GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

Alignment-free detection of horizontal gene transfer between closely related bacterial genomes.

PubMed

Domazet-Lošo, Mirjana; Haubold, Bernhard

2011-09-01

Bacterial epidemics are often caused by strains that have acquired their increased virulence through horizontal gene transfer. Due to this association with disease, the detection of horizontal gene transfer continues to receive attention from microbiologists and bioinformaticians alike. Most software for detecting transfer events is based on alignments of sets of genes or of entire genomes. But despite great advances in the design of algorithms and computer programs, genome alignment remains computationally challenging. We have therefore developed an alignment-free algorithm for rapidly detecting horizontal gene transfer between closely related bacterial genomes. Our implementation of this algorithm is called alfy for "ALignment Free local homologY" and is freely available from http://guanine.evolbio.mpg.de/alfy/. In this comment we demonstrate the application of alfy to the genomes of Staphylococcus aureus. We also argue that-contrary to popular belief and in spite of increasing computer speed-algorithmic optimization is becoming more, not less, important if genome data continues to accumulate at the present rate.

High-harmonic spectroscopy of aligned molecules

NASA Astrophysics Data System (ADS)

Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee

2017-01-01

High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.

Retro-detective control structures for free-space optical communication links.

PubMed

Jin, Xian; Barg, Jason E; Holzman, Jonathan F

2009-12-21

A corner-cube-based retro-detection photocell is introduced. The structure consists of three independent and mutually perpendicular photodiodes (PDs), whose differential photocurrents can be used to probe the alignment state of incident beams. These differential photocurrents are used in an actively-controlled triangulation procedure to optimize the communication channel alignment in a free-space optical (FSO) system. The active downlink and passive uplink communication capabilities of this system are demonstrated.

Pre-calculated protein structure alignments at the RCSB PDB website.

PubMed

Prlic, Andreas; Bliven, Spencer; Rose, Peter W; Bluhm, Wolfgang F; Bizon, Chris; Godzik, Adam; Bourne, Philip E

2010-12-01

With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org andreas@sdsc.edu; pbourne@ucsd.edu.

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

PubMed

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

2017-07-01

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

Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

PubMed

Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-04-01

Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Improved measurements of RNA structure conservation with generalized centroid estimators.

PubMed

Okada, Yohei; Saito, Yutaka; Sato, Kengo; Sakakibara, Yasubumi

2011-01-01

Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the minimum free energy (MFE) structure of an RNA sequence is regarded as the most stable structure, MFE alone could not be an appropriate measure for identifying ncRNAs since the free energy is heavily biased by the nucleotide composition. Therefore, instead of MFE itself, several alternative measures for identifying ncRNAs have been proposed such as the structure conservation index (SCI) and the base pair distance (BPD), both of which employ MFE structures. However, these measurements are unfortunately not suitable for identifying ncRNAs in some cases including the genome-wide search and incur high false discovery rate. In this study, we propose improved measurements based on SCI and BPD, applying generalized centroid estimators to incorporate the robustness against low quality multiple alignments. Our experiments show that our proposed methods achieve higher accuracy than the original SCI and BPD for not only human-curated structural alignments but also low quality alignments produced by CLUSTAL W. Furthermore, the centroid-based SCI on CLUSTAL W alignments is more accurate than or comparable with that of the original SCI on structural alignments generated with RAF, a high quality structural aligner, for which twofold expensive computational time is required on average. We conclude that our methods are more suitable for genome-wide alignments which are of low quality from the point of view on secondary structures than the original SCI and BPD.

Matt: local flexibility aids protein multiple structure alignment.

PubMed

Menke, Matthew; Berger, Bonnie; Cowen, Lenore

2008-01-01

Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root mean squared deviation (RMSD) of Matt alignments is shown to largely separate decoys from homologous protein structures in the SABmark benchmark dataset. We postulate that Matt's strong performance comes from its ability to model proteins in different conformational states and, perhaps even more important, its ability to model backbone distortions in more distantly related proteins.

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

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

2013-06-18

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

Alignment of RNA molecules: Binding energy and statistical properties of random sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valba, O. V., E-mail: valbaolga@gmail.com; Nechaev, S. K., E-mail: sergei.nechaev@gmail.com; Tamm, M. V., E-mail: thumm.m@gmail.com

2012-02-15

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energymore » between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.« less

Local-global alignment for finding 3D similarities in protein structures

DOEpatents

Zemla, Adam T [Brentwood, CA

2011-09-20

A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

Protein local structure alignment under the discrete Fréchet distance.

PubMed

Zhu, Binhai

2007-12-01

Protein structure alignment is a fundamental problem in computational and structural biology. While there has been lots of experimental/heuristic methods and empirical results, very few results are known regarding the algorithmic/complexity aspects of the problem, especially on protein local structure alignment. A well-known measure to characterize the similarity of two polygonal chains is the famous Fréchet distance, and with the application of protein-related research, a related discrete Fréchet distance has been used recently. In this paper, following the recent work of Jiang et al. we investigate the protein local structural alignment problem using bounded discrete Fréchet distance. Given m proteins (or protein backbones, which are 3D polygonal chains), each of length O(n), our main results are summarized as follows: * If the number of proteins, m, is not part of the input, then the problem is NP-complete; moreover, under bounded discrete Fréchet distance it is NP-hard to approximate the maximum size common local structure within a factor of n(1-epsilon). These results hold both when all the proteins are static and when translation/rotation are allowed. * If the number of proteins, m, is a constant, then there is a polynomial time solution for the problem.

Microstructure and phase behavior in colloids and liquid crystals

NASA Astrophysics Data System (ADS)

Lohr, Matthew Alan

This thesis describes our investigation of microstructure and phase behavior in colloids and liquid crystals. The first set of experiments explores the phase behavior of helical packings of thermoresponsive microspheres inside glass capillaries as a function of volume fraction. Stable helical packings are observed with long-range orientational order. Some of these packings evolve abruptly to disordered states as the volume fraction is reduced. We quantify these transitions using correlation functions and susceptibilities of an orientational order parameter. The emergence of coexisting metastable packings, as well as coexisting ordered and disordered states, is also observed. These findings support the notion of phase-transition-like behavior in quasi-one-dimensional systems. The second set of experiments investigates cross-over behavior from glasses with attractive interactions to sparse gel-like states. In particular, the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions are measured as a function of packing fraction. A crossover from glassy to sparse gel-like states is indicated by an excess of low-frequency phonon modes. This change in vibrational mode distribution appears to arise from highly localized vibrations that tend to involve individual and/or small clusters of particles with few local bonds. These mode behaviors and corresponding structural insights may serve as a useful signature for glass-gel transitions in wider classes of attractive packings. A third set of experiments explores the director structures of aqueous lyotropic chromonic liquid crystal (LCLC) films created on square lattice cylindrical-micropost substrates. The structures are manipulated by modulating of the concentration-dependent elastic properties of LCLC s via drying. Nematic LCLC films exhibit preferred bistable alignment along the diagonals of the micropost lattice. Columnar LCLC films form two distinct director and defect configurations: a diagonally aligned director pattern with local squares of defects, and an off-diagonal configuration with zig-zag defects. The formation of these patterns appears to be tied to the relative free energy costs of splay and bend deformations in the precursor nematic films. The observed nematic and columnar configurations are understood numerically using a Landau-de Gennes free energy model. This work provides first examