtained during the first flight in September 2015.

  16. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

    Science.gov (United States)

    Wang, Kai; Singh, Darshan; Zeng, Zheng; Coleman, Stephen J; Huang, Yan; Savich, Gleb L; He, Xiaping; Mieczkowski, Piotr; Grimm, Sara A; Perou, Charles M; MacLeod, James N; Chiang, Derek Y; Prins, Jan F; Liu, Jinze

    2010-10-01

    The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥ 75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice. PMID:20802226

  17. 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...

  18. Detection of Off-normal Images for NIF Automatic Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Candy, J V; Awwal, A S; McClay, W A; Ferguson, S W; Burkhart, S C

    2005-07-11

    One of the major purposes of National Ignition Facility at Lawrence Livermore National Laboratory is to accurately focus 192 high energy laser beams on a nanoscale (mm) fusion target at the precise location and time. The automatic alignment system developed for NIF is used to align the beams in order to achieve the required focusing effect. However, if a distorted image is inadvertently created by a faulty camera shutter or some other opto-mechanical malfunction, the resulting image termed ''off-normal'' must be detected and rejected before further alignment processing occurs. Thus the off-normal processor acts as a preprocessor to automatic alignment image processing. In this work, we discuss the development of an ''off-normal'' pre-processor capable of rapidly detecting the off-normal images and performing the rejection. Wide variety of off-normal images for each loop is used to develop the criterion for rejections accurately.

  19. Monitoring, alignment and control of the RICH detectors

    CERN Document Server

    D'Ambrosio, C; Gaspar, C; Laub, M; Lindner, R; Muheim, F; Papanestis, A; Soler, FJP

    2001-01-01

    The physical quantities of the RICH detectors need to be monitored throughout the duration of the experiment to ensure that their performance remains within the design specifications. The present note describes all the physical quantities that need to be monitored and a description of possible devices that could be implemented to achieve the specified level of control. In addition, the angular resolution of the RICH detectors depends on an accurate alignment of the system. Proposals for this alignment procedure are described.

  20. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

    Science.gov (United States)

    Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

    2015-11-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography.

  1. 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.

  2. 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.

  3. A laser shaft alignment system with dual PSDs

    Institute of Scientific and Technical Information of China (English)

    JIAO Guo-hua; LI Yu-lin; ZHANG Dong-bo; LI Tong-hai; HU Bao-wen

    2006-01-01

    Shaft alignment is an important technique during installation and maintenance of a rotating machine. A high-precision laser alignment system has been designed with dual PSDs (Position Sensing Detector) to change traditional manual way of shaft alignment and to make the measurement easier and more accurate. The system is comprised of two small measuring units (laser transmitter and detector) and a PDA (Personal Digital Assistant) with measurement software. The laser alignment system with dual PSDs was improved on a single PSD system, and yields higher measurement accuracy than the previous design, and has been successful for designing and implements actual shaft alignment. In the system, the range of offset measurement is ±4 mm, and the resolution is 1.5 μm, with accuracy being less than 2 μm.

  4. The Laser Shaft Alignment System with Dual PSDs

    Institute of Scientific and Technical Information of China (English)

    JIAO Guohua; LI Yulin; ZHANG Dongbo; LI Tonghai; HU Baowen

    2006-01-01

    Shaft alignment is an important technique during installation and maintenance of a rotating machine. A high-precision laser alignment system has been designed with dual PSDs (Position Sensing Detector) to change traditional manual way of shaft alignment and to make the measurement easier and more accurate. The system is comprised of two small measuring units (laser transmitter and detector) and a PDA (Personal Digital Assistant) with the measurement software. The laser alignment system with dual PSDs was improved on a single PSD system, and it gets higher measurement accuracy than the previous design, and it has been succeeded in designing and implement for actual shaft alignment. In the system, the range of offset measurement is ±4 mm, and the resolution is 1.5 μm, and the accuracy is less than 2 μm.

  5. A context dependent pair hidden Markov model for statistical alignment

    CERN Document Server

    Arribas-Gil, Ana

    2011-01-01

    This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and context dependent mutation rates relying on the observation of two homologous sequences. The procedure is based on a generalized pair-hidden Markov structure, where conditional on the alignment path, the nucleotide sequences follow a Markov distribution. We use a stochastic approximation expectation maximization (saem) algorithm to give accurate estimators of parameters and alignments. We provide results both on simulated data and vertebrate genomes, which are known to have a high mutation rate from CG dinucleotide. In particular, we establish that the method improves the accuracy of the alignment of a human pseudogene and its functional gene.

  6. Absorber Alignment Measurement Tool for Solar Parabolic Trough Collectors: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Stynes, J. K.; Ihas, B.

    2012-04-01

    As we pursue efforts to lower the capital and installation costs of parabolic trough solar collectors, it is essential to maintain high optical performance. While there are many optical tools available to measure the reflector slope errors of parabolic trough solar collectors, there are few tools to measure the absorber alignment. A new method is presented here to measure the absorber alignment in two dimensions to within 0.5 cm. The absorber alignment is measured using a digital camera and four photogrammetric targets. Physical contact with the receiver absorber or glass is not necessary. The alignment of the absorber is measured along its full length so that sagging of the absorber can be quantified with this technique. The resulting absorber alignment measurement provides critical information required to accurately determine the intercept factor of a collector.

  7. MUSE alignment onto VLT

    Science.gov (United States)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure

    2014-07-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  8. Intramedullary versus extramedullary alignment of the tibial component in the Triathlon knee

    LENUS (Irish Health Repository)

    Cashman, James P

    2011-08-20

    Abstract Background Long term survivorship in total knee arthroplasty is significantly dependant on prosthesis alignment. Our aim was determine which alignment guide was more accurate in positioning of the tibial component in total knee arthroplasty. We also aimed to assess whether there was any difference in short term patient outcome. Method A comparison of intramedullary versus extramedullary alignment jig was performed. Radiological alignment of tibial components and patient outcomes of 103 Triathlon total knee arthroplasties were analysed. Results Use of the intramedullary was found to be significantly more accurate in determining coronal alignment (p = 0.02) while use of the extramedullary jig was found to give more accurate results in sagittal alignment (p = 0.04). There was no significant difference in WOMAC or SF-36 at six months. Conclusion Use of an intramedullary jig is preferable for positioning of the tibial component using this knee system.

  9. Intramedullary versus extramedullary alignment of the tibial component in the Triathlon knee

    Directory of Open Access Journals (Sweden)

    Synnott Keith

    2011-08-01

    Full Text Available Abstract Background Long term survivorship in total knee arthroplasty is significantly dependant on prosthesis alignment. Our aim was determine which alignment guide was more accurate in positioning of the tibial component in total knee arthroplasty. We also aimed to assess whether there was any difference in short term patient outcome. Method A comparison of intramedullary versus extramedullary alignment jig was performed. Radiological alignment of tibial components and patient outcomes of 103 Triathlon total knee arthroplasties were analysed. Results Use of the intramedullary was found to be significantly more accurate in determining coronal alignment (p = 0.02 while use of the extramedullary jig was found to give more accurate results in sagittal alignment (p = 0.04. There was no significant difference in WOMAC or SF-36 at six months. Conclusion Use of an intramedullary jig is preferable for positioning of the tibial component using this knee system.

  10. Three-time rapid transfer alignment method of SINS/GPS navigation system of high-speed marine missile

    Institute of Scientific and Technical Information of China (English)

    WANG Si; DENG Zheng-long; SU Ling-feng

    2008-01-01

    The transfer alignment of SINS/GPS navigation system of a high-speed marine missile was investiga-ted. With the help of the big acceleration of a high-speed missile, the transfer alignment was changed into a three-time alignment. The azimuth alignment was coarsely finished in 10s in the first time alignment, the hori-zontal alignment was accurately and rapidly finished in the second time alignment, and the azimuth alignment was accurately finished in the third time alignment. Because the second time alignment and the third time align-ment were finished by GPS after the missile was launched, the horizontal alignment and the second azimuth a-lignment got rid of the influence of the warship body flexibility deforming. The precision and rapidity of the hori-zontal alignment were prominently increased due to the vertical launch of the marine missile with the big accel-eration. Simulation verifies the effectiveness of the proposed alignment method.

  11. 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.

  12. Inflation by alignment

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, C.P. [PH -TH Division, CERN,CH-1211, Genève 23 (Switzerland); Department of Physics & Astronomy, McMaster University,1280 Main Street West, Hamilton ON (Canada); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo ON (Canada); Roest, Diederik [Van Swinderen Institute for Particle Physics and Gravity, University of Groningen,Nijenborgh 4, 9747 AG Groningen (Netherlands)

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  13. Evaluation of microRNA alignment techniques.

    Science.gov (United States)

    Ziemann, Mark; Kaspi, Antony; El-Osta, Assam

    2016-08-01

    Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

  14. Orbit IMU alignment: Error analysis

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

    A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

  15. Nuclear reactor alignment plate configuration

    Science.gov (United States)

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  16. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;

    E-health promises to enable and support active patient participation in chronic care. However, these fairly recent innovations are complicated matters and emphasize significant challenges, such as patients’ and clinicians’ different ways of conceptualizing disease and illness. Informed by insights...... from medical phenomenology and our own empirical work in telemonitoring and medical care of heart patients, we propose a design rationale for e-health systems conceptualized as the ‘alignment of concerns’....

  17. Alignment reference device

    Science.gov (United States)

    Patton, Gail Y.; Torgerson, Darrel D.

    1987-01-01

    An alignment reference device provides a collimated laser beam that minimizes angular deviations therein. A laser beam source outputs the beam into a single mode optical fiber. The output end of the optical fiber acts as a source of radiant energy and is positioned at the focal point of a lens system where the focal point is positioned within the lens. The output beam reflects off a mirror back to the lens that produces a collimated beam.

  18. Alignment as a Teacher Variable

    Science.gov (United States)

    Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

    2007-01-01

    With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

  19. Approximate protein structural alignment in polynomial time.

    Science.gov (United States)

    Kolodny, Rachel; Linial, Nathan

    2004-08-17

    Alignment of protein structures is a fundamental task in computational molecular biology. Good structural alignments can help detect distant evolutionary relationships that are hard or impossible to discern from protein sequences alone. Here, we study the structural alignment problem as a family of optimization problems and develop an approximate polynomial-time algorithm to solve them. For a commonly used scoring function, the algorithm runs in O(n(10)/epsilon(6)) time, for globular protein of length n, and it detects alignments that score within an additive error of epsilon from all optima. Thus, we prove that this task is computationally feasible, although the method that we introduce is too slow to be a useful everyday tool. We argue that such approximate solutions are, in fact, of greater interest than exact ones because of the noisy nature of experimentally determined protein coordinates. The measurement of similarity between a pair of protein structures used by our algorithm involves the Euclidean distance between the structures (appropriately rigidly transformed). We show that an alternative approach, which relies on internal distance matrices, must incorporate sophisticated geometric ingredients if it is to guarantee optimality and run in polynomial time. We use these observations to visualize the scoring function for several real instances of the problem. Our investigations yield insights on the computational complexity of protein alignment under various scoring functions. These insights can be used in the design of scoring functions for which the optimum can be approximated efficiently and perhaps in the development of efficient algorithms for the multiple structural alignment problem. PMID:15304646

  20. GPCODON ALIGNMENT: A GLOBAL PAIRWISE CODON BASED SEQUENCE ALIGNMENT APPROACH

    Directory of Open Access Journals (Sweden)

    Zeinab A. Fareed

    2016-02-01

    Full Text Available The alignment of two DNA sequences is a basic step in the analysis of biological data. Sequencing a long DNA sequence is one of the most interesting problems in bioinformatics. Several techniques have been developed to solve this sequence alignment problem like dynamic programming and heuristic algorithms. In this paper, we introduce (GPCodon alignment a pairwise DNA-DNA method for global sequence alignment that improves the accuracy of pairwise sequence alignment. We use a new scoring matrix to produce the final alignment called the empirical codon substitution matrix. Using this matrix in our technique enabled the discovery of new relationships between sequences that could not be discovered using traditional matrices. In addition, we present experimental results that show the performance of the proposed technique over eleven datasets of average length of 2967 bps. We compared the efficiency and accuracy of our techniques against a comparable tool called “Pairwise Align Codons” [1].

  1. Nimble Protein Sequence Alignment in Grid (NPSAG

    Directory of Open Access Journals (Sweden)

    K. Somasundaram

    2008-01-01

    Full Text Available In Bio-Informatics application, the analysis of protein sequence is a kind of computation driven science which has rapidly and quickly growing biological data. Also databases used in these applications are heterogeneous in nature and alignment of protein sequence using physical techniques is expensive, slow and results are not always guaranteed/accurate. So this application requires cross-platform, cost-effective and more computing power algorithm for sequence matching and searching a sequence in database. Grid is one of the most emerging technologies of cost effective computing paradigm for large class of data and compute intensive application which enables large-scale aggregation and sharing of computational data and other resources across institutional boundaries. We proposed the Grid architecture for searching of distributed, heterogeneous genomic databases which contained protein sequences to speed up the analysis of large scale sequence data and performed sequence alignment for residues match.

  2. 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...

  3. CELT optics Alignment Procedure

    Science.gov (United States)

    Mast, Terry S.; Nelson, Jerry E.; Chanan, Gary A.; Noethe, Lothar

    2003-01-01

    The California Extremely Large Telescope (CELT) is a project to build a 30-meter diameter telescope for research in astronomy at visible and infrared wavelengths. The current optical design calls for a primary, secondary, and tertiary mirror with Ritchey-Chretién foci at two Nasmyth platforms. The primary mirror is a mosaic of 1080 actively-stabilized hexagonal segments. This paper summarizes a CELT report that describes a step-by-step procedure for aligning the many degrees of freedom of the CELT optics.

  4. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;

    2014-01-01

    The emergence of patient-centered eHealth systems introduces new challenges, where patients come to play an increasingly important role. Realizing the promises requires an in-depth understanding of not only the technology, but also the needs of both clinicians and patients. However, insights from...... medical phenomenology bring forth how physicians and patients focus on different aspects of illness and that they often have starkly divergent concerns. This has important implications for the design of eHealth systems that seek to engage patients as active participants. We emphasize the crucial...... as a design rationale for successful eHealth, termed 'alignment of concerns'....

  5. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A

    2008-01-01

    The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider at CERN. In order to achieve its physics goals, the ATLAS tracking requires that the positions of the silicon detector elements have to be known to a precision better than 10 μm. Several track-based alignment algorithms have been developed for the Inner Detector. An extensive validation has been performed with simulated events and real data coming from the ATLAS. Results from such validation are reported in this paper.

  6. TSGC and JSC Alignment

    Science.gov (United States)

    Sanchez, Humberto

    2013-01-01

    NASA and the SGCs are, by design, intended to work closely together and have synergistic Vision, Mission, and Goals. The TSGC affiliates and JSC have been working together, but not always in a concise, coordinated, nor strategic manner. Today we have a couple of simple ideas to present about how TSGC and JSC have started to work together in a more concise, coordinated, and strategic manner, and how JSC and non-TSG Jurisdiction members have started to collaborate: Idea I: TSGC and JSC Technical Alignment Idea II: Concept of Clusters.

  7. A rank-based sequence aligner with applications in phylogenetic analysis.

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

    Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  8. Aligned Immobilization of Proteins Using AC Electric Fields.

    Science.gov (United States)

    Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

    2016-03-01

    Protein molecules are aligned and immobilized from solution by AC electric fields. In a single-step experiment, the enhanced green fluorescent proteins are immobilized on the surface as well as at the edges of planar nanoelectrodes. Alignment is found to follow the molecules' geometrical shape with their longitudinal axes parallel to the electric field. Simultaneous dielectrophoretic attraction and AC electroosmotic flow are identified as the dominant forces causing protein movement and alignment. Molecular orientation is determined by fluorescence microscopy based on polarized excitation of the proteins' chromophores. The chromophores' orientation with respect to the whole molecule supports X-ray crystal data. PMID:26779699

  9. Computing alignment plots efficiently

    CERN Document Server

    Krusche, Peter

    2009-01-01

    Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used since it can be computed in linear time. However, the Hamming distance is a rather crude measure of string similarity, and using an alignment-based edit distance can greatly improve the sensitivity of the dot plot method. In this paper, we show how to compute alignment plots of the latter type efficiently. Given two strings of length m and n and a window size w, this problem consists in computing the edit distance between all pairs of substrings of length w, one from each input string. The problem can be solved by repeated application of the standard dynamic programming algorithm in time O(mnw^2). This paper gives an improved data-parallel algorithm, running in time $O(mnw/\\gamma/p)$ using vector operations that work on $\\gamma$ values in parallel and $p$ processors. We show ex...

  10. All about alignment

    CERN Multimedia

    2006-01-01

    The ALICE absorbers, iron wall and superstructure have been installed with great precision. The ALICE front absorber, positioned in the centre of the detector, has been installed and aligned. Weighing more than 400 tonnes, the ALICE absorbers and the surrounding support structures have been installed and aligned with a precision of 1-2 mm, hardly an easy task but a very important one. The ALICE absorbers are made of three parts: the front absorber, a 35-tonne cone-shaped structure, and two small-angle absorbers, long straight cylinder sections weighing 18 and 40 tonnes. The three pieces lined up have a total length of about 17 m. In addition to these, ALICE technicians have installed a 300-tonne iron filter wall made of blocks that fit together like large Lego pieces and a surrounding metal support structure to hold the tracking and trigger chambers. The absorbers house the vacuum chamber and are also the reference surface for the positioning of the tracking and trigger chambers. For this reason, the ab...

  11. 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.

  12. Theoretical study of determining orientation and alignment of symmetric top molecule using laser-induced fluorescence

    Institute of Scientific and Technical Information of China (English)

    丛书林; 韩克利; 楼南泉

    2000-01-01

    General expressions used for extracting the orientation and alignment parameters of a symmetric top molecule from laser-induced fluorescence (LIF) intensity are derived by employing the density matrix approach. The molecular orientation and alignment are described by molecular state multipoles. Excitation and detection are circularly and linearly polarized lights, respectively. In general cases, the LIF intensity is a complex function of the initial molecular state multipoles, the dynamic factors and the excitation-detection geometrical factors. It contains a population, ten orientation and fourteen alignment multipoles. The problem of how to extract the initial molecular state multipoles from the resolved LIF intensity is discussed.

  13. Array tomography: semiautomated image alignment.

    Science.gov (United States)

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. Successful array tomography requires that the captured images be properly stacked and aligned, and the software to achieve these ends is freely available. This protocol describes the construction of volumetric image stacks from images of fluorescently labeled arrays for three-dimensional image visualization, analysis, and archiving. PMID:21041400

  14. Onorbit IMU alignment error budget

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  15. Dust alignment in astrophysical environments

    Science.gov (United States)

    Lazarian, Alex; Thiem Hoang, Chi

    Dust is known to be aligned in interstellar medium and the arising polarization is extensively used to trace magnetic fields. What process aligns dust grains was one of the most long-standing problems of astrophysics in spite of the persistent efforts to solve it. For years the Davis-Greenstein paramagnetic alignment was the primary candidate for explaining grain alignment. However, the situation is different now and the most promising mechanism is associated with radiative torques (RATs) acting on irregular grains. I shall present the analytical theory of RAT alignment, discuss the observational tests that support this theory. I shall also discuss in what situations we expect to see the dominance of paramagnetic alignment.

  16. Nuclear reactor internals alignment configuration

    Science.gov (United States)

    Gilmore, Charles B.; Singleton, Norman R.

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  17. On aligning trees

    CERN Document Server

    Calder, J

    1997-01-01

    The increasing availability of corpora annotated for linguistic structure prompts the question: if we have the same texts, annotated for phrase structure under two different schemes, to what extent do the annotations agree on structuring within the text? We suggest the term tree alignment to indicate the situation where two markup schemes choose to bracket off the same text elements. We propose a general method for determining agreement between two analyses. We then describe an efficient implementation, which is also modular in that the core of the implementation can be reused regardless of the format of markup used in the corpora. The output of the implementation on the Susanne and Penn treebank corpora is discussed.

  18. The alignment strategy of HADES

    Energy Technology Data Exchange (ETDEWEB)

    Pechenova, O., E-mail: O.Pechenova@gsi.de [Institut für Kernphysik, Johann Wolfgang Goethe-Universität, 60438 Frankfurt (Germany); Pechenov, V. [GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt (Germany); Galatyuk, T. [GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt (Germany); Technische Universität Darmstadt, D-64289 Darmstadt (Germany); Hennino, T. [Institut de Physique Nucléaire (UMR 8608), CNRS/IN2P3 – Université Paris Sud, F-91406 Orsay Cedex (France); Holzmann, R. [GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt (Germany); Kornakov, G. [Departamento de Física de Partículas, Univ. de Santiago de Compostela, 15706 Santiago de Compostela (Spain); Technische Universität Darmstadt, D-64289 Darmstadt (Germany); Markert, J.; Müntz, C. [Institut für Kernphysik, Johann Wolfgang Goethe-Universität, 60438 Frankfurt (Germany); Salabura, P. [Smoluchowski Institute of Physics, Jagiellonian University of Kraków, 30-059 Kraków (Poland); Schmah, A. [Lawrence Berkeley National Laboratory, Berkeley (United States); Schwab, E. [GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt (Germany); Stroth, J. [Institut für Kernphysik, Johann Wolfgang Goethe-Universität, 60438 Frankfurt (Germany); GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt (Germany)

    2015-06-11

    The global as well as intrinsic alignment of any spectrometer impacts directly on its performance and the quality of the achievable physics results. An overview of the current alignment procedure of the DiElectron Spectrometer HADES is presented with an emphasis on its main features and its accuracy. The sequence of all steps and procedures is given, including details on photogrammetric and track-based alignment.

  19. Does improved instrumentation result in better component alignment in total knee arthroplasty?

    OpenAIRE

    Mo Hassaballa; Vijaya Budnar; Herbert Gbejuade; Ian Learmonth

    2011-01-01

    Accurate component alignment and joint line reproduction in total knee replacement (TKR) is crucial for successful clinical outcome. Advances in instrumentation and better understanding of the biomechanics can help to achieve better three dimensional alignments of TKR components and joint line restoration. We compared the accuracy of component alignment and joint line restoration with the use of 2 different TKR instrumentation kits (an older Gobot and a newer Xcelerate). Retrospective study o...

  20. High accuracy alignment facility for the receiver and transmitter of the BepiColombo Laser Altimeter

    OpenAIRE

    Chakraborty, Sumita; Affolter, Michael; Gunderson, Kurt; Neubert, Jakob; Thomas, Nicolas; Beck, Thomas; Gerber, Michael; Graf, Stefan; Piazza, Daniele; Pommerol, Antoine; Röthlisberger, Guillaume; Seiferlin, Karsten

    2012-01-01

    The accurate co-alignment of the transmitter to the receiver of the BepiColombo Laser Altimeter is a challenging task for which an original alignment concept had to be developed. We present here the design, construction and testing of a large collimator facility built to fulfill the tight alignment requirements. We describe in detail the solution found to attenuate the high energy of the instrument laser transmitter by an original beam splitting pentaprism group. We list the different steps o...

  1. Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics,that scale very poorly for large number, unsuitable. The second reason is that the alignment cannot be performed arbitrarily, because the position of the reads with respect to the original genome is important and has to be taken into account.In this report we present a short description of the multiple alignment system for pyrosequencing reads.

  2. Molecular Diagnostics

    OpenAIRE

    Choe, Hyonmin; Deirmengian, Carl A; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...

  3. Accurate pose estimation for forensic identification

    Science.gov (United States)

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk

    2010-04-01

    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  4. High-harmonic generation in aligned water molecules

    Science.gov (United States)

    Wang, Song; Devin, Julien; Hoffmann, Matthias; Cryan, James; Kaldun, Andreas; Bucksbaum, Philip

    2016-05-01

    In recent years, the use of high harmonic generation (HHG) in aligned molecular vapors has become a powerful tool to study ultrafast dynamics of electronic and nuclear wave packets. In our new experimental setup, we are able to orient H2 O and D2 O molecules using a single cycle terahertz (THz) pulse. Aligning water is especially interesting as the highest occupied molecular orbital (HOMO) of water contains a node in the xz plane of the molecular frame, allowing us to perform HHG from second highest occupied molecular orbital (HOMO-1) only, by setting the polarization of the fundamental laser along the z-axis of the aligned water molecules. We are particularly interested in the HOMO-1 state, as there is fast motion of the H-O-H angle leading to sub-wavelength dynamics. On this poster we present our all-optical alignment setup where HHG and single-cycle THz generation take place in high-vacuum, where measurements with arbitrary polarization angles between the two are possible. In addition, we discuss the effects of the molecular orientation on HHG, including symmetry breaking that could produce even harmonics and isotope effects between H2 O and D2 O due to different vibrational energies. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  5. Development of a new laser alignment device with Winston-Lutz phantom in radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Young Kyung; Min, Soonk; Jeong, Eun Hee; Jeong, Jong Hwi; Kim, Haksoo; Park, Jeong-Hoon; Shin, DongHo; Lee, Se Byeong [National Cancer Center, Goyang (Korea, Republic of); Choi, Sang Hyoun [Korea Cancer Center Hospital, Seoul (Korea, Republic of); Hwang, Ui-Jung [National Medical Center, Seoul (Korea, Republic of); Kwak, Jung Won [Asan Medical Center, Seoul (Korea, Republic of); Kim, Siyong [Virginia Commonwealth University, Richmond (United States)

    2015-10-15

    The lasers must be aligned precisely to the radiation isocenter. According to the report provided by the American Association of Physicists in Medicine (AAPM) Task Group 142, the localizing lasers should be aligned to within ±2 mm of radiation isocenter for non intensity modulated radiation therapy (IMRT), ±1 mm for IMRT, and less than ±1 mm for stereotactic radiosurgery (SRS) on a monthly basis. In this study, we developed and tested a new laser alignment device adopting an accurate, reproducible and straightforward alignment method in radiotherapy. The device consists of two laser alignments parts: the first part is an optical alignment part, and the second is a radiation alignment part. In the radiation alignment, a Winston-Lutz (W-L) phantom which was installed in the device was used. In this study, we developed a new laser alignment device with a W-L phantom for radiotherapy. Its performance was also tested in a conventional medical linac and a simulator. It was revealed that the device could align the patient-setup lasers in the treatment room accurately, precisely, and fast. We expect the device can be used as a quality assurance tool daily and monthly.

  6. Vacuum Alignment with more Flavors

    DEFF Research Database (Denmark)

    Ryttov, Thomas

    2014-01-01

    We study the alignment of the vacuum in gauge theories with $N_f$ Dirac fermions transforming according to a complex representation of the gauge group. The alignment of the vacuum is produced by adding a small mass perturbation to the theory. We study in detail the $N_f=2,3$ and $4$ case. For $N...

  7. CATO: The Clone Alignment Tool.

    Directory of Open Access Journals (Sweden)

    Peter V Henstock

    Full Text Available High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1 a top-level summary of the top candidate sequences aligned to each reference sequence, 2 a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3 a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow.

  8. Lexical alignment in triadic communication

    Directory of Open Access Journals (Sweden)

    Anouschka eFoltz

    2015-02-01

    Full Text Available Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment.

  9. Accurate phase-shift velocimetry in rock

    Science.gov (United States)

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  10. Alignment of flexible protein structures.

    Science.gov (United States)

    Shatsky, M; Fligelman, Z Y; Nussinov, R; Wolfson, H J

    2000-01-01

    We present two algorithms which align flexible protein structures. Both apply efficient structural pattern detection and graph theoretic techniques. The FlexProt algorithm simultaneously detects the hinge regions and aligns the rigid subparts of the molecules. It does it by efficiently detecting maximal congruent rigid fragments in both molecules and calculating their optimal arrangement which does not violate the protein sequence order. The FlexMol algorithm is sequence order independent, yet requires as input the hypothesized hinge positions. Due its sequence order independence it can also be applied to protein-protein interface matching and drug molecule alignment. It aligns the rigid parts of the molecule using the Geometric Hashing method and calculates optimal connectivity among these parts by graph-theoretic techniques. Both algorithms are highly efficient even compared with rigid structure alignment algorithms. Typical running times on a standard desktop PC (400 MHz) are about 7 seconds for FlexProt and about 1 minute for FlexMol.

  11. Alignments in the nobelium isotopes

    Institute of Scientific and Technical Information of China (English)

    ZHENG Shi-Zie; XU Fu-Rong; YUAN Cen-Xi; QI Chong

    2009-01-01

    Total-Routhian-Surface calculations have been performed to investigate the deformation and align-ment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist at low excitation energies. In neutron-deficient No isotopes, the superdeformed shapes can even become the ground states. Moreover, we plotted the kinematic moments of inertia of the No isotopes, which follow very nicely available experimental data. It is noted that, as the rotational frequency increases, align-ments develop at hω=0.2-0.3 MeV. Our calculations show that the occupation of the vj orbital plays an important role in the alignments of the No isotopes.

  12. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R

    2008-01-01

    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

  13. Space Mirror Alignment System

    Science.gov (United States)

    Jau, Bruno M.; McKinney, Colin; Smythe, Robert F.; Palmer, Dean L.

    2011-01-01

    An optical alignment mirror mechanism (AMM) has been developed with angular positioning accuracy of +/-0.2 arcsec. This requires the mirror s linear positioning actuators to have positioning resolutions of +/-112 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are 0.1 arc-sec angular mirror positioning accuracy, which translates into linear positioning resolutions at the actuator of 50 nm. The mechanism consists of a structure with sets of cross-directional flexures that enable the mirror s tip and tilt motion, a mirror with its kinematic mount, and two linear actuators. An actuator comprises a brushless DC motor, a linear ball screw, and a piezoelectric brake that holds the mirror s position while the unit is unpowered. An interferometric linear position sensor senses the actuator s position. The AMMs were developed for an Astrometric Beam Combiner (ABC) optical bench, which is part of an interferometer development. Custom electronics were also developed to accommodate the presence of multiple AMMs within the ABC and provide a compact, all-in-one solution to power and control the AMMs.

  14. Molecular Tools for Rapid and Accurate Detection of Black Truffle (Tuber melanosporum Vitt. in Inoculated Nursery Plants and Commercial Plantations in Chile Uso de Marcadores Moleculares para la Detección Rápida y Precisa de Trufa Negra (Tuber melanosporum Vitt. en Plantas de Vivero y Plantaciones Comerciales de Chile

    Directory of Open Access Journals (Sweden)

    Cecilia Cordero

    2011-09-01

    Full Text Available Truffle (Tuber melanosporum Vitt. culture is an agroforestry sector in Chile of increasing interest due to the high prices that truffles fetch in the national market and the recent evidence that its commercial production is possible in Chilean climatic and soil conditions. In this study, the efficiency of three methods of DNA extraction from a mix of 5 g of soil and roots from both nursery and field plants of Quercus ilex L. mycorrhized with T. melanosporum were evaluated, and a simple and reproducible protocol was established. Detection of T. melanosporum was performed by the technique of cleaved amplified polymorphic sequence (CAPS from amplicons generated with the primers ADL1 (5´-GTAACGATAAAGGCCATCTATAGG-3´ and ADL3 (5´-CGTTTTTCCTGAACTCTTCATCAC-3`, where a restriction fragment of 160 bp specific for T. melanosporum was generated, which allows the discrimination of this species from the rest of the species belonging to the Tuber sp. genus. Direct detection of T. melanosporum in one step was also obtained by polymerase chain reaction (PCR from total DNA isolated from mycorrhized roots and with the primers ITSML (5´-TGGCCATGTGTCAGATTTAGTA-3´ and ITSLNG (5´-TGATATGCTTAAGTTCAGCGGG-3´, generating a single amplicon of 440 bp. The molecular detection of T. melanosporum by the methods presented here will allow the rapid and accurate detection of mycorrhization of trees, both under nursery and field conditions. This technology will also provide more security to farmers by controlling the quality of the mycorrhized trees they will plant and also by following the mycorrhization status of established orchards.

  15. Protalign: a 3-dimensional protein alignment assessment tool.

    Science.gov (United States)

    Meads, D; Hansen, M D; Pang, A

    1999-01-01

    Protein fold recognition (sometimes called threading) is the prediction of a protein's 3-dimensional shape based on its similarity to a protein of known structure. Fold predictions are low resolution; that is, no effort is made to rotate the protein's component amino acid side chains into their correct spatial orientations. The goal is simply to recognize the protein family member that most closely resembles the target sequence of unknown structure and to create a sensible alignment of the target to the known structure (i.e., a structure-sequence alignment). To facilitate this type of structure prediction, we have designed a low resolution molecular graphics tool. ProtAlign introduces the ability to interact with and edit alignments directly in the 3-dimensional structure as well as in the usual 2-dimensional layout. It also contains several functions and features to help the user assess areas within the alignment. ProtAlign implements an open pipe architecture to allow other programs to access its molecular graphics capabilities. In addition, it is capable of "driving" other programs. Because amino acid side chain orientation is not relevant in fold recognition, we represent amino acid residues as abstract shapes or glyphs much like Lego (tm) blocks and we borrow techniques from comparative flow visualization using streamlines to provide clean depictions of the entire protein model. By creating a low resolution representation of protein structure, we are able to at least double the amount of information on the screen. At the same time, we create a view that is not as busy as the corresponding representations using traditional high resolution visualization methods which show detailed atomic structure. This eliminates distracting and possibly misleading visual clutter resulting from the mapping of protein alignment information onto a high resolution display of the known structure. This molecular graphics program is implemented in Open GL to facilitate porting to

  16. Local versus global biological network alignment

    Science.gov (United States)

    Meng, Lei; Striegel, Aaron; Milenković, Tijana

    2016-01-01

    Motivation: Network alignment (NA) aims to find regions of similarities between species’ molecular networks. There exist two NA categories: local (LNA) and global (GNA). LNA finds small highly conserved network regions and produces a many-to-many node mapping. GNA finds large conserved regions and produces a one-to-one node mapping. Given the different outputs of LNA and GNA, when a new NA method is proposed, it is compared against existing methods from the same category. However, both NA categories have the same goal: to allow for transferring functional knowledge from well- to poorly-studied species between conserved network regions. So, which one to choose, LNA or GNA? To answer this, we introduce the first systematic evaluation of the two NA categories. Results: We introduce new measures of alignment quality that allow for fair comparison of the different LNA and GNA outputs, as such measures do not exist. We provide user-friendly software for efficient alignment evaluation that implements the new and existing measures. We evaluate prominent LNA and GNA methods on synthetic and real-world biological networks. We study the effect on alignment quality of using different interaction types and confidence levels. We find that the superiority of one NA category over the other is context-dependent. Further, when we contrast LNA and GNA in the application of learning novel protein functional knowledge, the two produce very different predictions, indicating their complementarity. Our results and software provide guidelines for future NA method development and evaluation. Availability and implementation: Software: http://www.nd.edu/~cone/LNA_GNA Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27357169

  17. CMS Muon Alignment: System Description and first results

    CERN Document Server

    Sobron, M

    2008-01-01

    The CMS detector has been instrumented with a precise and complex opto-mechanical alignment subsystem that provides a common reference frame between Tracker and Muon detection systems by means of a net of laser beams. The system allows a continuous and accurate monitoring of the muon chambers positions with respect to the Tracker body. Preliminary results of operation during the test of the CMS 4T solenoid magnet, performed in 2006, are presented. These measurements complement the information provided by the use of survey techniques and the results of alignment algorithms based on muon tracks crossing the detector.

  18. Long Read Alignment with Parallel MapReduce Cloud Platform.

    Science.gov (United States)

    Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

    2015-01-01

    Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

  19. 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.

  20. Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets

    DEFF Research Database (Denmark)

    Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin;

    2013-01-01

    We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecules...

  1. Magnetic axis alignment and the Poisson alignment reference system

    Science.gov (United States)

    Griffith, Lee V.; Schenz, Richard F.; Sommargren, Gary E.

    1989-01-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This paper begins with a review of the motivation for developing an alignment system that will assure better than 100 micrometer accuracy in the alignment of the magnetic axis throughout an FEL. The paper describes techniques for identifying the magnetic axis of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development and use of the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. An error budget shows that the Poisson alignment reference system will make it possible to meet the alignment tolerances for an FEL.

  2. Electron transport in molecular junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun

    the lowest unoccupied molecular level (LUMO) of the 44BP molecule hybridizes strongly with Ni 3d orbitals, the gating is auxiliary by the so-called spinterface. Finally, the correlation effect of the image charge beyond the energy level renormalization has been studied. It is shown that the finite response...... groups. The failure of the DFT based description is due to the strong energy level pinning when the BDA molecule is in contact with Au contacts. The effect of contact geometries on the conductance and the thermopower has also been addressed. It is found that both GW and the DFT+∑ with a certain image...... charge position are in quantitative agreement with the experiments, while pure DFT is not. This is the consequence of the accurate energy level alignment, where the DFT+∑ method corrects the self-interaction error in the standard DFT functional and uses a static image charge model to include the image...

  3. BFAST: an alignment tool for large scale genome resequencing.

    Directory of Open Access Journals (Sweden)

    Nils Homer

    Full Text Available BACKGROUND: 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. METHODOLOGY: 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. CONCLUSIONS: 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.

  4. Harmonic Analysis of Linac Alignment

    CERN Document Server

    McCrady, Rodney C

    2005-01-01

    We have analyzed the requirements on alignment of the focusing elements (quadrupole doublets) in the Los Alamos Neutron Science Center (LANSCE) side coupled linac. The analysis is performed in terms of harmonics of the quardrupole spacing. This allows us to determine the effect of intentional deviations from a straight line, such as following the curvature of the Earth, and of unintentional deviations introduced by measurement and alignment errors. Results are compared to measured positions of the doublets.

  5. Expressive alignment language and implementation

    OpenAIRE

    Euzenat, Jérôme; Scharffe, François; Zimmermann, Antoine

    2007-01-01

    euzenat2007e This deliverable provides the description of an alignment language which is both expressive and independent from ontology languages. It defines the language through its abstract syntax and semantics depending on ontology language semantics. It then describes two concrete syntax: an exchange syntax in RDF/XML and a surface syntax for human consumption. Finally, it presents the current implementation of this expressive language within the Alignment API taking advantage of the OM...

  6. Towards accurate emergency response behavior

    International Nuclear Information System (INIS)

    Nuclear reactor operator emergency response behavior has persisted as a training problem through lack of information. The industry needs an accurate definition of operator behavior in adverse stress conditions, and training methods which will produce the desired behavior. Newly assembled information from fifty years of research into human behavior in both high and low stress provides a more accurate definition of appropriate operator response, and supports training methods which will produce the needed control room behavior. The research indicates that operator response in emergencies is divided into two modes, conditioned behavior and knowledge based behavior. Methods which assure accurate conditioned behavior, and provide for the recovery of knowledge based behavior, are described in detail

  7. Score distributions of gapped multiple sequence alignments down to the low-probability tail

    Science.gov (United States)

    Fieth, Pascal; Hartmann, Alexander K.

    2016-08-01

    Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10-160, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments.

  8. MAGSAT: Vector magnetometer absolute sensor alignment determination

    Science.gov (United States)

    Acuna, M. H.

    1981-01-01

    A procedure is described for accurately determining the absolute alignment of the magnetic axes of a triaxial magnetometer sensor with respect to an external, fixed, reference coordinate system. The method does not require that the magnetic field vector orientation, as generated by a triaxial calibration coil system, be known to better than a few degrees from its true position, and minimizes the number of positions through which a sensor assembly must be rotated to obtain a solution. Computer simulations show that accuracies of better than 0.4 seconds of arc can be achieved under typical test conditions associated with existing magnetic test facilities. The basic approach is similar in nature to that presented by McPherron and Snare (1978) except that only three sensor positions are required and the system of equations to be solved is considerably simplified. Applications of the method to the case of the MAGSAT Vector Magnetometer are presented and the problems encountered discussed.

  9. Optical alignment of Centaur's inertial guidance system

    Science.gov (United States)

    Gordan, Andrew L.

    1987-01-01

    During Centaur launch operations the launch azimuth of the inertial platform's U-accelerometer input axis must be accurately established and maintained. This is accomplished by using an optically closed loop system with a long-range autotheodolite whose line of sight was established by a first-order survey. A collimated light beam from the autotheodolite intercepts a reflecting Porro prism mounted on the platform azimuth gimbal. Thus, any deviation of the Porro prism from its predetermined heading is optically detected by the autotheodolite. The error signal produced is used to torque the azimuth gimbal back to its required launch azimuth. The heading of the U-accelerometer input axis is therefore maintained automatically. Previously, the autotheodolite system could not distinguish between vehicle sway and rotational motion of the inertial platform unless at least three prisms were used. One prism was mounted on the inertial platform to maintain azimuth alignment, and two prisms were mounted externally on the vehicle to track sway. For example, the automatic azimuth-laying theodolite (AALT-SV-M2) on the Saturn vehilce used three prisms. The results of testing and modifying the AALT-SV-M2 autotheodolite to simultaneously monitor and maintain alignment of the inertial platform and track the sway of the vehicle from a single Porro prism.

  10. 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.

  11. Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

    Science.gov (United States)

    Lyons, John L.

    Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S

  12. Accurate Ellipsometric Magnetic-Field Sensor Used to Align the LNE Watt Balance Magnetic Circuit

    OpenAIRE

    Ouedraogo, K; Topsu, S; Gayhmouni, J; Chassagne, L; Alayli, Y; Juncar, P.; Gournay, P; Bielsa, F; Geneves, G.

    2011-01-01

    International audience Magnetic-…eld sensors based on the Faraday e¤ect in a Tb 3 Ga 5 O 12 crystal are investigated in terms of their sensitivity, accuracy and directionality. The possibility of an increased sensitivity of such Faraday e¤ect sensors due to the application of multipass sensitive elements is considered. Signal-to-noise measurements on 5 mm diameter 20 mm long sample yield magnetic …elds equivalent noise of 300 nT=Hz 1=2 (= 1 s). The sensor has a sensitivity of 5.457(1) rad=...

  13. Double Photoionization of Spatially Aligned D{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Doerner, R.; Jagutzki, O.; Mergel, V.; Achler, M.; Moshammer, R.; Braeuning-Demian, A.; Spielberger, L.; McGuire, J.H.; Schmidt-Boecking, H. [Institut fuer Kernphysik, Universitaet Frankfurt, August Euler Strasse 6, D60486 Frankfurt (Germany); Braeuning, H.; Osipov, T.; Cocke, C.L. [Department of Physics, Kansas State University, Manhattan, Kansas 66506 (United States); Braeuning, H.; Prior, M.H.; Bozek, J.D. [Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Feagin, J.M. [Department of Physics, California State University-Fullerton, Fullerton, California 92834 (United States); Berrah, N. [Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008 (United States)

    1998-12-01

    The four-body breakup of spatially aligned D{sub 2} by 58.8 eV photons from the Advanced Light Source has been investigated by measuring the three dimensional momentum vectors of both fragment ions and one of the two electrons in coincidence. Energy and angular correlation between ions and electrons is discussed. We find rotational symmetry of the electron angular distribution around the polarization vector of the light and significant differences between helium and D{sub 2} as well as between molecular alignment parallel and perpendicular to the polarization axis. {copyright} {ital 1998} {ital The American Physical Society }

  14. Alignment dependent enhancement of the photo-electron cutoff for multi-photon ionization of molecules

    OpenAIRE

    Smeenk, C.T.L.; Arissian, L; Sokolov, A. V.; Spanner, M.; Lee, K F; Staudte, A.; Villeneuve, D. M.; Corkum, P B

    2013-01-01

    The multiphoton ionization rate of molecules depends on the alignment of the molecular axis with respect to the ionizing laser polarization. By studying molecular frame photo-electron angular distributions from N$_2$, O$_2$ and benzene, we illustrate how the angle-dependent ionization rate affects the photo-electron cutoff energy. We find alignment can enhance the high energy cutoff of the photo-electron spectrum when probing along a nodal plane or when ionization is otherwise suppressed. Thi...

  15. Field-free long-lived alignment of molecules in extreme rotational states

    CERN Document Server

    Milner, A A; Milner, V

    2015-01-01

    We introduce a new optical tool - a "two-dimensional optical centrifuge", capable of aligning molecules in extreme rotational states. Unlike the conventional centrifuge, which confines the molecules in the plane of their rotation, its two-dimensional version aligns the molecules along a well-defined axis, similarly to the effect of a single linearly polarized laser pulse, but at a much higher level of rotational excitation. The increased robustness of ultra-high rotational states with respect to collisions results in a longer life time of the created alignment in dense media, offering new possibilities for studying and utilizing aligned molecular ensembles under ambient conditions.

  16. Adiabatic field-free alignment of asymmetric top molecules with an optical centrifuge

    CERN Document Server

    Korobenko, A

    2015-01-01

    We use an optical centrifuge to align asymmetric top $\\mathrm{SO_2}$ molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment which persists after the molecules are released from the centrifuge. Periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 degrees, permanent field-free alignment offers new ways of controlling molecules with laser light.

  17. Accurate Modeling of Advanced Reflectarrays

    DEFF Research Database (Denmark)

    Zhou, Min

    Analysis and optimization methods for the design of advanced printed re ectarrays have been investigated, and the study is focused on developing an accurate and efficient simulation tool. For the analysis, a good compromise between accuracy and efficiency can be obtained using the spectral domain...

  18. DIDA: Distributed Indexing Dispatched Alignment.

    Directory of Open Access Journals (Sweden)

    Hamid Mohamadi

    Full Text Available One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA, and is free for academic use.

  19. A test facility of active alignment system at KEK

    International Nuclear Information System (INIS)

    A test facility with one control axis has been constructed at KEK to investigate a super-accurate alignment technique for the JLC (Japan Linear Collider) project. The facility consists of a stabilized laser system and a vibration control stage equipped with piezo transducers. Results of the first test show that the distance of about 28 cm is kept stable to 50 nm or better up to the frequency of 20 Hz, against the sine wave disturbance with a 500 nm amplitude

  20. Long Read Alignment with Parallel MapReduce Cloud Platform

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulhakim Al-Absi

    2015-01-01

    Full Text Available Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner’s Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.

  1. Active network alignment: a matching-based approach

    CERN Document Server

    Malmi, Eric; Gionis, Aristides

    2016-01-01

    Network alignment is the problem of matching the nodes of two graphs, maximizing the similarity of the matched nodes and the edges between them. This problem is encountered in a wide array of applications - from biological networks to social networks to ontologies - where multiple networked data sources need to be integrated. Due to the difficulty of the task, an accurate alignment can rarely be found without human assistance. Thus, it is of great practical importance to develop network alignment algorithms that can optimally leverage experts who are able to provide the correct alignment for a small number of nodes. Yet, only a handful of existing works address this active network alignment setting. The majority of the existing active methods focus on absolute queries ("are nodes $a$ and $b$ the same or not?"), whereas we argue that it is generally easier for a human expert to answer relative queries ("which node in the set $\\{b_1, \\ldots, b_n\\}$ is the most similar to node $a$?"). This paper introduces a nov...

  2. Geodetic alignment of laser power installations

    International Nuclear Information System (INIS)

    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

  3. Photosensitive Polymers for Liquid Crystal Alignment

    Science.gov (United States)

    Mahilny, U. V.; Stankevich, A. I.; Trofimova, A. V.; Muravsky, A. A.; Murauski, A. A.

    The peculiarities of alignment of liquid crystal (LC) materials by the layers of photocrosslinkable polymers with side benzaldehyde groups are considered. The investigation of mechanism of photostimulated alignment by rubbed benzaldehyde layer is performed. The methods of creation of multidomain aligning layers on the basis of photostimulated rubbing alignment are described.

  4. Overlay improvement by ASML HOWA 5th alignment strategy

    Science.gov (United States)

    Wang, Raf; Chiang, CY; Hsu, Wilson; Yang, Richer; Shih, Todd; Chen, Jackie; Chiu, Jonathan; Lin, Wythe

    2009-12-01

    Overlay control is more challenging when DRAM volume production continues to shrink its critical dimention (CD) to 70nm and beyond. Effected by process, the overlay behavior at wafer edge is quite different from wafer center. The big contribution to worse overlay at wafer edge which causes yield loss is misalignment. The analysis in wafer edge suggests that high order uncorrectable overlay residuals are often observed by certain process impact. Therefore, the basic linear model used for alignment correction is not sufficient and it is necessary to introduce an advanced alignment correction model for wafer edge overlay improvement. In this study, we demonstrated the achievement of moderating the poor overlay at wafer edge area by using a high order wafer alignment strategy. The mechanism is to use non-linear correction methods of high order models ( up to 5th order), with support by the function High Order Wafer Alignment (known as HOWA) in scanner. Instead of linear model for the 6 overlay parameters which come from average result, HOWA alignment strategy can do high order fitting through the wafer to get more accurate overlay parameters which represent the local wafer grid distortion better. As a result, the overlay improvement for wafer edge is achieved. Since alignment is a wafer dependent correction, with HOWA the wafer to wafer overlay variation can be improved dynamically as well. In addition, the effects of different mark quantity and sampling distribution from HOWA are also introduced in this paper. The results of this study indicate that HOWA can reduce uncorrectable overlay residual by 30~40% and improve wafer-to-wafer overlay variation significantly. We conclude that HOWA is a noteworthy strategy for overlay improvement. Moreover, optimized alignment mark numbers and distribution layout are also key factors to make HOWA successful.

  5. Accurate genome relative abundance estimation based on shotgun metagenomic reads.

    Directory of Open Access Journals (Sweden)

    Li C Xia

    Full Text Available Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have developed a unified probabilistic framework (named GRAMMy by explicitly modeling read assignment ambiguities, genome size biases and read distributions along the genomes. Maximum likelihood method is employed to compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy. GRAMMy has been demonstrated to give estimates that are accurate and robust across both simulated and real read benchmark datasets. We applied GRAMMy to a collection of 34 metagenomic read sets from four metagenomics projects and identified 99 frequent species (minimally 0.5% abundant in at least 50% of the data-sets in the human gut samples. Our results show substantial improvements over previous studies, such as adjusting the over-estimated abundance for Bacteroides species for human gut samples, by providing a new reference-based strategy for metagenomic sample comparisons. GRAMMy can be used flexibly with many read assignment tools (mapping, alignment or composition-based even with low-sensitivity mapping results from huge short-read datasets. It will be increasingly useful as an accurate and robust tool for abundance estimation with the growing size of read sets and the expanding database of reference genomes.

  6. Alignment method for parabolic trough solar concentrators

    Science.gov (United States)

    Diver, Richard B.

    2010-02-23

    A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

  7. Strategic Alignment and New Product Development

    DEFF Research Database (Denmark)

    Acur, Nuran; Kandemir, Destan; Boer, Harry

    2012-01-01

    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......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...... 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...

  8. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  9. Topology independent protein structural alignment

    Directory of Open Access Journals (Sweden)

    DasGupta Bhaskar

    2007-10-01

    Full Text Available Abstract Background Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein structures, and the more general cases of non-cyclic permutations between similar structures, which are related by non-topological rearrangement beyond circular permutation. We present a method based on an approximation algorithm that finds sequence-order independent structural alignments that are close to optimal. We formulate the structural alignment problem as a special case of the maximum-weight independent set problem, and solve this computationally intensive problem approximately by iteratively solving relaxations of a corresponding integer programming problem. The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps. Results Using a novel similarity score and a statistical model for significance p-value, we are able to discover previously unknown circular permuted proteins between nucleoplasmin-core protein and auxin binding protein, between aspartate rasemase and 3-dehydrogenate dehydralase, as well as between migration inhibition factor and arginine repressor which involves an additional strand-swapping. We also report the finding of non-cyclic permuted protein structures existing in nature between AML1/core binding factor and ribofalvin synthase. Our method can be used for large scale alignment of protein structures regardless of the topology. Conclusion The approximation algorithm introduced in this work can find good solutions for the problem of protein structure alignment. Furthermore, this algorithm can detect topological differences between two spatially similar protein structures. The alignment between MIF and the arginine repressor demonstrates our algorithm's ability to detect structural similarities even when spatial

  10. Post ionization alignment of the fragmentation of molecules in an ultrashort intense laser field

    International Nuclear Information System (INIS)

    We studied the angular distributions of the fragmented ions of diatomic molecules in an intense linearly polarized short laser pulse. In addition to the well-known dynamic alignment of the neutral molecules before ionization, we identified a more important post ionization alignment effect of the molecular ions. The latter is modelled quantum mechanically as resulting from the breakup of a rotating linear rotor. We showed that only for very short pulses are the two alignment mechanisms not important. In this case the angular distributions of the fragmented ions mimic the shape of the electronic density of the outermost molecular orbital

  11. Position list word aligned hybrid

    DEFF Research Database (Denmark)

    Deliege, Francois; Pedersen, Torben Bach

    2010-01-01

    of storage space. This paper presents the Position List Word Aligned Hybrid (PLWAH) compression scheme that improves significantly over WAH compression by better utilizing the available bits and new CPU instructions. For typical bit distributions, PLWAH compressed bitmaps are often half the size of WAH......Compressed bitmap indexes are increasingly used for efficiently querying very large and complex databases. The Word Aligned Hybrid (WAH) bitmap compression scheme is commonly recognized as the most efficient compression scheme in terms of CPU efficiency. However, WAH compressed bitmaps use a lot...

  12. A Genetic Algorithm on Multiple Sequences Alignment Problems in Biology

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the possible sequence alignments in order to find an optimal one for which the "distance" between sequences is minimum. In biology informatics area, it is a more important and difficult problem due to the long length (100 at least) of sequence, this cause the compute complexity and large memory require. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment, this give an obvious encoding of each path. This problem can be solved by applying genetic algorithm, which is more efficient than dynamic programming and hidden Markov model using commomly now.

  13. Profitable capitation requires accurate costing.

    Science.gov (United States)

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages. PMID:8788799

  14. Controlling single-molecule junction conductance by molecular interactions.

    Science.gov (United States)

    Kitaguchi, Y; Habuka, S; Okuyama, H; Hatta, S; Aruga, T; Frederiksen, T; Paulsson, M; Ueba, H

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  15. ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

    Science.gov (United States)

    Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

    2006-12-15

    We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

  16. Theoretical and practical feasibility demonstration of a micrometric remotely controlled pre-alignment system for the CLIC linear collider

    CERN Document Server

    Mainaud Durand, H; Chritin, N; Griffet, S; Kemppinen, J; Sosin, M; Touze, T

    2011-01-01

    The active pre-alignment of the Compact Linear Collider (CLIC) is one of the key points of the project: the components must be pre-aligned w.r.t. a straight line within a few microns over a sliding window of 200 m, along the two linacs of 20 km each. The proposed solution consists of stretched wires of more than 200 m, overlapping over half of their length, which will be the reference of alignment. Wire Positioning Sensors (WPS), coupled to the supports to be pre-aligned, will perform precise and accurate measurements within a few microns w.r.t. these wires. A micrometric fiducialisation of the components and a micrometric alignment of the components on common supports will make the strategy of pre-alignment complete. In this paper, the global strategy of active pre-alignment is detailed and illustrated by the latest results demonstrating the feasibility of the proposed solution.

  17. Aligned natural inflation with modulations

    Science.gov (United States)

    Choi, Kiwoon; Kim, Hyungjin

    2016-08-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  18. Laser-Beam-Alignment Controller

    Science.gov (United States)

    Krasowski, M. J.; Dickens, D. E.

    1995-01-01

    In laser-beam-alignment controller, images from video camera compared to reference patterns by fuzzy-logic pattern comparator. Results processed by fuzzy-logic microcontroller, which sends control signals to motor driver adjusting lens and pinhole in spatial filter.

  19. Aligned natural inflation with modulations

    CERN Document Server

    Choi, Kiwoon

    2015-01-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  20. Aligned natural inflation with modulations

    Directory of Open Access Journals (Sweden)

    Kiwoon Choi

    2016-08-01

    Full Text Available The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  1. Aligned natural inflation with modulations

    OpenAIRE

    Kiwoon Choi; Hyungjin Kim

    2016-01-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  2. Self crimped and aligned fibers

    Directory of Open Access Journals (Sweden)

    Thinakaran Senthilram

    2011-05-01

    Full Text Available Electrospinning is one of the most successful means of producing nanofibers with enormous application potential. New methods of producing nanofibers without high voltages are presently being explored by researchers around the globe. In the present work, a facile method of producing aligned and crimped fibers with polycaprolactone by rotating the needle assembly is described.

  3. Chemical control over the energy-level alignment in a two-terminal junction

    Science.gov (United States)

    Yuan, Li; Franco, Carlos; Crivillers, Núria; Mas-Torrent, Marta; Cao, Liang; Sangeeth, C. S. Suchand; Rovira, Concepció; Veciana, Jaume; Nijhuis, Christian A.

    2016-07-01

    The energy-level alignment of molecular transistors can be controlled by external gating to move molecular orbitals with respect to the Fermi levels of the source and drain electrodes. Two-terminal molecular tunnelling junctions, however, lack a gate electrode and suffer from Fermi-level pinning, making it difficult to control the energy-level alignment of the system. Here we report an enhancement of 2 orders of magnitude of the tunnelling current in a two-terminal junction via chemical molecular orbital control, changing chemically the molecular component between a stable radical and its non-radical form without altering the supramolecular structure of the junction. Our findings demonstrate that the energy-level alignment in self-assembled monolayer-based junctions can be regulated by purely chemical modifications, which seems an attractive alternative to control the electrical properties of two-terminal junctions.

  4. Chemical control over the energy-level alignment in a two-terminal junction

    Science.gov (United States)

    Yuan, Li; Franco, Carlos; Crivillers, Núria; Mas-Torrent, Marta; Cao, Liang; Sangeeth, C. S. Suchand; Rovira, Concepció; Veciana, Jaume; Nijhuis, Christian A.

    2016-01-01

    The energy-level alignment of molecular transistors can be controlled by external gating to move molecular orbitals with respect to the Fermi levels of the source and drain electrodes. Two-terminal molecular tunnelling junctions, however, lack a gate electrode and suffer from Fermi-level pinning, making it difficult to control the energy-level alignment of the system. Here we report an enhancement of 2 orders of magnitude of the tunnelling current in a two-terminal junction via chemical molecular orbital control, changing chemically the molecular component between a stable radical and its non-radical form without altering the supramolecular structure of the junction. Our findings demonstrate that the energy-level alignment in self-assembled monolayer-based junctions can be regulated by purely chemical modifications, which seems an attractive alternative to control the electrical properties of two-terminal junctions. PMID:27456200

  5. On the importance of having accurate data for astrophysical modelling

    Science.gov (United States)

    Lique, Francois

    2016-06-01

    The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.

  6. Grain Alignment and CMB Polarization Studies

    CERN Document Server

    Lazarian, A

    2008-01-01

    Polarized microwave emission from dust is an important foreground that may contaminate polarized CMB studies unless carefully accounted for. Modeling of polarization from dust requires a quantitative understanding of grain alignment. I review the current status of grain alignment theory outlining recent advances in quantitative description of the alignment. In particular, I show that the grain-alignment theory is a predictive one, and its results nicely match observations. Those indicate that the most important process of alignment is related to radiative torques acting on irregular grains. The recently developed analytical model of radiative torque alignment has proven to be a very efficient tool for predicting the degree of grain alignment. We expect the alignment theory to further mature before CMBPol flight, which would ensure a better accounting for the dust-related polarization. At the same time, CMBPol should provide the additional testing of grain alignment, clarifying the reliability of polarimetry f...

  7. In-Flight Self-Alignment Method Aided by Geomagnetism for Moving Basement of Guided Munitions

    Directory of Open Access Journals (Sweden)

    Shuang-biao Zhang

    2015-01-01

    Full Text Available Due to power-after-launch mode of guided munitions of high rolling speed, initial attitude of munitions cannot be determined accurately, and this makes it difficult for navigation and control system to work effectively and validly. An in-flight self-alignment method aided by geomagnetism that includes a fast in-flight coarse alignment method and an in-flight alignment model based on Kalman theory is proposed in this paper. Firstly a fast in-flight coarse alignment method is developed by using gyros, magnetic sensors, and trajectory angles. Then, an in-flight alignment model is derived by investigation of the measurement errors and attitude errors, which regards attitude errors as state variables and geomagnetic components in navigation frame as observed variables. Finally, fight data of a spinning projectile is used to verify the performance of the in-flight self-alignment method. The satisfying results show that (1 the precision of coarse alignment can attain below 5°; (2 the attitude errors by in-flight alignment model converge to 24′ at early of the latter half of the flight; (3 the in-flight alignment model based on Kalman theory has better adaptability, and show satisfying performance.

  8. Quantitatively accurate calculations of conductance and thermopower of molecular junctions

    DEFF Research Database (Denmark)

    Markussen, Troels; Jin, Chengjun; Thygesen, Kristian Sommer

    2013-01-01

    ) connected to gold electrodes using first‐principles calculations. We find excellent agreement with experiments for both molecules when exchange–correlation effects are described by the many‐body GW approximation. In contrast, results from standard density functional theory (DFT) deviate from experiments......‐principles calculations when exchange–correlation effects are taken properly into account....

  9. Accurate Kirkwood-Buff Integrals from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; O'Connell, John P.; Peters, Günther H.J.;

    2010-01-01

    theoretical limiting behaviour on the corresponding direct correlation function. The method is evaluated for the pure Lennard-Jones and Stockmayer fluids. The results are verified by comparing pure fluid isothermal compressibilities obtained from the KB integrals with values from derivatives of equations of...

  10. RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.

    Science.gov (United States)

    Wilson, Gavin W; Stein, Lincoln D

    2015-10-15

    RNA-seq is a key technology for understanding the biology of the cell because of its ability to profile transcriptional and post-transcriptional regulation at single nucleotide resolutions. Compared to DNA sequencing alignment algorithms, RNA-seq alignment algorithms have a diminished ability to accurately detect and map base pair substitutions, gaps, discordant pairs and repetitive regions. These shortcomings adversely affect experiments that require a high degree of accuracy, notably the ability to detect RNA editing. We have developed RNASequel, a software package that runs as a post-processing step in conjunction with an RNA-seq aligner and systematically corrects common alignment artifacts. Its key innovations are a two-pass splice junction alignment system that includes de novo splice junctions and the use of an empirically determined estimate of the fragment size distribution when resolving read pairs. We demonstrate that RNASequel produces improved alignments when used in conjunction with STAR or Tophat2 using two simulated datasets. We then show that RNASequel improves the identification of adenosine to inosine RNA editing sites on biological datasets. This software will be useful in applications requiring the accurate identification of variants in RNA sequencing data, the discovery of RNA editing sites and the analysis of alternative splicing.

  11. Library preparation for highly accurate population sequencing of RNA viruses

    Science.gov (United States)

    Acevedo, Ashley; Andino, Raul

    2015-01-01

    Circular resequencing (CirSeq) is a novel technique for efficient and highly accurate next-generation sequencing (NGS) of RNA virus populations. The foundation of this approach is the circularization of fragmented viral RNAs, which are then redundantly encoded into tandem repeats by ‘rolling-circle’ reverse transcription. When sequenced, the redundant copies within each read are aligned to derive a consensus sequence of their initial RNA template. This process yields sequencing data with error rates far below the variant frequencies observed for RNA viruses, facilitating ultra-rare variant detection and accurate measurement of low-frequency variants. Although library preparation takes ~5 d, the high-quality data generated by CirSeq simplifies downstream data analysis, making this approach substantially more tractable for experimentalists. PMID:24967624

  12. Accurate determination of antenna directivity

    DEFF Research Database (Denmark)

    Dich, Mikael

    1997-01-01

    The derivation of a formula for accurate estimation of the total radiated power from a transmitting antenna for which the radiated power density is known in a finite number of points on the far-field sphere is presented. The main application of the formula is determination of directivity from power......-pattern measurements. The derivation is based on the theory of spherical wave expansion of electromagnetic fields, which also establishes a simple criterion for the required number of samples of the power density. An array antenna consisting of Hertzian dipoles is used to test the accuracy and rate of convergence...

  13. Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

    Science.gov (United States)

    Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

    2016-07-01

    It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016. PMID:26939754

  14. Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

    Science.gov (United States)

    Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

    2016-07-01

    It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016.

  15. $H_{2}^{+}$ ion in strong magnetic field an accurate calculation

    CERN Document Server

    López, J C; Turbiner, A V

    1997-01-01

    Using a unique trial function we perform an accurate calculation of the ground state $1\\sigma_g$ of the hydrogenic molecular ion $H^+_2$ in a constant uniform magnetic field ranging $0-10^{13}$ G. We show that this trial function also makes it possible to study the negative parity ground state $1\\sigma_u$.

  16. Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks

    OpenAIRE

    Farid Amir-Ghiasvand; Abbas Nowzari-Dalini; Vida Momenzadeh

    2014-01-01

    To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce Pin-Align, a new tool for local alignment of protein-protein interaction networks. Pin-Align accuracy is tested on protein...

  17. High accuracy alignment facility for the receiver and transmitter of the BepiColombo Laser Altimeter.

    Science.gov (United States)

    Chakraborty, Sumita; Affolter, Michael; Gunderson, Kurt; Neubert, Jakob; Thomas, Nicolas; Beck, Thomas; Gerber, Michael; Graf, Stefan; Piazza, Daniele; Pommerol, Antoine; Roethlisberger, Guillaume; Seiferlin, Karsten

    2012-07-10

    The accurate co-alignment of the transmitter to the receiver of the BepiColombo Laser Altimeter is a challenging task for which an original alignment concept had to be developed. We present here the design, construction and testing of a large collimator facility built to fulfill the tight alignment requirements. We describe in detail the solution found to attenuate the high energy of the instrument laser transmitter by an original beam splitting pentaprism group. We list the different steps of the calibration of the alignment facility and estimate the errors made at each of these steps. We finally prove that the current facility is ready for the alignment of the flight instrument. Its angular accuracy is 23 μrad. PMID:22781273

  18. Local graph alignment and motif search in biological networks

    Science.gov (United States)

    Berg, Johannes; Lässig, Michael

    2004-10-01

    Interaction networks are of central importance in postgenomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks or protein interaction maps. The main challenge in the analysis of these data is to read off biological functions from the topology of the network. Topological motifs, i.e., patterns occurring repeatedly at different positions in the network, have recently been identified as basic modules of molecular information processing. In this article, we discuss motifs derived from families of mutually similar but not necessarily identical patterns. We establish a statistical model for the occurrence of such motifs, from which we derive a scoring function for their statistical significance. Based on this scoring function, we develop a search algorithm for topological motifs called graph alignment, a procedure with some analogies to sequence alignment. The algorithm is applied to the gene regulation network of Escherichia coli.

  19. Inverse Problem Approach for the Alignment of Electron Tomographic Series

    International Nuclear Information System (INIS)

    In the refining industry, morphological measurements of particles have become an essential part in the characterization catalyst supports. Through these parameters, one can infer the specific physico-chemical properties of the studied materials. One of the main acquisition techniques is electron tomography (or nano-tomography). 3D volumes are reconstructed from sets of projections from different angles made by a Transmission Electron Microscope (TEM). This technique provides a real three-dimensional information at the nano-metric scale. A major issue in this method is the misalignment of the projections that contributes to the reconstruction. The current alignment techniques usually employ fiducial markers such as gold particles for a correct alignment of the images. When the use of markers is not possible, the correlation between adjacent projections is used to align them. However, this method sometimes fails. In this paper, we propose a new method based on the inverse problem approach where a certain criterion is minimized using a variant of the Nelder and Mead simplex algorithm. The proposed approach is composed of two steps. The first step consists of an initial alignment process, which relies on the minimization of a cost function based on robust statistics measuring the similarity of a projection to its previous projections in the series. It reduces strong shifts resulting from the acquisition between successive projections. In the second step, the pre-registered projections are used to initialize an iterative alignment-refinement process which alternates between (i) volume reconstructions and (ii) registrations of measured projections onto simulated projections computed from the volume reconstructed in (i). At the end of this process, we have a correct reconstruction of the volume, the projections being correctly aligned. Our method is tested on simulated data and shown to estimate accurately the translation, rotation and scale of arbitrary transforms. We

  20. Nanofiber alignment of a small diameter elastic electrospun scaffold

    Science.gov (United States)

    Patel, Jignesh

    Cardiovascular disease is the leading cause of death in western countries with coronary heart disease making up 50% of these deaths. As a treatment option, tissue engineered grafts have great potential. Elastic scaffolds that mimic arterial extracellular matrix (ECM) may hold the key to creating viable vascular grafts. Electrospinning is a widely used scaffold fabrication technique to engineer tubular scaffolds. In this study, we investigated how the collector rotation speed altered the nanofiber alignment which may improve mechanical characteristics making the scaffold more suitable for arterial grafts. The scaffold was fabricated from a blend of PCL/Elastin. 2D Fast Fourier Transform (FFT) image processing tool and MatLab were used to quantitatively analyze nanofiber orientation at different collector speeds (13500 to 15500 rpm). Both Image J and MatLab showed graphical peaks indicating predominant fiber orientation angles. A collector speed of 15000 rpm was found to produce the best nanofiber alignment with narrow peaks at 90 and 270 degrees, and a relative amplitude of 200. This indicates a narrow distribution of circumferentially aligned nanofibers. Collector speeds below and above 15000 rpm caused a decrease in fiber alignment with a broader orientation distribution. Uniformity of fiber diameter was also measured. Of 600 measures from the 15000 rpm scaffolds, the fiber diameter range from 500 nm to 899 nm was most prevalent. This diameter range was slightly larger than native ECM which ranges from 50 nm to 500 nm. The second most prevalent diameter range had an average of 404 nm which is within the diameter range of collagen. This study concluded that with proper electrospinning technique and collector speed, it is possible to fabricate highly aligned small diameter elastic scaffolds. Image J 2D FFT results confirmed MatLab findings for the analyses of circumferentially aligned nanofibers. In addition, MatLab analyses simplified the FFT orientation data

  1. Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

    Directory of Open Access Journals (Sweden)

    Liu Jun S

    2004-10-01

    Full Text Available Abstract Background Certain protein families are highly conserved across distantly related organisms and belong to large and functionally diverse superfamilies. The patterns of conservation present in these protein sequences presumably are due to selective constraints maintaining important but unknown structural mechanisms with some constraints specific to each family and others shared by a larger subset or by the entire superfamily. To exploit these patterns as a source of functional information, we recently devised a statistically based approach called contrast hierarchical alignment and interaction network (CHAIN analysis, which infers the strengths of various categories of selective constraints from co-conserved patterns in a multiple alignment. The power of this approach strongly depends on the quality of the multiple alignments, which thus motivated development of theoretical concepts and strategies to improve alignment of conserved motifs within large sets of distantly related sequences. Results Here we describe a hidden Markov model (HMM, an algebraic system, and Markov chain Monte Carlo (MCMC sampling strategies for alignment of multiple sequence motifs. The MCMC sampling strategies are useful both for alignment optimization and for adjusting position specific background amino acid frequencies for alignment uncertainties. Associated statistical formulations provide an objective measure of alignment quality as well as automatic gap penalty optimization. Improved alignments obtained in this way are compared with PSI-BLAST based alignments within the context of CHAIN analysis of three protein families: Giα subunits, prolyl oligopeptidases, and transitional endoplasmic reticulum (p97 AAA+ ATPases. Conclusion While not entirely replacing PSI-BLAST based alignments, which likewise may be optimized for CHAIN analysis using this approach, these motif-based methods often more accurately align very distantly related sequences and thus can

  2. Energy level alignment in Au/pentacene/PTCDA trilayer stacks

    OpenAIRE

    Sehati, Parisa; Braun, Slawomir; Fahlman, Mats

    2013-01-01

    Ultraviolet photoelectron spectroscopy is used to investigate the energy level alignment and molecular orientation at the interfaces in Au/pentacene/PTCDA trilayer stacks. We deduced a standing orientation for pentacene grown on Au while we conclude a flat lying geometry for PTCDA grown onto pentacene. We propose that the rough surface of polycrystalline Au induces the standing geometry in pentacene. It is further shown that in situ deposition of PTCDA on pentacene can influence the orientati...

  3. Preparation of the CMS tracker alignment for the LHC Run-2

    Energy Technology Data Exchange (ETDEWEB)

    Lelek, Aleksandra; Mankel, Rainer; Schroeder, Matthias; Kleinwort, Claus [DESY, Notkestrasse 85, 22607 Hamburg (Germany)

    2015-07-01

    The CMS tracker is the world's largest silicon detector and consists of more than 25000 sensors. A precise knowledge of their position is crucial for an accurate reconstruction of higher-level objects such as particle trajectories (tracks) and jets. Using a track-based alignment procedure, which minimizes the residuals between the measured and predicted hit positions in the detector, the position and orientation of the sensors are determined to the level of 10 μm and 10 μrad, respectively. In the presentation, the impact of the alignment precision on the object reconstruction is investigated and alignment strategies for the upcoming LHC Run-2 are discussed.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-12-14

    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.

  5. A hybrid retention time alignment algorithm for SWATH-MS data.

    Science.gov (United States)

    Wu, Long; Amon, Sabine; Lam, Henry

    2016-08-01

    Recently, data-independent acquisition (DIA) MS has gained popularity as a qualitative-quantitative workflow for proteomics. One outstanding problem in the analysis of DIA-MS data is alignment of chromatographic retention times across multiple samples, which facilitates peptide identification and accurate quantification. Here, we present a novel hybrid (profile-based and feature-based) algorithm for LC-MS alignment and test it on sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) (a type of DIA) data. Our algorithm uses a profile-based dynamic time warping algorithm to obtain a coarse alignment and corrects large retention time shifts, and then uses a feature-based bipartite matching algorithm to match feature to feature at a fine scale. We evaluated our method by comparing our aligned feature pairs to peptide identification results of pseudo-MS2 spectra exported by DIA-Umpire, a recently reported tool for deconvoluting DIA-MS data. We proposed that our method can be used to align DIA-MS data prior to identification, and the alignment can be used to delete noise peaks or screen for differentially changed features. We found that a simple alignment-enabled denoising scheme can reduce the number of pseudo-MS2 spectra exported by DIA-Umpire by up to around 40%, while retaining a comparable number of identifications. Finally, we demonstrated the utility of our tool for accurate label-free relative quantification across multiple SWATH runs.

  6. Aligning seminars with Bologna requirements

    DEFF Research Database (Denmark)

    Lueg, Klarissa; Lueg, Rainer; Lauridsen, Ole

    2015-01-01

    Changes in public policy, such as the Bologna Process, require students to be equipped with multifunctional competencies to master relevant tasks in unfamiliar situations. Achieving this goal might imply a change in many curricula toward deeper learning. As a didactical means to achieve deep...... learning results, the authors suggest reciprocal peer tutoring (RPT); as a conceptual framework the authors suggest the SOLO (Structure of Observed Learning Outcomes) taxonomy and constructive alignment as suggested by Biggs and Tang. Our study presents results from the introduction of RPT in a large...... course. The authors find that RPT produces satisfying learning outcomes, active students, and ideal constructive alignments of the seminar content with the exam, the intended learning outcomes, and the requirements of the Bologna Process. Our data, which comprise surveys and evaluations from both faculty...

  7. Prism Window for Optical Alignment

    Science.gov (United States)

    Tang, Hong

    2008-01-01

    A prism window has been devised for use, with an autocollimator, in aligning optical components that are (1) required to be oriented parallel to each other and/or at a specified angle of incidence with respect to a common optical path and (2) mounted at different positions along the common optical path. The prism window can also be used to align a single optical component at a specified angle of incidence. Prism windows could be generally useful for orienting optical components in manufacture of optical instruments. "Prism window" denotes an application-specific unit comprising two beam-splitter windows that are bonded together at an angle chosen to obtain the specified angle of incidence.

  8. Aligned mesoporous architectures and devices.

    Energy Technology Data Exchange (ETDEWEB)

    Brinker, C. Jeffrey; Lu, Yunfeng (University of California Los Angeles, Los Angeles, CA)

    2011-03-01

    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

  9. Accurate ab initio spin densities

    CERN Document Server

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

  10. The Accurate Particle Tracer Code

    CERN Document Server

    Wang, Yulei; Qin, Hong; Yu, Zhi

    2016-01-01

    The Accurate Particle Tracer (APT) code is designed for large-scale particle simulations on dynamical systems. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and non-linear problems. Under the well-designed integrated and modularized framework, APT serves as a universal platform for researchers from different fields, such as plasma physics, accelerator physics, space science, fusion energy research, computational mathematics, software engineering, and high-performance computation. The APT code consists of seven main modules, including the I/O module, the initialization module, the particle pusher module, the parallelization module, the field configuration module, the external force-field module, and the extendible module. The I/O module, supported by Lua and Hdf5 projects, provides a user-friendly interface for both numerical simulation and data analysis. A series of new geometric numerical methods...

  11. Accurate thickness measurement of graphene

    Science.gov (United States)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  12. Accurate thickness measurement of graphene.

    Science.gov (United States)

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  13. Intrinsic Galaxy Alignments and Weak Gravitational Lensing

    CERN Document Server

    Heavens, A F

    2001-01-01

    Gravitational lensing causes background galaxy images to become aligned, and the statistical characteristics of the image alignments can then be used to constrain the power spectrum of mass fluctuations. Analyses of gravitational lensing assume that intrinsic galaxy alignments are negligible, but if this assumption does not hold, then the interpretation of image alignments will be in error. As gravitational lensing experiments become more ambitious and seek very low-level alignments arising from lensing by large-scale structure, it becomes more important to estimate the level of intrinsic alignment in the galaxy population. In this article, I review the cluster of independent theoretical studies of this issue, as well as the current observational status. Theoretically, the calculation of intrinsic alignments is by no means straightforward, but some consensus has emerged from the existing works, despite each making very different assumptions. This consensus is that a) intrinsic alignments are a small but non-n...

  14. RDF Graph Alignment with Bisimulation

    OpenAIRE

    Buneman, Peter; Staworko, Sławek

    2016-01-01

    We investigate the problem of aligning two RDF databases, an essential problem in understanding the evolution of ontologies. Our approaches address three fundamental challenges: 1) the use of "blank" (null) names, 2) ontology changes in which different names are used to identify the same entity, and 3) small changes in the data values as well as small changes in the graph structure of the RDF database. We propose approaches inspired by the classical notion of graph bisimulation and extend the...

  15. From Word Alignment to Word Senses, via Multilingual Wordnets

    Directory of Open Access Journals (Sweden)

    Dan Tufis

    2006-05-01

    Full Text Available Most of the successful commercial applications in language processing (text and/or speech dispense with any explicit concern on semantics, with the usual motivations stemming from the computational high costs required for dealing with semantics, in case of large volumes of data. With recent advances in corpus linguistics and statistical-based methods in NLP, revealing useful semantic features of linguistic data is becoming cheaper and cheaper and the accuracy of this process is steadily improving. Lately, there seems to be a growing acceptance of the idea that multilingual lexical ontologisms might be the key towards aligning different views on the semantic atomic units to be used in characterizing the general meaning of various and multilingual documents. Depending on the granularity at which semantic distinctions are necessary, the accuracy of the basic semantic processing (such as word sense disambiguation can be very high with relatively low complexity computing. The paper substantiates this statement by presenting a statistical/based system for word alignment and word sense disambiguation in parallel corpora. We describe a word alignment platform which ensures text pre-processing (tokenization, POS-tagging, lemmatization, chunking, sentence and word alignment as required by an accurate word sense disambiguation.

  16. Structural analysis of aligned RNAs.

    Science.gov (United States)

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  17. Reconstruction of the Electron Density of Molecules with Single-Axis Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Starodub, Dmitri

    2011-08-12

    Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. We present two methods of structure solution for this case. One is based on the iterative projection algorithms for phase retrieval applied to the coefficients of the cylindrical harmonic expansion of the molecular electron density. Another is the holographic approach utilizing presence of the strongly scattering reference atom for a specific molecule.

  18. Alignment dependent ultrafast electron-nuclear dynamics in high-order harmonic generation

    CERN Document Server

    Li, Mu-Zi; Bian, Xue-Bin

    2016-01-01

    We investigated the high-order harmonic generation (HHG) process of diatomic molecular ion $\\mathrm{H}_2^+$ in non-Born-Oppenheimer approximations. The corresponding three-dimensional time-dependent Schr\\"odinger equation is solved with arbitrary alignment angles. It is found that the nuclear motion can lead to spectral modulation of HHG. Redshifts are unique in molecular HHG which decrease with the increase of alignment angles of the molecules and are sensitive to the initial vibrational states. It can be used to extract the ultrafast electron-nuclear dynamics and image molecular structure.

  19. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  20. Beam alignment system for laser welding system

    International Nuclear Information System (INIS)

    The patent describes a beam alignment system for laser welding work pieces, such as fuel rod grids for nuclear fuel assemblies. The apparatus for performing various laser-machining comprises a beam alignment system including alignment target means, as well as means for emitting, directing and focusing the laser beam. (U.K.)

  1. Vertically aligned nanostructure scanning probe microscope tips

    Science.gov (United States)

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  2. Alignment of lower-limb prostheses.

    Science.gov (United States)

    Zahedi, M S; Spence, W D; Solomonidis, S E; Paul, J P

    1986-04-01

    Alignment of a prosthesis is defined as the position of the socket relative to the other prosthetic components of the limb. During dynamic alignment the prosthetist, using subjective judgment and feedback from the patient, aims to achieve the most suitable limb geometry for best function and comfort. Until recently it was generally believed that a patient could only be satisfied with a unique "optimum alignment." The purpose of this systematic study of lower-limb alignment parameters was to gain an understanding of the factors that make a limb configuration or optimum alignment, acceptable to the patient, and to obtain a measure of the variation of this alignment that would be acceptable to the amputee. In this paper, the acceptable range of alignments for 10 below- and 10 above-knee amputees are established. Three prosthetists were involved in the majority of the 183 below-knee and 100 above-knee fittings, although several other prosthetists were also involved. The effects of each different prosthetist on the established range of alignment for each patient are reported to be significant. It is now established that an amputee can tolerate several alignments ranging in some parameters by as much as 148 mm in shifts and 17 degrees in tilts. This paper describes the method of defining and measuring the alignment of lower-limb prostheses. It presents quantitatively established values for bench alignment position and the range of adjustment required for incorporation into the design of new alignment units.

  3. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  4. Shift dynamics of capillary self-alignment

    NARCIS (Netherlands)

    Arutinov, G.; Mastrangeli, M.; Smits, E.C.P.; Heck, G.V.; Schoo, H.F.M.; Toonder, J.J.M. den; Dietzel, A.H.

    2014-01-01

    This paper describes the dynamics of capillary self-alignment of components with initial shift offsets from matching receptor sites. The analysis of the full uniaxial self-alignment dynamics of foil-based mesoscopic dies from pre-alignment to final settling evidenced three distinct, sequential regim

  5. Inferring comprehensible business/ICT alignment rules

    NARCIS (Netherlands)

    B. Cumps; D. Martens; M. De Backer; R. Haesen; S. Viaene; G. Dedene; B. Baesens; M. Snoeck

    2009-01-01

    We inferred business rules for business/ICT alignment by applying a novel rule induction algorithm on a data set containing rich alignment information polled from 641 organisations in 7 European countries. The alignment rule set was created using AntMiner+, a rule induction technique with a reputati

  6. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

    Directory of Open Access Journals (Sweden)

    Grossman Lawrence I

    2007-09-01

    Full Text Available Abstract Background Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence. Results Here we report an online codon-preserved alignment tool (OCPAT that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s from at least one species; however, functional annotation clustering of the ~1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved. Conclusion The OCPAT program facilitates large-scale evolutionary and

  7. Direct Uniaxial Alignment of a Donor-Acceptor Semiconducting Polymer Using Single-Step Solution Shearing.

    Science.gov (United States)

    Shaw, Leo; Hayoz, Pascal; Diao, Ying; Reinspach, Julia Antonia; To, John W F; Toney, Michael F; Weitz, R Thomas; Bao, Zhenan

    2016-04-13

    The alignment of organic semiconductors (OSCs) in the active layers of electronic devices can confer desirable properties, such as enhanced charge transport properties due to better ordering, charge transport anisotropy for reduced device cross-talk, and polarized light emission or absorption. The solution-based deposition of highly aligned small molecule OSCs has been widely demonstrated, but the alignment of polymeric OSCs in thin films deposited directly from solution has typically required surface templating or complex pre- or postdeposition processing. Therefore, single-step solution processing and the charge transport enhancement afforded by alignment continue to be attractive. We report here the use of solution shearing to tune the degree of alignment in poly(diketopyrrolopyrrole-terthiophene) thin films by controlling the coating speed. A maximum dichroic ratio of ∼7 was achieved on unpatterned substrates without any additional pre- or postdeposition processing. The degree of polymer alignment was found to be a competition between the shear alignment of polymer chains in solution and the complex thin film drying process. Contrary to previous reports, no charge transport anisotropy was observed because of the small crystallite size relative to the channel length, a meshlike morphology, and the likelihood of increased grain boundaries in the direction transverse to coating. In fact, the lack of aligned morphological structures, coupled with observed anisotropy in X-ray diffraction data, suggests the alignment of polymer molecules in both the crystalline and the amorphous regions of the films. The shear speed at which maximum dichroism is achieved can be controlled by altering deposition parameters such as temperature and substrate treatment. Modest changes in molecular weight showed negligible effects on alignment, while longer polymer alkyl side chains were found to reduce the degree of alignment. This work demonstrates that solution shearing can be used

  8. Mitotic Protein CSPP1 Interacts with CENP-H Protein to Coordinate Accurate Chromosome Oscillation in Mitosis.

    Science.gov (United States)

    Zhu, Lijuan; Wang, Zhikai; Wang, Wenwen; Wang, Chunli; Hua, Shasha; Su, Zeqi; Brako, Larry; Garcia-Barrio, Minerva; Ye, Mingliang; Wei, Xuan; Zou, Hanfa; Ding, Xia; Liu, Lifang; Liu, Xing; Yao, Xuebiao

    2015-11-01

    Mitotic chromosome segregation is orchestrated by the dynamic interaction of spindle microtubules with the kinetochores. During chromosome alignment, kinetochore-bound microtubules undergo dynamic cycles between growth and shrinkage, leading to an oscillatory movement of chromosomes along the spindle axis. Although kinetochore protein CENP-H serves as a molecular control of kinetochore-microtubule dynamics, the mechanistic link between CENP-H and kinetochore microtubules (kMT) has remained less characterized. Here, we show that CSPP1 is a kinetochore protein essential for accurate chromosome movements in mitosis. CSPP1 binds to CENP-H in vitro and in vivo. Suppression of CSPP1 perturbs proper mitotic progression and compromises the satisfaction of spindle assembly checkpoint. In addition, chromosome oscillation is greatly attenuated in CSPP1-depleted cells, similar to what was observed in the CENP-H-depleted cells. Importantly, CSPP1 depletion enhances velocity of kinetochore movement, and overexpression of CSPP1 decreases the speed, suggesting that CSPP1 promotes kMT stability during cell division. Specific perturbation of CENP-H/CSPP1 interaction using a membrane-permeable competing peptide resulted in a transient mitotic arrest and chromosome segregation defect. Based on these findings, we propose that CSPP1 cooperates with CENP-H on kinetochores to serve as a novel regulator of kMT dynamics for accurate chromosome segregation.

  9. A Vondrak Low Pass Filter for IMU Sensor Initial Alignment on a Disturbed Base

    Directory of Open Access Journals (Sweden)

    Zengke Li

    2014-12-01

    Full Text Available The initial alignment of the Inertial Measurement Unit (IMU is an important process of INS to determine the coordinate transformation matrix which is used in the integration of Global Positioning Systems (GPS with Inertial Navigation Systems (INS. In this paper a novel alignment method for a disturbed base, such as a vehicle disturbed by wind outdoors, implemented with the aid of a Vondrak low pass filter, is proposed. The basic principle of initial alignment including coarse alignment and fine alignment is introduced first. The spectral analysis is processed to compare the differences between the characteristic error of INS force observation on a stationary base and on disturbed bases. In order to reduce the high frequency noise in the force observation more accurately and more easily, a Vondrak low pass filter is constructed based on the spectral analysis result. The genetic algorithms method is introduced to choose the smoothing factor in the Vondrak filter and the corresponding objective condition is built. The architecture of the proposed alignment method with the Vondrak low pass filter is shown. Furthermore, simulated experiments and actual experiments were performed to validate the new algorithm. The results indicate that, compared with the conventional alignment method, the Vondrak filter could eliminate the high frequency noise in the force observation and the proposed alignment method could improve the attitude accuracy. At the same time, only one parameter needs to be set, which makes the proposed method easier to implement than other low-pass filter methods.

  10. Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Shunichi Kosugi

    Full Text Available Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in 'targeted' alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.

  11. Measures of frontal plane lower limb alignment obtained from static radiographs and dynamic gait analysis.

    Science.gov (United States)

    Hunt, Michael A; Birmingham, Trevor B; Jenkyn, Thomas R; Giffin, J Robert; Jones, Ian C

    2008-05-01

    Currently, lower limb alignment is measured statically from radiographs that may not accurately represent the condition of the limb when moving and weight-bearing. Thus, the purpose of the present study was to introduce and examine a novel measure of dynamic lower limb alignment obtained during walking in patients with knee OA. In this cross-sectional study, standing, full-length lower limb radiographs were acquired from 80 individuals with confirmed knee OA, who also underwent three-dimensional gait analyses with reflective markers placed on the segments of the lower limb. Frontal plane lower limb alignment was measured using the static radiographs (mechanical axis) and gait analyses (marker-based alignment) by identifying the centres of the hip, knee, and ankle from both methods. Simple linear regression indicated these measures were highly correlated (r=0.84), however, 30% of the variance in the marker-based measure of lower limb alignment was not explained by the mechanical axis despite using the same anatomical landmarks. Results from this study suggest that a valid measure of dynamic lower limb alignment can be obtained from a standard quantitative gait analysis and highlight the differences in measures of lower limb alignment obtained in static and dynamic situations. Future research into the clinical utility of measures of dynamic alignment in the treatment of OA may aid in the development of interventions specifically tailored to one's dynamic lower limb biomechanics during gait.

  12. Alignment of wave functions for angular momentum projection

    CERN Document Server

    Taniguchi, Yasutaka

    2016-01-01

    Angular momentum projection is used to obtain eigen states of angular momentum from general wave functions. Multi-configuration mixing calculation with angular momentum projection is an important microscopic method in nuclear physics. For accurate multi-configuration mixing calculation with angular momentum projection, concentrated distribution of $z$ components $K$ of angular momentum in the body-fixed frame ($K$-distribution) is favored. Orientation of wave functions strongly affects $K$-distribution. Minimization of variance of $\\hat{J}_z$ is proposed as an alignment method to obtain wave functions that have concentrated $K$-distribution. Benchmark calculations are performed for $\\alpha$-$^{24}$Mg cluster structure, triaxially superdeformed states in $^{40}$Ar, and Hartree-Fock states of some nuclei. The proposed alignment method is useful and works well for various wave functions to obtain concentrated $K$-distribution.

  13. A More Accurate Fourier Transform

    CERN Document Server

    Courtney, Elya

    2015-01-01

    Fourier transform methods are used to analyze functions and data sets to provide frequencies, amplitudes, and phases of underlying oscillatory components. Fast Fourier transform (FFT) methods offer speed advantages over evaluation of explicit integrals (EI) that define Fourier transforms. This paper compares frequency, amplitude, and phase accuracy of the two methods for well resolved peaks over a wide array of data sets including cosine series with and without random noise and a variety of physical data sets, including atmospheric $\\mathrm{CO_2}$ concentrations, tides, temperatures, sound waveforms, and atomic spectra. The FFT uses MIT's FFTW3 library. The EI method uses the rectangle method to compute the areas under the curve via complex math. Results support the hypothesis that EI methods are more accurate than FFT methods. Errors range from 5 to 10 times higher when determining peak frequency by FFT, 1.4 to 60 times higher for peak amplitude, and 6 to 10 times higher for phase under a peak. The ability t...

  14. AGORA: Assembly Guided by Optical Restriction Alignment

    Directory of Open Access Journals (Sweden)

    Lin Henry C

    2012-08-01

    Full Text Available Abstract Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs. Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. However, optical maps have not previously been used within the genome assembly process. Here, we use optical map information within the popular de Bruijn graph assembly paradigm to eliminate paths in the de Bruijn graph which are not consistent with the optical map and help determine the correct reconstruction of the genome. Results We developed a new algorithm called AGORA: Assembly Guided by Optical Restriction Alignment. AGORA is the first algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. Our simulations on bacterial genomes show that AGORA is effective at producing assemblies closely matching the reference sequences. Additionally, we show that noise in the optical map can have a strong impact on the final assembly quality for some complex genomes, and we also measure how various characteristics of the starting de Bruijn graph may impact the quality of the final assembly. Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly. Conclusions Our work shows that optical maps can be used effectively to assemble genomes within the de Bruijn graph assembly framework. Our experiments also provide insights into the characteristics of the mapping data that most affect the performance of our algorithm, indicating the

  15. Photogeneration and enhanced charge transport in aligned smectic liquid crystalline organic semiconductor

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Sanjoy; Ellman, Brett, E-mail: bellman@kent.edu [Department of Physics, Kent State University, Kent, Ohio 44242 (United States); Tripathi, Suvagata; Twieg, Robert J. [Department of Chemistry, Kent State University, Kent, Ohio 44242 (United States)

    2015-10-07

    Liquid crystalline organic semiconductors are emerging candidates for applications in electronic and photonic devices. One of the most attractive aspects of such materials is the potential, in principle, to easily control and manipulate the molecular alignment of the semiconductor over large length scales. Here, we explore the consequences of alignment in a model smectic liquid crystalline semiconductor, and find that the photogeneration efficiency is a strong function of incident polarization in aligned samples. A straightforward theory shows that such behavior is a general feature of aligned materials, regardless of the details of photophysics. Furthermore, we uncover tentative evidence that the mobility of aligned samples is substantially enhanced. Both of these phenomena are of significant technological importance.

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

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    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...... alignment by 'reverse translation' of the aligned protein sequences. In the resulting DNA alignment, gaps occur in groups of three corresponding to entire codons, and analogous codon positions are therefore always lined up. These features are useful when constructing multiple DNA alignments for phylogenetic...

  17. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2007-07-01

    Full Text Available Abstract Background Antigen presenting cells (APCs sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC and three mouse H2-IA alleles. Results The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR, we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. Conclusion

  18. Molecular characterisation of Brucella species.

    Science.gov (United States)

    Scholz, H C; Vergnaud, G

    2013-04-01

    The genus Brucella (Mayer and Shaw, 1920) currently consists often species with validly published names. Within most species further differentiation into biovars exists. Genetically, all Brucella species are highly related to each other, exhibiting sequence similarity values of 98% to 100% in aligned regions (core genome). The population structure is clonal. Despite this close genetic relatedness, the various species can be clearly distinguished from each other by application of high-resolution molecular typing tools, in addition to assessment of phenotype and host preference. Accurate species delineation can be achieved by conventional multiplex polymerase chain reaction (PCR), single nucleotide polymorphism (SNP) analysis and multilocus sequence typing (MLST) or multilocus sequence analysis (MLSA). The last is also suitable for phylogenetic reconstructions, owing to the highly clonal evolution of the different species. Highly discriminatory multilocus variable number of tandem repeats (VNTR) analysis (MLVA) allows both species delineation and differentiation of individual isolates and thus represents a perfect first-line toolfor molecular epidemiological studies within outbreak investigations. More recently,whole genome sequencing (WGS)and the resulting global genome-wide SNP analysis have become available. These novel approaches should help in further understanding the evolution, host specificity and pathogenicity of the genus Brucella.

  19. Stark-selected beam of ground-state OCS molecules characterized by revivals of impulsive alignment

    CERN Document Server

    Nielsen, Jens H; Bisgaard, Christer Z; Stapelfeldt, Henrik; Filsinger, Frank; Friedrich, Bretislav; Meijer, Gerard; Küpper, Jochen

    2011-01-01

    We make use of an inhomogeneous electrostatic dipole field to impart a quantum-state-dependent deflection to a pulsed beam of OCS molecules, and show that those molecules residing in the absolute ground state, $X ^1\\Sigma^+$, $\\ket{00^00}$, J=0, can be separated out by selecting the most deflected part of the molecular beam. Past the deflector, we irradiate the molecular beam by a linearly polarized pulsed nonresonant laser beam that impulsively aligns the OCS molecules. Their alignment, monitored via velocity-map imaging, is measured as a function of time, and the time dependence of the alignment is used to determine the quantum state composition of the beam. We find significant enhancements of the alignment (\\costhetasqtd $= 0.84$) and of state purity ($> 92$%) for a state-selected, deflected beam compared with an undeflected beam.

  20. Galaxy alignments: Theory, modelling and simulations

    CERN Document Server

    Kiessling, Alina; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L; Rassat, Anais

    2015-01-01

    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 large-scale structure tend to align the shapes and angular momenta of nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments 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 ...

  1. Aligning Sequences by Minimum Description Length

    Directory of Open Access Journals (Sweden)

    John S. Conery

    2008-01-01

    Full Text Available This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions of similarity in the sequences. To retrieve the original set of sequences, a receiver generates all strings that match the expression. An alignment algorithm uses minimum description length to encode and explore alternative expressions; the expression with the shortest encoding provides the best overall alignment. When two substrings contain letters that are similar according to a substitution matrix, a code length function based on conditional probabilities defined by the matrix will encode the substrings with fewer bits. In one experiment, alignments produced with this new method were found to be comparable to alignments from CLUSTALW. A second experiment measured the accuracy of the new method on pairwise alignments of sequences from the BAliBASE alignment benchmark.

  2. Pupil Alignment Measuring Technique and Alignment Reference for Instruments or Optical Systems

    Science.gov (United States)

    Hagopian, John G.

    2010-01-01

    A technique was created to measure the pupil alignment of instruments in situ by measuring calibrated pupil alignment references (PARs) in instruments. The PAR can also be measured using an alignment telescope or an imaging system. PAR allows the verification of the science instrument (SI) pupil alignment at the integrated science instrument module (ISIM) level of assembly at ambient and cryogenic operating temperature. This will allow verification of the ISIM+SI alignment, and provide feedback to realign the SI if necessary.

  3. NON-ALIGNEMENT IN AFRICA

    Directory of Open Access Journals (Sweden)

    G. Jacobs

    2012-02-01

    Full Text Available The first indications to the Western world that African non-alignment had achieved conscious political form became apparent only in the late 1940's. This strand of thought within the tapestry of Africanism reached its zenith with the declarations of Kwame Nkrumah, Jomo Kenyatta and Julius Nyerere in the years after the Pan-African Congress in Manchester in 1945. The causes of the movement go back far beyond the first official expressions of an African solidarity in the 1940's. As a mature expression of group attitudes tqwards foreign pol icy, nonalignment can be traced back to the roots of African nationalism.

  4. The Cluster Substructure - Alignment Connection

    CERN Document Server

    Plionis, M

    2002-01-01

    Using the APM cluster data we investigate whether the dynamical status of clusters is related to the large-scale structure of the Universe. We find that cluster substructure is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically young clusters are more clustered than the overall cluster population. These are strong indications that cluster develop in a hierarchical fashion by anisotropy merging along the large-scale filamentary superclusters within which they are embedded.

  5. The Substructure-Alignment Connection

    CERN Document Server

    Plionis, M; Plionis, Manolis; Basilakos, Spyros

    2001-01-01

    Using a sample of 903 APM clusters we investigate whether their dynamical status, as evidenced by the presence of significant substructures, is related to the large-scale structure of the Universe. We find that the cluster dynamical activity is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically active clusters are more clustered than the overall cluster population. These are strong indications that clusters develop in a hierarchical fashion by anisotropic merging along the large-scale filaments within which they are embedded.

  6. Automated quantification of aligned collagen for human breast carcinoma prognosis

    Directory of Open Access Journals (Sweden)

    Jeremy S Bredfeldt

    2014-01-01

    Full Text Available Background: Mortality in cancer patients is directly attributable to the ability of cancer cells to metastasize to distant sites from the primary tumor. This migration of tumor cells begins with a remodeling of the local tumor microenvironment, including changes to the extracellular matrix and the recruitment of stromal cells, both of which facilitate invasion of tumor cells into the bloodstream. In breast cancer, it has been proposed that the alignment of collagen fibers surrounding tumor epithelial cells can serve as a quantitative image-based biomarker for survival of invasive ductal carcinoma patients. Specific types of collagen alignment have been identified for their prognostic value and now these tumor associated collagen signatures (TACS are central to several clinical specimen imaging trials. Here, we implement the semi-automated acquisition and analysis of this TACS candidate biomarker and demonstrate a protocol that will allow consistent scoring to be performed throughout large patient cohorts. Methods: Using large field of view high resolution microscopy techniques, image processing and supervised learning methods, we are able to quantify and score features of collagen fiber alignment with respect to adjacent tumor-stromal boundaries. Results: Our semi-automated technique produced scores that have statistically significant correlation with scores generated by a panel of three human observers. In addition, our system generated classification scores that accurately predicted survival in a cohort of 196 breast cancer patients. Feature rank analysis reveals that TACS positive fibers are more well-aligned with each other, are of generally lower density, and terminate within or near groups of epithelial cells at larger angles of interaction. Conclusion: These results demonstrate the utility of a supervised learning protocol for streamlining the analysis of collagen alignment with respect to tumor stromal boundaries.

  7. Strategies for active alignment of lenses

    Science.gov (United States)

    Langehanenberg, Patrik; Heinisch, Josef; Wilde, Chrisitan; Hahne, Felix; Lüerß, Bernd

    2015-10-01

    Today's optical systems require up-to-date assembly and joining technology. The trend of keeping dimensions as small as possible while maintaining or increasing optical imaging performance leaves little to no room for mechanical lens adjustment equipment that may remain in the final product. In this context active alignment of optical elements opens up possibilities for the fast and cost-economic manufacturing of lenses and lens assemblies with highest optical performance. Active alignment for lens manufacturing is the precise alignment of the optical axis of a lens with respect to an optical or mechanical reference axis (e.g. housing) including subsequent fixation by glue. In this contribution we will describe different approaches for active alignment and outline strengths and limitations of the different methods. Using the SmartAlign principle, highest quality cemented lenses can be manufactured without the need for high precision prealignment, while the reduction to a single alignment step greatly reduces the cycle time. The same strategies can also be applied to bonding processes. Lenses and lens groups can be aligned to both mechanical and optical axes to maximize the optical performance of a given assembly. In hybrid assemblies using both mechanical tolerances and active alignment, SmartAlign can be used to align critical lens elements anywhere inside the system for optimized total performance. Since all geometrical parameters are re-measured before each alignment, this process is especially suited for complex and time-consuming production processes where the stability of the reference axis would otherwise be critical. For highest performance, lenses can be actively aligned using up to five degrees of freedom. In this way, SmartAlign enables the production of ultra-precise mounted lenses with an alignment precision below 1 μm.

  8. The propensity of molecules to spatially align in intense light fields

    CERN Document Server

    Banerjee, S; Kumar, G R

    2001-01-01

    The propensity of molecules to spatially align along the polarization vector of intense, pulsed light fields is related to readily-accessible parameters (molecular polarizabilities, moment of inertia, peak intensity of the light and its pulse duration). Predictions can now be made of which molecules can be spatially aligned, and under what circumstances, upon irradiation by intense light. Accounting for both enhanced ionization and hyperpolarizability, it is shown that {\\it all} molecules can be aligned, even those with the smallest static polarizability, when subjected to the shortest available laser pulses (of sufficient intensity).

  9. Electronic states of model hydrocarbon chromophores investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy on aligned samples

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Hoffmann, Søren Vrønning; Jones, Nykola;

    2010-01-01

    Conventional UV-VIS absorption spectroscopy provides information on transition energies and intensities. Linear dichroism (LD) spectroscopy on aligned molecular samples yields additional information on transition moment directions, thereby frequently leading to resolution of otherwise overlapping...

  10. Accurate free energy calculation along optimized paths.

    Science.gov (United States)

    Chen, Changjun; Xiao, Yi

    2010-05-01

    The path-based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10-ALA peptide and find that the calculated free energy changes in helix-helix and helix-hairpin transitions are both self-convergent and cross-convergent. We also calculate the free energy differences between different stable states of beta-hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation.

  11. A DNA sequence alignment algorithm using quality information and a fuzzy inference method

    Institute of Scientific and Technical Information of China (English)

    Kwangbaek Kim; Minhwan Kim; Youngwoon Woo

    2008-01-01

    DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods.In this paper.We propose a DNA sequence alignment that Uses quality information and a fuzzy inference method developed based on the characteristics of DNA fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods that uses DNA sequence quality information.In conventional algorithms.DNA sequence alignment scores are calculated by the global sequence alignment algorithm proposed by Needleman-Wunsch,which is established by using quality information of each DNA fragment.However,there may be errors in the process of calculating DNA sequence alignment scores when the quality of DNA fragment tips is low.because only the overall DNA sequence quality information are used.In our proposed method.an exact DNA sequence alignment can be achieved in spite of the low quality of DNA fragment tips by improvement of conventional algorithms using quality information.Mapping score parameters used to calculate DNA sequence alignment scores are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments.From the experiments by applying real genome data of National Center for Bioteclmology Information,we could see that the proposed method is more efficient than conventional algorithms.

  12. Galaxy alignment on large and small scales

    Science.gov (United States)

    Kang, X.; Lin, W. P.; Dong, X.; Wang, Y. O.; Dutton, A.; Macciò, A.

    2016-10-01

    Galaxies are not randomly distributed across the universe but showing different kinds of alignment on different scales. On small scales satellite galaxies have a tendency to distribute along the major axis of the central galaxy, with dependence on galaxy properties that both red satellites and centrals have stronger alignment than their blue counterparts. On large scales, it is found that the major axes of Luminous Red Galaxies (LRGs) have correlation up to 30Mpc/h. Using hydro-dynamical simulation with star formation, we investigate the origin of galaxy alignment on different scales. It is found that most red satellite galaxies stay in the inner region of dark matter halo inside which the shape of central galaxy is well aligned with the dark matter distribution. Red centrals have stronger alignment than blue ones as they live in massive haloes and the central galaxy-halo alignment increases with halo mass. On large scales, the alignment of LRGs is also from the galaxy-halo shape correlation, but with some extent of mis-alignment. The massive haloes have stronger alignment than haloes in filament which connect massive haloes. This is contrary to the naive expectation that cosmic filament is the cause of halo alignment.

  13. Redshift and luminosity evolution of the intrinsic alignments of galaxies in Horizon-AGN

    Science.gov (United States)

    Chisari, N.; Laigle, C.; Codis, S.; Dubois, Y.; Devriendt, J.; Miller, L.; Benabed, K.; Slyz, A.; Gavazzi, R.; Pichon, C.

    2016-09-01

    Intrinsic galaxy shape and angular momentum alignments can arise in cosmological large-scale structure due to tidal interactions or galaxy formation processes. Cosmological hydrodynamical simulations have recently come of age as a tool to study these alignments and their contamination to weak gravitational lensing. We probe the redshift and luminosity evolution of intrinsic alignments in Horizon-AGN between z = 0 and 3 for galaxies with an r-band absolute magnitude of Mr ≤ -20. Alignments transition from being radial at low redshifts and high luminosities, dominated by the contribution of ellipticals, to being tangential at high redshift and low luminosities, where discs dominate the signal. This cannot be explained by the evolution of the fraction of ellipticals and discs alone: intrinsic evolution in the amplitude of alignments is necessary. The alignment amplitude of elliptical galaxies alone is smaller in amplitude by a factor of ≃2, but has similar luminosity and redshift evolution as in current observations and in the non-linear tidal alignment model at projected separations of ≳1 Mpc. Alignments of discs are null in projection and consistent with current low-redshift observations. The combination of the two populations yields an overall amplitude a factor of ≃4 lower than observed alignments of luminous red galaxies with a steeper luminosity dependence. The restriction on accurate galaxy shapes implies that the galaxy population in the simulation is complete only to Mr ≤ -20. Higher resolution simulations will be necessary to avoid extrapolation of the intrinsic alignment predictions to the range of luminosities probed by future surveys.

  14. Correlated Terahertz and High Harmonic Generation from Aligned Nitrogen Molecules

    Science.gov (United States)

    Huang, Yindong; Meng, Chao; Wang, Xiaowei; Lv, Zhihui; Zhang, Dongwen; Chen, Wenbo; Zhao, Jing; Yuan, Jianmin; Zhao, Zengxiu

    2016-05-01

    When laser beams are focused on atoms and molecules, wide spectral range of photons can be radiated from the source. In the region of high energy, high harmonic generation (HHG), covering tens to hundreds electron volts, emit within the attosecond timescale. In the low energy region, terahertz wave generation (TWG) can also be generated. Synchronizing TWG with HHG is to take snapshot of the electronic dynamics with time-scale spanning over 6 orders of magnitudes. In this abstract, we report the joint measurements on TWG and HHG from pre-aligned molecules. By calibrating the angular ionization rates with the alignment dependent TWG, we reconstruct the photoionization cross section (PICS) of nitrogen in one run of experiment. The measured PICS is found to be consistent with theoretical predications, although some discrepancies exist. This all-optical method provides a new alternative for investigating molecular structures (Yindong Huang et al., Phys. Rev. Lett. 115, 123002, 2015).

  15. Theory for the alignment of cortical feature maps during development

    KAUST Repository

    Bressloff, Paul C.

    2010-08-23

    We present a developmental model of ocular dominance column formation that takes into account the existence of an array of intrinsically specified cytochrome oxidase blobs. We assume that there is some molecular substrate for the blobs early in development, which generates a spatially periodic modulation of experience-dependent plasticity. We determine the effects of such a modulation on a competitive Hebbian mechanism for the modification of the feedforward afferents from the left and right eyes. We show how alternating left and right eye dominated columns can develop, in which the blobs are aligned with the centers of the ocular dominance columns and receive a greater density of feedforward connections, thus becoming defined extrinsically. More generally, our results suggest that the presence of periodically distributed anatomical markers early in development could provide a mechanism for the alignment of cortical feature maps. © 2010 The American Physical Society.

  16. 38 CFR 4.46 - Accurate measurement.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  17. Planar self-aligned imprint lithography for coplanar plasmonic nanostructures fabrication

    KAUST Repository

    Wan, Weiwei

    2014-03-01

    Nanoimprint lithography (NIL) is a cost-efficient nanopatterning technology because of its promising advantages of high throughput and high resolution. However, accurate multilevel overlay capability of NIL required for integrated circuit manufacturing remains a challenge due to the high cost of achieving mechanical alignment precision. Although self-aligned imprint lithography was developed to avoid the need of alignment for the vertical layered structures, it has limited usage in the manufacture of the coplanar structures, such as integrated plasmonic devices. In this paper, we develop a new process of planar self-alignment imprint lithography (P-SAIL) to fabricate the metallic and dielectric structures on the same plane. P-SAIL transfers the multilevel imprint processes to a single-imprint process which offers higher efficiency and less cost than existing manufacturing methods. Such concept is demonstrated in an example of fabricating planar plasmonic structures consisting of different materials. © 2014 Springer-Verlag Berlin Heidelberg.

  18. Program for PET image alignment: Effects on calculated differences in cerebral metabolic rates for glucose

    International Nuclear Information System (INIS)

    A program was developed to align positron emission tomography images from multiple studies on the same subject. The program allowed alignment of two images with a fineness of one-tenth the width of a pixel. The indications and effects of misalignment were assessed in eight subjects from a placebo-controlled double-blind crossover study on the effects of cocaine on regional cerebral metabolic rates for glucose. Visual examination of a difference image provided a sensitive and accurate tool for assessing image alignment. Image alignment within 2.8 mm was essential to reduce variability of measured cerebral metabolic rates for glucose. Misalignment by this amount introduced errors on the order of 20% in the computed metabolic rate for glucose. These errors propagate to the difference between metabolic rates for a subject measured in basal versus perturbed states

  19. Molecular alignment and orientation in short pulse laser fields

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1999-01-01

    An analytical expression for the propagator associated with impulsive excitation is derived based on the Magnus expansion. We apply this expression to the excitation of angular motion out of a rotational eigenstate for a linear polar molecule in a plane polarized electromagnetic field. We show...

  20. Galaxy alignments: Observations and impact on cosmology

    CERN Document Server

    Kirk, Donnacha; Hoekstra, Henk; Joachimi, Benjamin; Kitching, Thomas D; Mandelbaum, Rachel; Sifón, Cristóbal; Cacciato, Marcello; Choi, Ami; Kiessling, Alina; Leonard, Adrienne; Rassat, Anais; Schäfer, Björn Malte

    2015-01-01

    Galaxy shapes are not randomly oriented, rather they are statistically aligned in a way that can depend on formation environment, history and galaxy type. Studying the alignment of galaxies can therefore deliver important information about the astrophysics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of intrinsic alignments, divided by galaxy type, scale and environment. We also cover the statistics and formalism necessary to understand the observations in the literature. With the emergence of weak gravitational lensing as a precision probe of cosmology, galaxy alignments took on an added importance because they can mimic cosmic shear, the effect of gravitational lensing by large-scale structure on observed galaxy shapes. This makes intrinsic alignments an important systematic effect in weak lensing studies. We quantify the impact of intrinsic alignments on cosmic shear surveys and finish by reviewing practical mitigat...

  1. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.;

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment...... methods to misalign, or even refuse to align, homologous ncRNAs, consequently obscuring that structural signal. We have used CMfinder, a structure-oriented local alignment tool, to search the ENCODE regions of vertebrate multiple alignments. In agreement with other studies, we find a large number...... of potential RNA structures in the ENCODE regions. We report 6587 candidate regions with an estimated false-positive rate of 50%. More intriguingly, many of these candidates may be better represented by alignments taking the RNA secondary structure into account than those based on primary sequence alone, often...

  2. Self-transport and self-alignment of microchips using microscopic rain

    Science.gov (United States)

    Chang, Bo; Shah, Ali; Zhou, Quan; Ras, Robin H. A.; Hjort, Klas

    2015-10-01

    Alignment of microchips with receptors is an important process step in the construction of integrated micro- and nanosystems for emerging technologies, and facilitating alignment by spontaneous self-assembly processes is highly desired. Previously, capillary self-alignment of microchips driven by surface tension effects on patterned surfaces has been reported, where it was essential for microchips to have sufficient overlap with receptor sites. Here we demonstrate for the first time capillary self-transport and self-alignment of microchips, where microchips are initially placed outside the corresponding receptor sites and can be self-transported by capillary force to the receptor sites followed by self-alignment. The surface consists of hydrophilic silicon receptor sites surrounded by superhydrophobic black silicon. Rain-induced microscopic droplets are used to form the meniscus for the self-transport and self-alignment. The boundary conditions for the self-transport have been explored by modeling and confirmed experimentally. The maximum permitted gap between a microchip and a receptor site is determined by the volume of the liquid and by the wetting contrast between receptor site and substrate. Microscopic rain applied on hydrophilic-superhydrophobic patterned surfaces greatly improves the capability, reliability and error-tolerance of the process, avoiding the need for accurate initial placement of microchips, and thereby greatly simplifying the alignment process.

  3. Island method for estimating the statistical significance of profile-profile alignment scores

    Directory of Open Access Journals (Sweden)

    Poleksic Aleksandar

    2009-04-01

    Full Text Available Abstract Background In the last decade, a significant improvement in detecting remote similarity between protein sequences has been made by utilizing alignment profiles in place of amino-acid strings. Unfortunately, no analytical theory is available for estimating the significance of a gapped alignment of two profiles. Many experiments suggest that the distribution of local profile-profile alignment scores is of the Gumbel form. However, estimating distribution parameters by random simulations turns out to be computationally very expensive. Results We demonstrate that the background distribution of profile-profile alignment scores heavily depends on profiles' composition and thus the distribution parameters must be estimated independently, for each pair of profiles of interest. We also show that accurate estimates of statistical parameters can be obtained using the "island statistics" for profile-profile alignments. Conclusion The island statistics can be generalized to profile-profile alignments to provide an efficient method for the alignment score normalization. Since multiple island scores can be extracted from a single comparison of two profiles, the island method has a clear speed advantage over the direct shuffling method for comparable accuracy in parameter estimates.

  4. Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+.

    Directory of Open Access Journals (Sweden)

    Jorge González-Domínguez

    Full Text Available The growth of next-generation sequencing (NGS datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the CUSHAW3 aligner show that our implementation based on dynamic scheduling obtains good scalability on multi-core clusters. Through our evaluation, we are able to complete the single-end and paired-end alignments of 246 million reads of length 150 base-pairs in 11.54 and 16.64 minutes, respectively, using 32 nodes with four AMD Opteron 6272 16-core CPUs per node. In contrast, the multi-threaded original tool needs 2.77 and 5.54 hours to perform the same alignments on the 64 cores of one node. The source code of our parallel implementation is publicly available at the CUSHAW3 homepage (http://cushaw3.sourceforge.net.

  5. A distributed system for fast alignment of next-generation sequencing data

    Science.gov (United States)

    Srimani, Jaydeep K.; Wu, Po-Yen; Phan, John H.; Wang, May D.

    2016-01-01

    We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

  6. Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+.

    Science.gov (United States)

    González-Domínguez, Jorge; Liu, Yongchao; Schmidt, Bertil

    2016-01-01

    The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the CUSHAW3 aligner show that our implementation based on dynamic scheduling obtains good scalability on multi-core clusters. Through our evaluation, we are able to complete the single-end and paired-end alignments of 246 million reads of length 150 base-pairs in 11.54 and 16.64 minutes, respectively, using 32 nodes with four AMD Opteron 6272 16-core CPUs per node. In contrast, the multi-threaded original tool needs 2.77 and 5.54 hours to perform the same alignments on the 64 cores of one node. The source code of our parallel implementation is publicly available at the CUSHAW3 homepage (http://cushaw3.sourceforge.net). PMID:26731399

  7. Recursions for Statistical Multiple Alignment

    DEFF Research Database (Denmark)

    Hein, Jotun; Pedersen, Christian Nørgaard Storm; Jensen, Jens Ledet

    2002-01-01

    Algorithms are presented that allow the calculation of the probability of a set of sequences related by a binary tree that have evolved according to the Thorne–Kishino–Felsenstein model for a fixed set of parameters. The algorithms are based on a Markov chain generating sequences and their alignm...... but probabilistically different. The running time of the algorithms is , where Li is the length of the ith observed sequences and d is the number of sequences. An alternative recursion is also formulated that uses only a Markov chain involving the inner nodes of a tree....... and their alignment at nodes in a tree. Depending on whether the complete realization of this Markov chain is decomposed into the first transition and the rest of the realization or the last transition and the first part of the realization, two kinds of recursions are obtained that are computationally similar...

  8. Fiscal State-Citizen Alignment

    DEFF Research Database (Denmark)

    Celik, Tim Holst

    2016-01-01

    to the 2008 crisis and the larger post-1970s politico-economic constellation. The crisis can be perceived as a particular articulation of an age-old state-household dynamic—a dialectical alignment of the mode of fiscal state-crafting with the ethos of the state-citizen nexus—characterized by a heightened......The 2008 crisis ended the growth bubble of the 2000s, which Organisation for Economic Co-operation and Development (OECD) governments facilitated through the normative/political-regulatory promotion of household indebtedness. Historically contextualizing this state-citizen relationship......, this article maps out four episodes of sovereign fiscalism, namely, debt-taking in the Italian city-states, the making of the absolutist tax/fiscal state, the eighteenth/nineteenth century elaboration of the economic citizen, and the postwar era of managed capitalism. Finally, it applies this framework...

  9. Using Student Reflections to Explore Curriculum Alignment

    OpenAIRE

    Marina Harvey; Chris Baumann

    2012-01-01

    The concept of curriculum alignment is held as a guiding principle of good curriculum design in higher education. Curriculum alignment can be mapped using a variety of strategies and tools. This paper reports on a project that expands the horizons of curriculum review by applying a novel methodology, word clouds, to investigate the use of student reflections for exploring curriculum alignment.Students, from Australia and Denmark, engaged in written reflections about their learning in a Busine...

  10. Measurement of alignment between standards and assessment

    OpenAIRE

    Näsström, Gunilla

    2008-01-01

    Many educational systems of today are standards-based and aim at for alignment, i.e. consistency, among the components of the educational system: standards, teaching and assessment. To conclude whether the alignment is sufficiently high, analyses with a useful model are needed. This thesis investigates the usefulness of models for analyzing alignment between standards and assessments, with emphasis on one method: Bloom’s revised taxonomy. The thesis comprises an introduction and five articles...

  11. FUSE: Multiple Network Alignment via Data Fusion

    OpenAIRE

    Gligorijević, Vladimir; Malod-Dognin, Noël; Pržulj, Nataša

    2014-01-01

    Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. The objective of a multiple network alignment is to create clusters of nodes that are evolutionarily conserved and functionally consistent across all networks. Unfortunately, the alignment methods ...

  12. Alignment performance monitoring for ASML systems

    Science.gov (United States)

    Chung, Woong-Jae; Temchenko, Vlad; Hauck, Tarja; Schmidt, Sebastian

    2006-03-01

    In today's semiconductor industry downscaling of the IC design puts a stringent requirement on pattern overlay control. Tighter overlay requirements lead to exceedingly higher rework rates, meaning additional costs to manufacturing. Better alignment control became a target of engineering efforts to decrease rework rate for high-end technologies. Overlay performance is influenced by known parameters such as "Shift, Scaling, Rotation, etc", and unknown parameters defined as "Process Induced Variation", which are difficult to control by means of a process automation system. In reality, this process-induced variation leads to a strong wafer to wafer, or lot to lot variation, which are not easy to detect in the mass-production environment which uses sampling overlay measurements for only several wafers in a lot. An engineering task of finding and correcting a root cause for Process Induced Variations of overlay performance will be greatly simplified if the unknown parameters could be tracked for each wafer. This paper introduces an alignment performance monitoring method based on analysis of automatically generated "AWE" files for ASML scanner systems. Because "AWE" files include alignment results for each aligned wafer, it is possible to use them for monitoring, controlling and correcting the causes of "process induced" overlay performance without requiring extra measurement time. Since "AWE" files include alignment information for different alignment marks, it is also possible to select and optimize the best alignment recipe for each alignment strategy. Several case studies provided in our paper will demonstrate how AWE file analysis can be used to assist engineer in interpreting pattern alignment data. Since implementing our alignment data monitoring method, we were able to achieve significant improvement of alignment and overlay performance without additional overlay measurement time. We also noticed that the rework rate coming from alignment went down and

  13. COS to FGS Alignment {NUV}

    Science.gov (United States)

    Hartig, George

    2009-07-01

    DESCRIPTION: In order to determine the location of the COS reference frame with respect to the FGS reference frames, NUV MIRRORA images will be obtained of an astrometric target and field. Astrometric guide stars and targets must be employed for this activity in order to facilitate the alignment wth the FGS. Images will be obtained at the initial pointing and at positions offset in V2 and in V3. Starting with the original blind pointing, obtain MIRRORA image exposures in a 5x5 POS-TARG grid centered on initial pointing; repeat the image sequence at two bracketing focus positions in same visit. Following completion of third pattern, return to nominal focus and perform 5x5 ACQ/SEARCH target acquisition and obtain one TIME-TAG MIRRORA image and one ACCUM verification exposure. Next perform an ACQ/IMAGE target acquisition followed by an ACCUM verification exposure. Also obtain ACCUM verification exposure for each of the two alternate focus positions used previously. Using MIRRORB obtain ACCUM confirmation image at nominal focus and ACCUM images at alternate focus positions and then perform an ACQ/IMAGE and confirming image at nominal focus. Analyze imagery, uplink pointing offset as offset 11469A and adjust nominal focus via patchable constant uplinked with subsequent visit of this program; update aperture locations via modified SIAF file uplinked with subsequent SMS. Use updated focus and offset pointing as input for COS 09 {program 11469 - NUV Optics Alignment and Focus} {note the SIAF update is not a prerequisite for COS 09 to proceed, but the pointing offset and focus update are}.

  14. Installation and Alignment of Neutron Guides for In-pile Plug Assembly and Primary Shutter

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jin Won; Cho, Yeong Garp [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2008-12-15

    The HANARO will be equipped with a neutron guide system, in order to transport cold neutrons from the neutron source to the neutron scattering instruments in the neutron guide hall near the reactor building. The neutron guide system of HANARO consists of the in-pile plug assembly with in-pile guides, the primary shutter with in-shutter guides, the neutron guides in the guide shielding room with dedicated secondary shutters, and the neutron guides connected to the instruments in the neutron guide hall. Neutron guides have rectangular shapes of glass which is specially coated inside by Ni and Ti. It is very important to align neutron guides accurately in order to minimize a loss of cold neutrons which are transferred to scattering instruments. The alignment is one of significant factors together with a reflectivity and a manufacturing accuracy, which decide the performance of neutron guides. So it is necessary to develop special alignment tools and techniques to align neutron guides successfully. There is some limit of accessibility and workability to use optical measurement while aligning neutron guides of the in-pile plug assembly and the primary shutter because of a high radiation level at the CN beam port. So we adopted a laser tracker as the measurement system to align neutron guides accurately in a radiation environment. The laser tracker enables to measure coordinates of neutron guides at far and offset positions of the beam port. This report describes a method of neutron guides alignment for the in-pile plug assembly and the primary shutter using a laser tracker. The result of the installation and the alignment of neutron guides is also presented.

  15. Alignment of neutron guides for the in-pile plug assembly and the primary shutter

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jin Won; Cho, Yeong Garp; Cho, Sang Jin; Lee, Jung Hee [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2009-05-15

    KAERI has been developing a neutron guide system for cold neutron research facilities in HANARO since 2003. The neutron guide system plays an important role in transporting cold neutrons from the cold neutron source to the neutron scattering instruments in the neutron guide hall. A beam port assigned for the cold neutron (CN) has been used for an 8-m SANS without neutron guides until early 2008. The old instrument at the CN beam port was removed and a completely new system has been installed, which is composed of an in-pile plug assembly with in-plug guides, a primary shutter with in-shutter guides, removable shielding blocks, and a vacuum system. It is very important to align the neutron guides accurately in order to minimize a loss of cold neutrons which are transferred to scattering instruments. The alignment is one of significant factors together with a reflectivity and a manufacturing accuracy, which decide the performance of neutron guides. So it is necessary to develop special alignment tools and techniques to align the neutron guides successfully. There exist some limits of accessibility and workability to use conventional optical measurements while aligning the neutron guides for the in-pile plug assembly and the primary shutter because of a high radiation level at the CN beam port. So we adopted a laser tracker as a measurement system to align the neutron guides in a radiation environment. The accurate alignment of neutron guides was safely achieved by a laser tracker through measuring the coordinates of neutron guides at far and offset positions of the beam port. This paper presents the successful result of the installation and alignment of neutron guides for the in pile plug assembly and the primary shutter using a laser tracker.

  16. Track Based Alignment of Composite Detector Structures

    CERN Document Server

    Karimäki, V; Schilling, F P

    2006-01-01

    An iterative algorithm for track based alignment is presented. The algorithm can be applied to rigid composite detector structures or to individual modules. The iterative process involves track reconstruction and alignment, in which the chi-2 function of the hit residuals of each alignable object is minimized. Six alignment parameters per structure or per module, three for location and three for orientation, can be computed. The method is computationally light and easily parallelizable. The performance of the method is demonstrated with simulated tracks in the CMS pixel detector and tracks reconstructed from experimental data recorded with a test beam setup.

  17. The twilight zone of cis element alignments.

    Science.gov (United States)

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2013-02-01

    Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

  18. IMAGA: INTRON MULTIPLE ALIGNMENT USING GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    V. AMOUDA,

    2010-11-01

    Full Text Available Multiple sequence alignment (MSA is one of the multi-dimensional problems in biology. This paper describes a new approach to solve MSA, a NP-hard problem using modified Genetic Algorithm with new mutation operator. A web based tool iMAGA (Intron Multiple Alignment using Genetic Algorithm is developed for aligning the intron sequences in order to find the pattern. It has two modules (i iExtractor/ iClassifier which extracts and classifies introns (ii iAligner/ Pattern Finder which aligns the intron sequences and finds the patterns. iAligner, the core module of the tool aligns any type of sequences (DNA, RNA, Protein & Intron. In this module GA is applied in which the chromosome consists of gap positions. On applying conventional mutation operator leads to problems like repetition and increase in number of gap positions. To overcome theseproblems, a newly designed mutation operator X-Shuffler is proposed.To validate the alignment, the sum-of-pairs score is used to compare iMAGA with widely used tools. The data sets chosen from the standard BaliBASE, SMART and OXBENCH benchmark alignment suite. To validate the pattern obtained using iMAGA tool, the similarity percentage of the pattern is compared with MEME, a widely used motif finder. Dataset of Saccharomyces Cerviceae with 254 intron sequences are used to prove this work. The tool is available at www.imaga.bicpu.edu.in.

  19. CCD Camera Lens Interface for Real-Time Theodolite Alignment

    Science.gov (United States)

    Wake, Shane; Scott, V. Stanley, III

    2012-01-01

    Theodolites are a common instrument in the testing, alignment, and building of various systems ranging from a single optical component to an entire instrument. They provide a precise way to measure horizontal and vertical angles. They can be used to align multiple objects in a desired way at specific angles. They can also be used to reference a specific location or orientation of an object that has moved. Some systems may require a small margin of error in position of components. A theodolite can assist with accurately measuring and/or minimizing that error. The technology is an adapter for a CCD camera with lens to attach to a Leica Wild T3000 Theodolite eyepiece that enables viewing on a connected monitor, and thus can be utilized with multiple theodolites simultaneously. This technology removes a substantial part of human error by relying on the CCD camera and monitors. It also allows image recording of the alignment, and therefore provides a quantitative means to measure such error.

  20. Multimodal Integration (Image and Text Using Ontology Alignment

    Directory of Open Access Journals (Sweden)

    Ahmad A.A. Shareha

    2009-01-01

    Full Text Available Problem statement: This study proposed multimodal integration method at the concept level to investigate information from multimodalities. The multimodal data was represented as two separate lists of concepts which were extracted from images and its related text. The concepts extracted from image analysis are often ambiguous, while the concepts extracted from text processing could be sense-ambiguous. The major problems that face the integration of the underlying modalities (image and text were: The difference in the coverage and the difference in the granularity level. Approach: This study proposed a novel application using ontology alignment to unify the underlying ontologies. The said lists of concepts were represented in a structured form within the corresponding ontologies then the two structural lists are enriched and matched based on the alignment, this matching represent the final knowledge. Results: The difference in the coverage was solved in this study using the alignment process and the difference in the granularity level was solved using the enrichment process. Thus, the proposed integration produced accurate integrated results. Conclusion: Thus, integration of these concepts allows the totality of the knowledge be expressed more precisely.

  1. Photoalignment - an alternative aligning technique for Liquid Crystal Displays

    Directory of Open Access Journals (Sweden)

    M.M. Chrzanowski

    2011-09-01

    Full Text Available Purpose: The main aim of this work is to present our investigation in the field of photoalignment. In this work we introduce useful photoalignment techniques and discuss in detail the results of photocrosslinking and photodegradation in photosensitive polymer materials.Design/methodology/approach: We describe the new procedure investigated in our laboratory for the following materials: HD-4100, HD-4110 and HD-8820 (DuPont Microsystems as well as the characteristics obtained for the thin polyimide layers: optical homogeneity, thickness, surface tension.Findings: Polyimide layers obtained on the glass/ITO substrates which were irradiated using linearly polarised ultraviolet light show the aligning properties for liquid crystal layers. The proposed new technology is fairly fine to obtain 2-3 cm2 layers.Research limitations/implications: The liquid crystal material alignment quality is not perfect, but the works are still in progress. In the next step we will try to use silan-derivative adhesion promoters to lower the aligning layers thickness. This solution will probably also have a big influence on the aligning layers homogeneity.Practical implications: We discuss an alternative technique of the rubbing method for composition of liquid crystal displays. Liquid crystal displays are widely used for many industrial and commercial applications. Multimedia and graphics and medical-imaging systems require top quality images. Such an image can be obtained under the condition of good liquid crystal alignment. Rubbing is a method conventionally used for these purposes. Unfortunately this technique has some disadvantages that are particularly visible in new generation displays. The usage of photodephiniable materials opens the route to obtain an appropriate molecular tilt and controlled anchoring energy as well as preparing layers that are suitable to providing diversified optical axes in one liquid crystal cell.Originality/value: Agents investigated in the

  2. 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.

  3. Multiscale Point Correspondence Using Feature Distribution and Frequency Domain Alignment

    Directory of Open Access Journals (Sweden)

    Zeng-Shun Zhao

    2012-01-01

    Full Text Available In this paper, a hybrid scheme is proposed to find the reliable point-correspondences between two images, which combines the distribution of invariant spatial feature description and frequency domain alignment based on two-stage coarse to fine refinement strategy. Firstly, the source and the target images are both down-sampled by the image pyramid algorithm in a hierarchical multi-scale way. The Fourier-Mellin transform is applied to obtain the transformation parameters at the coarse level between the image pairs; then, the parameters can serve as the initial coarse guess, to guide the following feature matching step at the original scale, where the correspondences are restricted in a search window determined by the deformation between the reference image and the current image; Finally, a novel matching strategy is developed to reject the false matches by validating geometrical relationships between candidate matching points. By doing so, the alignment parameters are refined, which is more accurate and more flexible than a robust fitting technique. This in return can provide a more accurate result for feature correspondence. Experiments on real and synthetic image-pairs show that our approach provides satisfactory feature matching performance.

  4. Bayesian coestimation of phylogeny and sequence alignment

    Directory of Open Access Journals (Sweden)

    Jensen Jens

    2005-04-01

    Full Text Available Abstract Background Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to first build a multiple alignment of these sequences, followed by a phylogenetic reconstruction step based on this multiple alignment. However, alignment and phylogenetic inference are fundamentally interdependent, and ignoring this fact leads to biased and overconfident estimations. Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both. Results We developed a fully Bayesian Markov chain Monte Carlo method for coestimating phylogeny and sequence alignment, under the Thorne-Kishino-Felsenstein model of substitution and single nucleotide insertion-deletion (indel events. In our earlier work, we introduced a novel and efficient algorithm, termed the "indel peeling algorithm", which includes indels as phylogenetically informative evolutionary events, and resembles Felsenstein's peeling algorithm for substitutions on a phylogenetic tree. For a fixed alignment, our extension analytically integrates out both substitution and indel events within a proper statistical model, without the need for data augmentation at internal tree nodes, allowing for efficient sampling of tree topologies and edge lengths. To additionally sample multiple alignments, we here introduce an efficient partial Metropolized independence sampler for alignments, and combine these two algorithms into a fully Bayesian co-estimation procedure for the alignment and phylogeny problem. Our approach results in estimates for the posterior distribution of evolutionary rate parameters, for the maximum a-posteriori (MAP phylogenetic tree, and for the posterior decoding alignment. Estimates for the evolutionary tree and multiple alignment are augmented with confidence estimates for each node height and alignment column

  5. Alignments between galaxies, satellite systems and haloes

    Science.gov (United States)

    Shao, Shi; Cautun, Marius; Frenk, Carlos S.; Gao, Liang; Crain, Robert A.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

    2016-08-01

    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the discs of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the `Evolution and Assembly of GaLaxies and their Environments' (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their haloes, with a median misalignment angle of 33° in both cases. While the centrals are better aligned with the inner 10 kpc halo, the satellite systems are better aligned with the entire halo indicating that satellites preferentially trace the outer halo. The central-satellite alignment is weak (median misalignment angle of 52°) and we find that around 20 per cent of systems have a misalignment angle larger than 78°, which is the value for the Milky Way. The central-satellite alignment is a consequence of the tendency of both components to align with the dark matter halo. As a consequence, when the central is parallel to the satellite system, it also tends to be parallel to the halo. In contrast, if the central is perpendicular to the satellite system, as in the case of the Milky Way and Andromeda, then the central-halo alignment is much weaker. Dispersion-dominated (spheroidal) centrals have a stronger alignment with both their halo and their satellites than rotation-dominated (disc) centrals. We also found that the halo, the central galaxy and the satellite system tend to be aligned with the surrounding large-scale distribution of matter, with the halo being the better aligned of the three.

  6. Aligning Optical Fibers by Means of Actuated MEMS Wedges

    Science.gov (United States)

    Morgan, Brian; Ghodssi, Reza

    2007-01-01

    Microelectromechanical systems (MEMS) of a proposed type would be designed and fabricated to effect lateral and vertical alignment of optical fibers with respect to optical, electro-optical, optoelectronic, and/or photonic devices on integrated circuit chips and similar monolithic device structures. A MEMS device of this type would consist of a pair of oppositely sloped alignment wedges attached to linear actuators that would translate the wedges in the plane of a substrate, causing an optical fiber in contact with the sloping wedge surfaces to undergo various displacements parallel and perpendicular to the plane. In making it possible to accurately align optical fibers individually during the packaging stages of fabrication of the affected devices, this MEMS device would also make it possible to relax tolerances in other stages of fabrication, thereby potentially reducing costs and increasing yields. In a typical system according to the proposal (see Figure 1), one or more pair(s) of alignment wedges would be positioned to create a V groove in which an optical fiber would rest. The fiber would be clamped at a suitable distance from the wedges to create a cantilever with a slight bend to push the free end of the fiber gently to the bottom of the V groove. The wedges would be translated in the substrate plane by amounts Dx1 and Dx2, respectively, which would be chosen to move the fiber parallel to the plane by a desired amount Dx and perpendicular to the plane by a desired amount Dy. The actuators used to translate the wedges could be variants of electrostatic or thermal actuators that are common in MEMS.

  7. Focal adhesion kinase regulation in stem cell alignment and spreading on nanofibers.

    Science.gov (United States)

    Andalib, Mohammad Nahid; Lee, Jeong Soon; Ha, Ligyeom; Dzenis, Yuris; Lim, Jung Yul

    2016-05-13

    While electrospun nanofibers have demonstrated the potential for novel tissue engineering scaffolds, very little is known about the molecular mechanism of how cells sense and adapt to nanofibers. Here, we revealed the role of focal adhesion kinase (FAK), one of the key molecular sensors in the focal adhesion complex, in regulating mesenchymal stem cell (MSC) shaping on nanofibers. We produced uniaxially aligned and randomly distributed nanofibers from poly(l-lactic acid) to have the same diameters (about 130 nm) and evaluated MSC behavior on these nanofibers comparing with that on flat PLLA control. C3H10T1/2 murine MSCs exhibited upregulations in FAK expression and phosphorylation (pY397) on nanofibrous cultures as assessed by immunoblotting, and this trend was even greater on aligned nanofibers. MSCs showed significantly elongated and well-spread morphologies on aligned and random nanofibers, respectively. In the presence of FAK silencing via small hairpin RNA (shRNA), cell elongation length in the aligned nanofiber direction (cell major axis length) was significantly decreased, while cells still showed preferred orientation along the aligned nanofibers. On random nanofibers, MSCs with FAK-shRNA showed impaired cell spreading resulting in smaller cell area and higher circularity. Our study provides new data on how MSCs shape their morphologies on aligned and random nanofibrous cultures potentially via FAK-mediated mechanism. PMID:27040763

  8. Energy level alignment in Au/pentacene/PTCDA trilayer stacks

    Science.gov (United States)

    Sehati, P.; Braun, S.; Fahlman, M.

    2013-09-01

    Ultraviolet photoelectron spectroscopy is used to investigate the energy level alignment and molecular orientation at the interfaces in Au/pentacene/PTCDA trilayer stacks. We deduced a standing orientation for pentacene grown on Au while we conclude a flat lying geometry for PTCDA grown onto pentacene. We propose that the rough surface of polycrystalline Au induces the standing geometry in pentacene. It is further shown that in situ deposition of PTCDA on pentacene can influence the orientation of the surface pentacene layer, flipping part of the surface pentacene molecules into a flat lying geometry, maximizing the orbital interaction across the pentacene-PTCDA heterojunction.

  9. Electronic structure of spatially aligned graphene nanoribbons on Au(788).

    Science.gov (United States)

    Linden, S; Zhong, D; Timmer, A; Aghdassi, N; Franke, J H; Zhang, H; Feng, X; Müllen, K; Fuchs, H; Chi, L; Zacharias, H

    2012-05-25

    We report on a bottom-up approach of the selective and precise growth of subnanometer wide straight and chevron-type armchair nanoribbons (GNRs) on a stepped Au(788) surface using different specific molecular precursors. This process creates spatially well-aligned GNRs, as characterized by STM. High-resolution direct and inverse photoemission spectroscopy of occupied and unoccupied states allows the determination of the energetic position and momentum dispersion of electronic states revealing the existence of band gaps of several electron volts for straight 7-armchair, 13-armchair, and chevron-type GNRs in the electronic structure. PMID:23003288

  10. Business and IT alignment in context

    NARCIS (Netherlands)

    Silvius, A.J.G.

    2013-01-01

    Already for more than two decades, the necessity and desirability of aligning business needs and information technology (IT) capabilities is considered to be one of the key issues in IT management. However, several studies report quite low scores on business and IT alignment (BIA). The question “Why

  11. Sambamba: fast processing of NGS alignment formats

    NARCIS (Netherlands)

    Tarasov, A.; Vilella, A.J.; Cuppen, E.; Nijman, I.J.; Prins, J.C.P.

    2015-01-01

    Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces proc

  12. Automatic alignment of hieroglyphs and transliteration

    OpenAIRE

    Nederhof, Mark Jan

    2009-01-01

    Automatic alignment has important applications in philology, facilitating study of texts on the basis of electronic resources produced by different scholars. A simple technique is presented to realise such alignment for Ancient Egyptian hieroglyphic texts and transliteration. Preliminary experiments with the technique are reported, and plans for future work are discussed. Postprint

  13. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao;

    2007-01-01

    BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more...

  14. Aligning the μs-ALEX Setup.

    Science.gov (United States)

    Kapanidis, Achillefs; Majumdar, Devdoot; Heilemann, Mike; Nir, Eyal; Weiss, Shimon

    2015-11-01

    To achieve single-molecule sensitivity and thus have the ability to detect single diffusing fluorophores, careful alignment of the microsecond-alternating laser excitation (μs-Alex) setup is crucial. The following protocol describes routine alignment for 2c-ALEX (532 nm/635 nm) with spectral windows G(550-620)R(650-750). PMID:26527766

  15. Compositions for directed alignment of conjugated polymers

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jinsang; Kim, Bong-Gi; Jeong, Eun Jeong

    2016-04-19

    Conjugated polymers (CPs) achieve directed alignment along an applied flow field and a dichroic ratio of as high as 16.67 in emission from well-aligned thin films and fully realized anisotropic optoelectronic properties of CPs in field-effect transistor (FET).

  16. Evaluating Alignment between Curriculum, Assessment, and Instruction

    Science.gov (United States)

    Martone, Andrea; Sireci, Stephen G.

    2009-01-01

    The authors (a) discuss the importance of alignment for facilitating proper assessment and instruction, (b) describe the three most common methods for evaluating the alignment between state content standards and assessments, (c) discuss the relative strengths and limitations of these methods, and (d) discuss examples of applications of each…

  17. Instructional Alignment under No Child Left Behind

    Science.gov (United States)

    Polikoff, Morgan S.

    2012-01-01

    The alignment of instruction with the content of standards and assessments is the key mediating variable separating the policy of standards-based reform (SBR) from the outcome of improved student achievement. Few studies have investigated SBR's effects on instructional alignment, and most have serious methodological limitations. This research uses…

  18. Optical packet switching without packet alignment

    DEFF Research Database (Denmark)

    Hansen, Peter Bukhave; Danielsen, Søren Lykke; Stubkjær, Kristian

    1998-01-01

    Operation without packet alignment of an all-optical packet switch is proposed and predicted feasible through a detailed traffic analysis. Packet alignment units are eliminated resulting in a simple switch architecture while optimal traffic performance is maintained through the flexibility provided...

  19. Alignment Nashville. Complementary Learning in Action

    Science.gov (United States)

    Bouffard, Suzanne; Malone, Helen

    2007-01-01

    This profile illustrates how Alignment Nashville brings together diverse community members and organizations to leverage existing resources in support of Nashville's youth and the Metro Nashville Public Schools. In addition to a diversified funding structure, Alignment leaders point to three factors that have helped them get the effort off the…

  20. Sambamba : Fast processing of NGS alignment formats

    NARCIS (Netherlands)

    Tarasov, Artem; Vilella, Albert J.; Cuppen, Edwin; Nijman, Isaac J.; Prins, Pjotr

    2015-01-01

    Summary: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically red

  1. The GEM Detector projective alignment simulation system

    International Nuclear Information System (INIS)

    Precision position knowledge (< 25 microns RMS) of the GEM Detector muon system at the Superconducting Super Collider Laboratory (SSCL) is an important physics requirement necessary to minimize sagitta error in detecting and tracking high energy muons that are deflected by the magnetic field within the GEM Detector. To validate the concept of the sagitta correction function determined by projective alignment of the muon detectors (Cathode Strip Chambers or CSCs), the basis of the proposed GEM alignment scheme, a facility, called the ''Alignment Test Stand'' (ATS), is being constructed. This system simulates the environment that the CSCs and chamber alignment systems are expected to experience in the GEM Detector, albeit without the 0.8 T magnetic field and radiation environment. The ATS experimental program will allow systematic study and characterization of the projective alignment approach, as well as general mechanical engineering of muon chamber mounting concepts, positioning systems and study of the mechanical behavior of the proposed 6 layer CSCs. The ATS will consist of a stable local coordinate system in which mock-ups of muon chambers (i.e., non-working mechanical analogs, representing the three superlayers of a selected barrel and endcap alignment tower) are implemented, together with a sufficient number of alignment monitors to overdetermine the sagitta correction function, providing a self-consistency check. This paper describes the approach to be used for the alignment of the GEM muon system, the design of the ATS, and the experiments to be conducted using the ATS

  2. Achieving Organisational Change through Values Alignment

    Science.gov (United States)

    Branson, Christopher M.

    2008-01-01

    Purpose: The purpose of this paper is to, first, establish the interdependency between the successful achievement of organisational change and the attainment of values alignment within an organisation's culture and then, second, to describe an effective means for attaining such values alignment. Design/methodology/approach: Literature from the…

  3. SOA-Driven Business-Software Alignment

    NARCIS (Netherlands)

    Shishkov, Boris; Sinderen, van Marten; Quartel, Dick

    2006-01-01

    The alignment of business processes and their supporting application software is a major concern during the initial software design phases. This paper proposes a design approach addressing this problem of business-software alignment. The approach takes an initial business model as a basis in derivin

  4. Vacuum alignment with(out) elementary scalars

    CERN Document Server

    Alanne, Tommi; Meroni, Aurora; Sannino, Francesco

    2016-01-01

    We systematically elucidate differences and similarities of the vacuum alignment issue in composite and renormalizable elementary extensions of the Standard Model featuring a pseudo-Goldstone Higgs. We also provide general conditions for the stability of the vacuum in the elementary framework, thereby extending previous studies of the vacuum alignment.

  5. STELLAR: fast and exact local alignments

    Directory of Open Access Journals (Sweden)

    Weese David

    2011-10-01

    Full Text Available Abstract Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de.

  6. Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.

    Directory of Open Access Journals (Sweden)

    Hsin-Nan Lin

    Full Text Available Most sequence alignment tools can successfully align protein sequences with higher levels of sequence identity. The accuracy of corresponding structure alignment, however, decreases rapidly when considering distantly related sequences (<20% identity. In this range of identity, alignments optimized so as to maximize sequence similarity are often inaccurate from a structural point of view. Over the last two decades, most multiple protein aligners have been optimized for their capacity to reproduce structure-based alignments while using sequence information. Methods currently available differ essentially in the similarity measurement between aligned residues using substitution matrices, Fourier transform, sophisticated profile-profile functions, or consistency-based approaches, more recently.In this paper, we present a flexible similarity measure for residue pairs to improve the quality of protein sequence alignment. Our approach, called SymAlign, relies on the identification of conserved words found across a sizeable fraction of the considered dataset, and supported by evolutionary analysis. These words are then used to define a position specific substitution matrix that better reflects the biological significance of local similarity. The experiment results show that the SymAlign scoring scheme can be incorporated within T-Coffee to improve sequence alignment accuracy. We also demonstrate that SymAlign is less sensitive to the presence of structurally non-similar proteins. In the analysis of the relationship between sequence identity and structure similarity, SymAlign can better differentiate structurally similar proteins from non- similar proteins. We show that protein sequence alignments can be significantly improved using a similarity estimation based on weighted n-grams. In our analysis of the alignments thus produced, sequence conservation becomes a better indicator of structural similarity. SymAlign also provides alignment visualization that

  7. Accelerated large-scale multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Lloyd Scott

    2011-12-01

    Full Text Available Abstract Background Multiple sequence alignment (MSA is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware. Results We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor. Conclusions Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from http://dna.cs.byu.edu/msa/.

  8. Bokeh Mirror Alignment for Cherenkov Telescopes

    CERN Document Server

    Ahnen, M L; Balbo, M; Bergmann, M; Biland, A; Blank, M; Bretz, T; Bruegge, K A; Buss, J; Domke, M; Dorner, D; Einecke, S; Hempfling, C; Hildebrand, D; Hughes, G; Lustermann, W; Mannheim, K; Mueller, S A; Neise, D; Neronov, A; Noethe, M; Overkemping, A -K; Paravac, A; Pauss, F; Rhode, W; Shukla, A; Temme, F; Thaele, J; Toscano, S; Vogler, P; Walter, R; Wilbert, A

    2016-01-01

    Imaging Atmospheric Cherenkov Telescopes (IACTs) need imaging optics with large apertures and high image intensities to map the faint Cherenkov light emitted from cosmic ray air showers onto their image sensors. Segmented reflectors fulfill these needs, and composed from mass production mirror facets they are inexpensive and lightweight. However, as the overall image is a superposition of the individual facet images, alignment remains a challenge. Here we present a simple, yet extendable method, to align a segmented reflector using its Bokeh. Bokeh alignment does not need a star or good weather nights but can be done even during daytime. Bokeh alignment optimizes the facet orientations by comparing the segmented reflectors Bokeh to a predefined template. The optimal Bokeh template is highly constricted by the reflector's aperture and is easy accessible. The Bokeh is observed using the out of focus image of a near by point like light source in a distance of about 10 focal lengths. We introduce Bokeh alignment ...

  9. Operational performance of the Antares alignment system

    International Nuclear Information System (INIS)

    A review of the operational performance of the alignment system for the large Antares optical system is presented. The alignment of twenty-four optical channels consisting of two hundred optical elements is verified and established as required prior to each target shot for this CO2 laser fusion test facility. The overall system design included features such as automatic operation, data base driven controls, self calibration, provisions for initial optical alignment set up, and system aided fault location. The system approach employed two alignment stations which sequentially viewed the 24 optical channels (sectors) and could be used for prealignments and calibrations. Closed-loop operations via the computer permit rapid mirror alignments. The performance of the applied techniques and devices is evaluated and compared to the required performance specifically from the standpoint of accuracy and shot rate. Overall system performance with verification by actual target shots is presented

  10. Semiautomatic beam-based LHC collimator alignment

    CERN Document Server

    Valentino, Gianluca; Bruce, Roderik; Wollmann, Daniel; Sammut, Nicholas; Rossi, Adriana; Redaelli, Stefano

    2012-01-01

    Full beam-based alignment of the LHC collimation system was a time-consuming procedure (up to 28 hours) as the collimators were set up manually. A yearly alignment campaign has been sufficient for now, although in the future due to tighter tolerances this may lead to a decrease in the cleaning efficiency if machine parameters such as the beam orbit drift over time. Automating the collimator setup procedure can reduce the beam time for collimator setup and allow for more frequent alignments, therefore reducing the risk of performance degradation. This article describes the design and testing of a semiautomatic algorithm as a first step towards a fully automatic setup procedure. The parameters used to measure the accuracy and performance of the alignment are defined and determined from experimental data. A comparison of these measured parameters at 450 GeV and 3.5 TeV with manual and semiautomatic alignment is provided.

  11. Multiple sequence alignment with arbitrary gap costs: computing an optimal solution using polyhedral combinatorics.

    Science.gov (United States)

    Althaus, Ernst; Caprara, Alberto; Lenhof, Hans-Peter; Reinert, Knut

    2002-01-01

    Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In this paper we propose for the first time a general formulation for multiple alignment with arbitrary gap-costs based on an integer linear program (ILP). In addition we describe a branch-and-cut algorithm to effectively solve the ILP to optimality. We evaluate the performances of our approach in terms of running time and quality of the alignments using the BAliBase database of reference alignments. The results show that our implementation ranks amongst the best programs developed so far.

  12. Laser tunneling from aligned molecules

    CERN Document Server

    Smeenk, C T L; Sokolov, A V; Spanner, M; Lee, K F; Staudte, A; Villeneuve, D M; Corkum, P B

    2013-01-01

    We study multi-photon ionization from N_2, O_2 and benzene using circularly polarized light. By examining molecular frame photo-electron angular distributions, we illustrate how multi-photon ionization acts a momentum-selective probe of the local electron density in the Dyson orbitals for these molecules. We find good agreement with calculations based on a tunneling model and including saturation effects.

  13. Silicon Alignment Pins: An Easy Way to Realize a Wafer-to-Wafer Alignment

    Science.gov (United States)

    Jung-Kubiak, Cecile; Reck, Theodore J.; Lin, Robert H.; Peralta, Alejandro; Gill, John J.; Lee, Choonsup; Siles, Jose; Toda, Risaku; Chattopadhyay, Goutam; Cooper, Ken B.; Mehdi, Imran; Thomas, Bertrand

    2013-01-01

    Submillimeter heterodyne instruments play a critical role in addressing fundamental questions regarding the evolution of galaxies as well as being a crucial tool in planetary science. To make these instruments compatible with small platforms, especially for the study of the outer planets, or to enable the development of multi-pixel arrays, it is essential to reduce the mass, power, and volume of the existing single-pixel heterodyne receivers. Silicon micromachining technology is naturally suited for making these submillimeter and terahertz components, where precision and accuracy are essential. Waveguide and channel cavities are etched in a silicon bulk material using deep reactive ion etching (DRIE) techniques. Power amplifiers, multiplier and mixer chips are then integrated and the silicon pieces are stacked together to form a supercompact receiver front end. By using silicon micromachined packages for these components, instrument mass can be reduced and higher levels of integration can be achieved. A method is needed to assemble accurately these silicon pieces together, and a technique was developed here using etched pockets and silicon pins to align two wafers together.

  14. Polyimide photo-alignment layers for inclined homeotropic alignment of liquid crystal molecules

    International Nuclear Information System (INIS)

    We have succeeded in realizing an inclined homeotropic alignment of liquid crystal (LC) molecules by using photo-aligned films of a polyimide containing azobenzene in the backbone structure. To induce such an LC alignment, a side chain structure was introduced into the backbone structure. The LC pretilt angle, measured from the surface normal, could be controlled up to 1.75o by varying the light exposure in oblique angle irradiation with unpolarized light. Its thermal stability was examined by annealing the LC cell at 100 deg. C. No change was observed in the pretilt angle even after annealing for 36 h, indicative of its excellent thermal stability. Since photo-alignment has patterning capability, the photo-aligned polyimide film is expected as a promising alignment film for multi-domain vertical alignment mode LC displays

  15. Theoretical analysis of nanoparticle-induced homeotropic alignment in nematic liquid crystals

    CERN Document Server

    Choudhary, Amit; Li, Guoqiang

    2015-01-01

    A theoretical analysis of homeotropic alignment induced by nanoparticles (NPs) in a nematic liquid crystal (NLC) sample cell is presented. It is found that such alignment on the surface of a NP causes a change in the orientation of the molecular director near the surface, which in turn induces variations in the elastic constants and free energy. The induced NLC properties allow coupling between nearby NPs, mediated by the NLC molecules. The rotation of the coupled NPs close to the substrate tends to induce a long-range orientation of the NLC molecular director, leading to modification in the alignment at the interface of NLC and substrate which induces the orientation from homogeneous (planar) to homeotropic (vertical) in the bulk material.

  16. Automatic laser beam alignment using blob detection for an environment monitoring spectroscopy

    Science.gov (United States)

    Khidir, Jarjees; Chen, Youhua; Anderson, Gary

    2013-05-01

    This paper describes a fully automated system to align an infra-red laser beam with a small retro-reflector over a wide range of distances. The component development and test were especially used for an open-path spectrometer gas detection system. Using blob detection under OpenCV library, an automatic alignment algorithm was designed to achieve fast and accurate target detection in a complex background environment. Test results are presented to show that the proposed algorithm has been successfully applied to various target distances and environment conditions.

  17. 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.

  18. Galaxy alignment on large and small scales

    CERN Document Server

    Kang, X; Wang, Y O; Dutton, A; Macciò, A

    2014-01-01

    Galaxies are not randomly distributed across the universe but showing different kinds of alignment on different scales. On small scales satellite galaxies have a tendency to distribute along the major axis of the central galaxy, with dependence on galaxy properties that both red satellites and centrals have stronger alignment than their blue counterparts. On large scales, it is found that the major axes of Luminous Red Galaxies (LRGs) have correlation up to 30Mpc/h. Using hydro-dynamical simulation with star formation, we investigate the origin of galaxy alignment on different scales. It is found that most red satellite galaxies stay in the inner region of dark matter halo inside which the shape of central galaxy is well aligned with the dark matter distribution. Red centrals have stronger alignment than blue ones as they live in massive haloes and the central galaxy-halo alignment increases with halo mass. On large scales, the alignment of LRGs is also from the galaxy-halo shape correlation, but with some ex...

  19. 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.

  20. 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.

  1. Alignment and Sensitive Detection of DNA by a Moving Interface

    Science.gov (United States)

    Bensimon, A.; Simon, A.; Chiffaudel, A.; Croquette, V.; Heslot, F.; Bensimon, D.

    1994-09-01

    In a process called "molecular combing," DNA molecules attached at one end to a solid surface were extended and aligned by a receding air-water interface and left to dry on the surface. Molecular combing was observed to extend the length of the bacteriophage λ DNA molecule to 21.5 ± 0.5 micrometers (unextended length, 16.2 micrometers). With the combing process, it was possible to (i) extend a chromosomal Escherichia coli DNA fragment (10^6 base pairs) and (ii) detect a minute quantity of DNA (10^3 molecules). These results open the way for a faster physical mapping of the genome and for the detection of small quantities of target DNA from a population of molecules.

  2. Rotational molecular dynamics of laser-manipulated bromotrifluoromethane studied by x-ray absorption

    International Nuclear Information System (INIS)

    We present a computational study of the rotational molecular dynamics of bromotrifluoromethane (CF3Br) molecules in gas phase. The rotation is manipulated with an off-resonant 800 nm laser. The molecules are treated as rigid rotors. Frequently, we use a computationally efficient linear rotor model for CF3Br, which we compare with selected results for full symmetric-rotor computations. The expectation value 2 θ>(t) is discussed. Especially, the transition from impulsive to adiabatic alignment, the temperature dependence of the maximally achievable alignment, and its intensity dependence are investigated. In a next step, we examine resonant x-ray absorption as an accurate tool to study laser manipulation of molecular rotation. Specifically, we investigate the impact of the x-ray pulse duration on the signal (particularly its temporal resolution) and study the temperature dependence of the achievable absorption. Most importantly, we demonstrated that using picosecond x-ray pulses, one can accurately measure the expectation value 2 θ>(t) for impulsively aligned CF3Br molecules. We point out that a control of the rotational dynamics opens up a novel way to imprint shapes onto long x-ray pulses on a picosecond time scale. For our computations, we determine the dynamic polarizability tensor of CF3Br using ab initio molecular linear-response theory in conjunction with wave function models of increasing sophistication: Coupled-cluster singles (CCS), second-order approximate coupled-cluster singles and doubles (CC2), and coupled-cluster singles and doubles (CCSD).

  3. Comparing quasiparticle H2O level alignment on anatase and rutile TiO2

    OpenAIRE

    Sun, Huijuan; Mowbray, Duncan J.; Migani, Annapaola; Zhao, Jin; Petek, Hrvoje; Rubio, Angel

    2015-01-01

    Knowledge of the molecular frontier levels' alignment in the ground state can be used to predict the photocatalytic activity of an interface. The position of the adsorbate's highest occupied molecular orbital (HOMO) levels relative to the substrate's valence band maximum (VBM) in the interface describes the favorability of photogenerated hole transfer from the VBM to the adsorbed molecule. This is a key quantity for assessing and comparing H$_2$O photooxidation activities on two prototypical ...

  4. Rotational Alignment Altered by Source Position Correlations

    Science.gov (United States)

    Jacobs, Chris S.; Heflin, M. B.; Lanyi, G. E.; Sovers, O. J.; Steppe, J. A.

    2010-01-01

    In the construction of modern Celestial Reference Frames (CRFs) the overall rotational alignment is only weakly constrained by the data. Therefore, common practice has been to apply a 3-dimensional No-Net-Rotation (NNR) constraint in order to align an under-construction frame to the ICRF. We present evidence that correlations amongst source position parameters must be accounted for in order to properly align a CRF at the 5-10 (mu)as level of uncertainty found in current work. Failure to do so creates errors at the 10-40 (mu)as level.

  5. Improved model for statistical alignment

    Energy Technology Data Exchange (ETDEWEB)

    Miklos, I.; Toroczkai, Z. (Zoltan)

    2001-01-01

    The statistical approach to molecular sequence evolution involves the stochastic modeling of the substitution, insertion and deletion processes. Substitution has been modeled in a reliable way for more than three decades by using finite Markov-processes. Insertion and deletion, however, seem to be more difficult to model, and thc recent approaches cannot acceptably deal with multiple insertions and deletions. A new method based on a generating function approach is introduced to describe the multiple insertion process. The presented algorithm computes the approximate joint probability of two sequences in 0(13) running time where 1 is the geometric mean of the sequence lengths.

  6. Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS

    OpenAIRE

    Gao, Chuan; Zhang, Fusheng; Zhang, Jun; Guo, Shunxing; Shao, Hongbo

    2009-01-01

    The internal transcribed spacer (ITS) sequences alignment and proteomic difference of Anoectochilus interspecies have been studied by means of ITS molecular identification and surface enhanced laser desorption ionization time of flight mass spectrography. Results showed that variety certification on Anoectochilus by ITS sequences can not determine species, and there is proteomic difference among Anoectochilus interspecies. Moreover, proteomic finger printings of five Anoectochilus species hav...

  7. Aligned Fibrous Scaffold Induced Aligned Growth of Corneal Stroma Cells in vitro Culture

    Institute of Scientific and Technical Information of China (English)

    GAO Yan; YAN Jing; CUI Xue-jun; WANG Hong-yan; WANG Qing

    2012-01-01

    To investigate the contribution of fibre arrangement to guiding the aligned growth of corneal stroma cells,aligned and randomly oriented fibrous scaffolds of gelatin and poly-L-lactic acid(PLLA) were fabricated by electrospinning.A comparative study of two different systems with corneal stroma cells on randomly organized and aligned fibres were conducted.The efficiency of the scaffolds for inducing the aligned growth of cells was assessed by morphological observation and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide(MTT) assay.Results show that the cells cultured on both randomly oriented and aligned scaffolds maintained normal morphology and well spreading as well as long term proliferation.Importantly,corneal stroma cells grew high orderly on the aligned scaffold,while the cells grew disordered on the randomly oriented scaffold.Moreover,the cells exhibited higher viability in aligned scaffold than that in randomly oriented scaffold.These results indcate that electrospinng to prepare aligned fibrous scaffolds has provided an effective approach to the aligned growth of corneal stroma cells in vitro.Our findings that fiber arrangement plays a crucial role in guiding the aligned growth of cells may be helpful to the development of better biomaterials for tissue engineered cornea.

  8. SU-E-T-484: A New Method of Aligning Patient Setup Lasers in Radiation Therapy

    International Nuclear Information System (INIS)

    Purpose: To develop a new method to align the patient setup lasers in radiation therapy and examine its validity and effectiveness. Methods: The new laser alignment method was realized by a device composed of both a metallic base plate and few acrylic transparent plates with a cross hair line on each of them. The holders of radiochromic films were prepared in the device to find a radiation isocenter. The right laser positions could be found optically by matching the shadows of all the cross hairs in the gantry head and the device. The repeatability and reproducibility (R and R) of laser alignments and the dependency of the alignment on the position error of the light source were evaluated by comparing the standard deviations and the means of the measured laser positions. After aligning the lasers optically, a radiation isocenter was found by a collimator spoke shot and the gantry spoke shot, and then the lasers were parallely translated to the isocenter. Results: In the R and R test, the standard deviation was 1.14 mm for the new method whereas it was 1.49 mm or 2.76 mm for the conventional method with either high- or low-precision levels. In the test of the dependency on the position error of the light source, the mean laser position was shifted by 5.3 mm corresponding to the shift of the light source, 4.8 mm for the new method, but for the conventional method the laser position was shifted more than 7 times than that. The positional shift could be corrected by a parallel translation to the isocenter in the new method. Conclusion: A new laser alignment method was devised for radiation therapy and tested successfully. The method enabled us to align the lasers easily and accurately without repetition, and all lasers could be finally aligned to the radiation isocenter

  9. SU-E-T-484: A New Method of Aligning Patient Setup Lasers in Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, U [National Medical Center in Korea, Seoul (Korea, Republic of); Lim, Y; Cho, K; Jeong, C; Kim, M; Jeong, J; Park, J; Shin, D; Lee, S; Kim, J [National Cancer Center in Korea, Goyang, Gyeonggi-do (Korea, Republic of); Choi, S [Korea Cancer Center Hospital, Seoul, Seoul (Korea, Republic of); Kwak, J; Yoon, K [ASAN medical center, Songpa-gu, Seoul (Korea, Republic of); Park, S [McLaren-Flint, Flint, MI (United States); Kim, S [Virginia Commonwealth University, Richmond, VA (United States)

    2014-06-01

    Purpose: To develop a new method to align the patient setup lasers in radiation therapy and examine its validity and effectiveness. Methods: The new laser alignment method was realized by a device composed of both a metallic base plate and few acrylic transparent plates with a cross hair line on each of them. The holders of radiochromic films were prepared in the device to find a radiation isocenter. The right laser positions could be found optically by matching the shadows of all the cross hairs in the gantry head and the device. The repeatability and reproducibility (R and R) of laser alignments and the dependency of the alignment on the position error of the light source were evaluated by comparing the standard deviations and the means of the measured laser positions. After aligning the lasers optically, a radiation isocenter was found by a collimator spoke shot and the gantry spoke shot, and then the lasers were parallely translated to the isocenter. Results: In the R and R test, the standard deviation was 1.14 mm for the new method whereas it was 1.49 mm or 2.76 mm for the conventional method with either high- or low-precision levels. In the test of the dependency on the position error of the light source, the mean laser position was shifted by 5.3 mm corresponding to the shift of the light source, 4.8 mm for the new method, but for the conventional method the laser position was shifted more than 7 times than that. The positional shift could be corrected by a parallel translation to the isocenter in the new method. Conclusion: A new laser alignment method was devised for radiation therapy and tested successfully. The method enabled us to align the lasers easily and accurately without repetition, and all lasers could be finally aligned to the radiation isocenter.

  10. Robust and Efficient Parametric Face Alignment

    NARCIS (Netherlands)

    Tzimiropoulos, Georgios; Zafeiriou, Stefanos; Pantic, Maja

    2011-01-01

    We propose a correlation-based approach to parametric object alignment particularly suitable for face analysis applications which require efficiency and robustness against occlusions and illumination changes. Our algorithm registers two images by iteratively maximizing their correlation coefficient

  11. Alignment of the NOMAD-STAR detector

    CERN Document Server

    Cervera-Villanueva, A

    2000-01-01

    This note describes the alignment of the NOMAD-STAR detector. This is the B/sub 4/C-silicon target installed in the NOMAD spectrometer in 1997. NOMAD-STAR is composed of modules of 12 silicon detectors each giving a total length of 72 cm. Ten of these modules (called ladders) are assembled to form a layer. There are five layers interleaved with passive boron carbide plates. The total surface of silicon is 1.14 m /sup 2/. Energetic muons from the flat-top of the CERN SPS cycle provide the necessary information to perform a very precise software alignment. This alignment is needed to ensure that the impact parameter measurement needed for the identification of taus in a detector like NOMAD-STAR will not be limited by the error in the alignment. (15 refs).

  12. Aligner for Elastic Collisions of Dropped Balls.

    Science.gov (United States)

    Mellen, Walter Roy

    1995-01-01

    Discusses an aligner that permits dropping a stack of any number of balls of different sizes, elasticities, hardnesses, or types to observe the rebound of the top ball. Experimental results allow a reasonable comparison with theory. (MVL)

  13. Alignment free characterization of 2D gratings

    CERN Document Server

    Madsen, Morten Hannibal; Hansen, Poul-Erik; Jørgensen, Jan Friis

    2015-01-01

    Fast characterization of 2-dimensional gratings is demonstrated using a Fourier lens optical system and a differential optimization algorithm. It is shown that both the grating specific parameters such as the basis vectors and the angle between them and the alignment of the sample, such as the rotation of the sample around the x-, y-, and z-axis, can be deduced from a single measurement. More specifically, the lattice vectors and the angle between them have been measured, while the corrections of the alignment parameters are used to improve the quality of the measurement, and hence reduce the measurement uncertainty. Alignment free characterization is demonstrated on both a 2D hexagonal grating with a period of 700 nm and a checkerboard grating with a pitch of 3000 nm. The method can also be used for both automatic alignment and in-line characterization of gratings.

  14. Precision alignment of permanent magnet drift tubes

    International Nuclear Information System (INIS)

    The Lawrence Berkeley National Laboratory (LBNL) technique of drift-tube alignment has been resurrected at Los Alamos for the precision alignment of 1-cm-core drift tubes that carry high gradient rare-earth-cobalt quadrupoles. Because the quadrupoles cannot be switched off, this technique is not applicable to a drift-tube assembly, but tests indicate that individual magnetic centers can be detected with a precision of +/-0.003 mm. Methods of transferring this information to machined alignment flats on the sides of the drift-tube body are discussed. With measurements of drift tubes designed for a 100-mA, 425-MHz drift-tube linac, offsets between the geometric and magnetic axes of up to +/-0.05 mm were detected following final assembly and welding. This degree of offset is serious if not accommodated, because it represents the entire alignment tolerance for the 40-cell tank. The measurement equipment and technique are described

  15. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander

    2007-01-01

    Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \\emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length $m$ by comparing them to a known related gene sequence of length n, $m = \\Theta(n)$. Gelfand et al.\\ gave an algorithm for spliced alignment running in time O(n^3). Kent et al.\\ considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n^{2.5}). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n^{2.25}). Our approach is based on a new framework of \\emph{quasi-local string comparison}.

  16. Robust and resistant 2D shape alignment

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Eiriksson, Hrafnkell

    2001-01-01

    We express the alignment of 2D shapes as the minimization of the norm of a linear vector function. The minimization is done in the \\$l\\_1\\$, \\$l\\_2\\$ and the \\$l\\_\\$\\backslash\\$infty\\$ norms using well known standard numerical methods. In particular, the \\$l\\_1\\$ and the \\$l\\_\\$\\backslash\\$infty\\......We express the alignment of 2D shapes as the minimization of the norm of a linear vector function. The minimization is done in the \\$l\\_1\\$, \\$l\\_2\\$ and the \\$l\\_\\$\\backslash\\$infty\\$ norms using well known standard numerical methods. In particular, the \\$l\\_1\\$ and the \\$l......\\_\\$\\backslash\\$infty\\$ norm alignments are formulated as linear programming problems. The linear vector function formulation along with the different norms results in alignment methods that are both resistant from influence from outliers, robust wrt. errors in the annotation and capable of handling missing datapoints...

  17. EURRECA—Framework for Aligning Micronutrient Recommendations

    NARCIS (Netherlands)

    Veer, van 't P.; Grammatikaki, E.; Matthys, C.; Raats, M.M.; Contor, L.

    2013-01-01

    There is currently no standard approach for deriving micronutrient recommendations, and large variations exist across Europe, causing confusion among consumers, food producers, and policy makers. More aligned information could influence dietary behaviors and potentially lead to a healthier populatio

  18. Accurate studies on dissociation energies of diatomic molecules

    Institute of Scientific and Technical Information of China (English)

    SUN; WeiGuo; FAN; QunChao

    2007-01-01

    The molecular dissociation energies of some electronic states of hydride and N2 molecules were studied using a parameter-free analytical formula suggested in this study and the algebraic method (AM) proposed recently. The results show that the accurate AM dissociation energies DeAM agree excellently with experimental dissociation energies Deexpt, and that the dissociation energy of an electronic state such as the 23△g state of 7Li2 whose experimental value is not available can be predicted using the new formula.

  19. Optimal Nonlinear Filter for INS Alignment

    Institute of Scientific and Technical Information of China (English)

    赵瑞; 顾启泰

    2002-01-01

    All the methods to handle the inertial navigation system (INS) alignment were sub-optimal in the past. In this paper, particle filtering (PF) as an optimal method is used for solving the problem of INS alignment. A sub-optimal two-step filtering algorithm is presented to improve the real-time performance of PF. The approach combines particle filtering with Kalman filtering (KF). Simulation results illustrate the superior performance of these approaches when compared with extended Kalman filtering (EKF).

  20. Strategic alignment: a performance tool for SMEs

    OpenAIRE

    Jouirou, Nihel; Kalika, Michel

    2004-01-01

    The purpose of this research is to investigate whether the alignment of IT with the strategy (particularly the partnership strategy or cooperation practice) and organizational structure of an SME could have a decisive influence on its performance. We constructed a model and tested it empirically using data from 381 SMEs operating in different sectors. A multivariate perspective, modelled with structural equations, was used to test the alignment between strategy, structure and IT. The alignmen...

  1. Unscented Kalman filter for SINS alignment

    Institute of Scientific and Technical Information of China (English)

    Zhou Zhanxin; Gao Yanan; Chen Jiabin

    2007-01-01

    In order to improve the filter accuracy for the nonlinear error model of strapdown inertial navigation system (SINS) alignment, Unscented Kalman Filter (UKF) is presented for simulation with stationary base and moving base of SINS alignment.Simulation results show the superior performance of this approach when compared with classical suboptimal techniques such as extended Kalman filter in cases of large initial misalignment.The UKF has good performance in case of small initial misalignment.

  2. Aligning sourcing activities with corporate strategy

    OpenAIRE

    Buczek, Kristopher

    2014-01-01

    In this paper I set out to discover how global firms ensure that sourcing activities are aligned with corporate strategy. In order to understand this, I broke the problem down into three specific questions, which were: 1) How does strategy flow through the sourcing departments of large firms? 2) What hurdles do sourcing departments face when trying to implement corporate strategy? 3) What tools are available in improving the alignment between corporate strategies and sourcing activi...

  3. Genome Update: alignment of bacterial chromosomes

    DEFF Research Database (Denmark)

    Ussery, David; Jensen, Mette; Poulsen, Tine Rugh;

    2004-01-01

    There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1⇓. The method of genome comparison this month is that of genome alignment and......, as an example, an alignment of seven Staphylococcus aureus genomes and one Staphylococcus epidermidis genome is presented....

  4. Orthodontics Align Crooked Teeth and Boost Self-Esteem

    Science.gov (United States)

    ... desktop! more... Orthodontics Align Crooked Teeth and Boost Self- esteem Article Chapters Orthodontics Align Crooked Teeth and Boost Self- esteem Orthodontics print full article print this chapter email ...

  5. LHCb VELO software alignment, Part I the alignment of the VELO modules in their half boxes

    CERN Document Server

    Viret, S; Petrie, D

    2005-01-01

    Software alignment of the Vertex Locator (VELO) is a critical stage of the LHCb alignment strategy. This note presents a demonstration of a potential algorithm to satisfy the requirements of this stage. A fast track-based software alignment procedure is described. This method is based on non-iterative least squares fitting. The first step of the algorithm, the alignment of the VELO modules in their half-boxes, is fully described and results obtained with simulated events are presented and discussed. The approach described in this document, and the tools developed, are also applicable to the alignment of the other LHCb sub-systems and the global relative alignment of the sub-detectors.

  6. Can technology improve alignment during knee arthroplasty.

    Science.gov (United States)

    Thienpont, Emmanuel; Fennema, Peter; Price, Andrew

    2013-09-01

    Component malalignment remains a concern in total knee arthroplasty (TKA); therefore, a series of technologies have been developed to improve alignment. The authors conducted a systematic review to compare computer-assisted navigation with conventional instrumentation, and assess the current evidence for patient-matched instrumentation and robot-assisted implantation. An extensive search of the PubMed database for relevant meta-analyses, systematic reviews and original articles was performed, with each study scrutinised by two reviewers. Data on study characteristics and outcomes were extracted from each study and compared. In total 30 studies were included: 10 meta-analyses comparing computer-assisted navigation and conventional instrumentation, 13 studies examining patient-matched instrumentation, and seven investigating robot-assisted implantation. Computer-assisted navigation showed significant and reproducible improvements in mechanical alignment over conventional instrumentation. Patient-matched instrumentation appeared to achieve a high degree of mechanical alignment, although the majority of studies were of poor quality. The data for robot-assisted surgery was less indicative. Computer-assisted navigation improves alignment during TKA over conventional instrumentation. For patient-matched instrumentation and robot-assisted implantation, alignment benefits have not been reliably demonstrated. For all three technologies, clinical benefits cannot currently be assumed, and further studies are required. Although current technologies to improve alignment during TKA appear to result in intra-operative benefits, their clinical impact remains unclear, and surgeons should take this into account when considering their adoption.

  7. Alignments between galaxies, satellite systems and haloes

    CERN Document Server

    Shao, Shi; Frenk, Carlos S; Gao, Liang; Crain, Robert A; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

    2016-01-01

    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the disks of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their haloes, with a median misalignment angle of $33^{\\circ}$ in both cases. While the centrals are better aligned with the inner $10$ kpc halo, the satellite systems are better aligned with the entire halo indicating that satellites preferentially trace the outer halo. The central - satellite alignment is weak (median misalignment angle of $52^{\\circ}$) and we find that around $20\\%$ of systems have a misalignment angle larger than $78^{\\circ}$, which is the value for the Milky Way. The central - satellite alignment is a conseq...

  8. An implicit spatial memory alignment effect.

    Science.gov (United States)

    Cerles, Mélanie; Gomez, Alice; Rousset, Stéphane

    2015-09-01

    The memory alignment effect is the advantage of reasoning from a perspective which is aligned with the frame of reference used to encode an environment in memory. It usually occurs when participants have to consciously take a perspective to perform a spatial memory task. The present experiment assesses whether the memory alignment effect can occur without requiring to consciously take a given perspective, when the misaligned perspective is only perceptively provided. In others words, does the memory alignment effect still arise when it is only implicitly prompted? Thirty participants learned a sequence of four objects' positions in a room from a north-as-up survey perspective. During the testing phase, they had to point to the direction of a target object from another object ('the reference') with a fixed north-up orientation. The background behind the reference object displayed either a uniform color (control condition) or a misaligned ground-level perspective. The latter displayed a reference object's position information which was either congruent with the studied environment (congruent misaligned condition) or incongruent (incongruent misaligned condition). Mean pointing errors were higher in the congruent misaligned condition than in the control condition, whereas the incongruent misaligned condition did not differ from the control one. The present study shows that the memory alignment effect can arise without requiring a conscious misaligned perspective taking. Moreover, the perceived misaligned perspective must share the same spatial content as the memorized spatial representation in order to induce an alignment effect. PMID:26233526

  9. Laboratory Building for Accurate Determination of Plutonium

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>The accurate determination of plutonium is one of the most important assay techniques of nuclear fuel, also the key of the chemical measurement transfer and the base of the nuclear material balance. An

  10. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization

    Directory of Open Access Journals (Sweden)

    Paten Benedict

    2011-05-01

    Full Text Available Abstract Background Continuing research into the global multiple sequence alignment problem has resulted in more sophisticated and principled alignment methods. Unfortunately these new algorithms often require large amounts of time and memory to run, making it nearly impossible to run these algorithms on large datasets. As a solution, we present two general methods, Crumble and Prune, for breaking a phylogenetic alignment problem into smaller, more tractable sub-problems. We call Crumble and Prune meta-alignment methods because they use existing alignment algorithms and can be used with many current alignment programs. Crumble breaks long alignment problems into shorter sub-problems. Prune divides the phylogenetic tree into a collection of smaller trees to reduce the number of sequences in each alignment problem. These methods are orthogonal: they can be applied together to provide better scaling in terms of sequence length and in sequence depth. Both methods partition the problem such that many of the sub-problems can be solved independently. The results are then combined to form a solution to the full alignment problem. Results Crumble and Prune each provide a significant performance improvement with little loss of accuracy. In some cases, a gain in accuracy was observed. Crumble and Prune were tested on real and simulated data. Furthermore, we have implemented a system called Job-tree that allows hierarchical sub-problems to be solved in parallel on a compute cluster, significantly shortening the run-time. Conclusions These methods enabled us to solve gigabase alignment problems. These methods could enable a new generation of biologically realistic alignment algorithms to be applied to real world, large scale alignment problems.

  11. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    Science.gov (United States)

    Nordmeyer, Robert A.; Snell, Gyorgy P.; Cornell, Earl W.; Kolbe, William F.; Yegian, Derek T.; Earnest, Thomas N.; Jaklevich, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    2007-09-25

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  12. Considerations for clinical read alignment and mutational profiling using next-generation sequencing

    Directory of Open Access Journals (Sweden)

    Gavin R Oliver

    2012-07-01

    Full Text Available Next-generation sequencing technologies are increasingly being applied in clinical settings, however the data are characterized by a range of platform-specific artifacts making downstream analysis problematic and error prone. One major application of NGS is in the profiling of clinically relevant mutations whereby sequences are aligned to a reference genome and potential mutations assessed and scored. Accurate sequence alignment is pivotal in reliable assessment of potential mutations however selection of appropriate alignment tools is a non-trivial task complicated by the availability of multiple solutions each with its own performance characteristics. Using BRCA1 as an example, we have simulated and mutated a test dataset based on Illumina sequencing technology. Our findings reveal key differences in the performances of a range of common commercial and open source tools and will be of importance to anyone using NGS to profile mutations in clinical or basic research.

  13. Comparison of robust H∞ filter and Kalman filter for initial alignment of inertial navigation system

    Institute of Scientific and Technical Information of China (English)

    HAO Yan-ling; CHEN Ming-hui; LI Liang-jun; XU Bo

    2008-01-01

    There are many filtering methods that can be used for the initial alignment of an integrated inertial navigation system.This paper discussed the use of GPS,but focused on two kinds of filters for the initial alignment of an integrated strapdown inertial navigation system (SINS).One method is based on the Kalman filter (KF),and the other is based on the robust filter.Simulation results showed that the filter provides a quick transient response and a little more accurate estimate than KF,given substantial process noise or unknown noise statistics.So the robust filter is an effective and useful method for initial alignment of SINS.This research should make the use of SINS more popular,and is also a step for further research.

  14. Direct sample positioning and alignment methodology for strain measurement by diffraction

    Science.gov (United States)

    Ratel, N.; Hughes, D. J.; King, A.; Malard, B.; Chen, Z.; Busby, P.; Webster, P. J.

    2005-05-01

    An ISO (International Organization for Standardization) TTA (Technology Trends Assessment) was published in 2001 for the determination of residual stress using neutron diffraction which identifies sample alignment and positioning as a key source of strain measurement error. Although the measurement uncertainty by neutron and synchrotron x-ray diffraction for an individual measurement of lattice strain is typically of the order of 10-100×10-6, specimens commonly exhibit strain gradients of 1000×10-6mm-1 or more, making sample location a potentially considerable source of error. An integrated approach to sample alignment and positioning is described which incorporates standard base-plates and sample holders, instrument alignment procedures, accurate digitization using a coordinate measuring machine and automatic generation of instrument control scripts. The methodology that has been developed is illustrated by the measurement of the transverse residual strain field in a welded steel T-joint using neutrons.

  15. Initial alignment method for free space optics laser beam

    Science.gov (United States)

    Shimada, Yuta; Tashiro, Yuki; Izumi, Kiyotaka; Yoshida, Koichi; Tsujimura, Takeshi

    2016-08-01

    The authors have newly proposed and constructed an active free space optics transmission system. It is equipped with a motor driven laser emitting mechanism and positioning photodiodes, and it transmits a collimated thin laser beam and accurately steers the laser beam direction. It is necessary to introduce the laser beam within sensible range of the receiver in advance of laser beam tracking control. This paper studies an estimation method of laser reaching point for initial laser beam alignment. Distributed photodiodes detect laser luminescence at respective position, and the optical axis of laser beam is analytically presumed based on the Gaussian beam optics. Computer simulation evaluates the accuracy of the proposed estimation methods, and results disclose that the methods help us to guide the laser beam to a distant receiver.

  16. Alignment of the magnetic circuit of the BIPM watt balance

    Science.gov (United States)

    Bielsa, F.; Lu, Y. F.; Lavergne, T.; Kiss, A.; Fang, H.; Stock, M.

    2015-12-01

    The International Bureau of Weights and Measures (BIPM) is developing a watt balance for the forthcoming redefinition of the kilogram. An improved version of the apparatus, based on a new closed magnetic circuit is now being assembled. The new apparatus will significantly reduce the type B uncertainty due to misalignment of the magnetic circuit as this work demonstrates. We present two techniques recently developed to accurately align the magnetic field of the circuit perpendicular to the direction defined by the local acceleration of gravity. Uncertainty below 30 μrad was achieved for both techniques which fulfils the requirements for the BIPM watt balance to enable a Planck constant determination at the 1  ×  10-8 level.

  17. Multiple Fading Factors Kalman Filter for SINS Static Alignment Application

    Institute of Scientific and Technical Information of China (English)

    GAO Weixi; MIAO Lingjuan; NI Maolin

    2011-01-01

    To solve the problem that the standard Kalman filter cannot give the optimal solution when the system model and stochastic information are unknown accurately,single fading factor Kalman filter is suitable for simple systems.But for complex systems with multi-variable,it may not be sufficient to use single fading factor as a multiplier for the covariance matrices.In this paper,a new multiple fading factors Kalman filtering algorithm is presented.By calculating the unbiased estimate of the innovation sequence covariance using fenestration,the fading factor matrix is obtained.Adjusting the covariance matrix of prediction error Pk|k-1 using fading factor matrix,the algorithm provides different rates of fading for different filter channels.The proposed algorithm is applied to strapdown inertial navigation system(SINS) initial alignment,and simulation and experimental results demonstrate that,the alignment accuracy can be upgraded dramatically when the actual system noise characteristics are different from the pre-set values.The new algorithm is less sensitive to uncertainty noise and has better estimation effect of the parameters.Therefore,it is of significant value in practical applications.

  18. The Alignment and Assembly for EAST Tokamak Device

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    EAST (HT-7U) is a large fusion experimental device. It is a full superconducting tokamak with 1 MA of plasma current, 1000 s of plasma duration, high elongation and triangularity. It mainly consists of superconducting magnets of poloidal and toroidal field (PF& TF),vacuum vessel (VV), thermal radiation shield (TRS) and cryostat vessel (CV). The significant difficulty for assembly of EAST is tight installation tolerances, which are in the order of several tenth of a millimeter. In particular, the alignment of plasma facing components to the magnetic axis of the device is less than ± 0.5 mm.At present, a reasonable assembly process of EAST has been defined, and based on it, the alignment method for EAST, including the survey control network, the location of the main components in different directions, the magnetic axis determination and the accurate positioning of the plasma facing components inside of the vacuum vessel and so on, has been defined by using the sophisticated optical metrology system (SOMS).This paper describes the assembly procedure of EAST and the installation tolerances associated with the main components. Meanwhile, how to establish the assembly survey control network,magnetic axis determination methods, are introduced in detail.

  19. Statistical study of epicentre alignment in the broader Aegean area

    Directory of Open Access Journals (Sweden)

    E. Papadirnitriou

    1994-06-01

    Full Text Available Accurate data concerning shallow (h = 60 km earthquakes (Ms =4.5 that occurred in the broader Aegean area are used to point out the presence of linear seismogenic structures (seismolineaments. The earthquake data were analyzed by the use of a specific algorithm, and the directions of the best alignment of epicentres were found. The algorithm is based on statistical criteria applied within a circular area with the aim of searching for the best direction of alignment; this is then tested, to discriminate whether or not the pattern could stem from a random distribution of epicentres, or whether it is effectively the result of a linear seismic structure; the procedure is repeated to cover the whole area examined. The resulting lineaments can be regarded as individual tectonic units, as they usually coincide with known active faults or fault systems. An interpretation is given of the spatio-temporal evolution of the seismicity along the lineaments in terms of the asperity model.

  20. Alignment-dependent fluorescence emission induced by tunnel ionization of carbon dioxide from lower-lying orbitals

    CERN Document Server

    Yao, Jinping; Jia, Xinyan; Hao, Xiaolei; Zeng, Bin; Jing, Chenrui; Chu, Wei; Ni, Jielei; Zhang, Haisu; Xie, Hongqiang; Zhang, Chaojin; Zhao, Zengxiu; Chen, Jing; Liu, Xiaojun; Cheng, Ya; Xu, Zhizhan

    2013-01-01

    We show that fluorescence emission induced by strong field tunnel ionization of carbon dioxide from its lower-lying orbitals exhibits a peculiar molecular alignment dependence. The experimentally measured alignment-dependence of the fluorescence agrees with the alignment-dependence of the ionization probability calculated in the framework of the strong field approximation. Our results demonstrate the feasibility of an all-optical approach for shedding more light on the ionization mechanisms of molecules from their lower-lying orbitals in tunnel ionization regime.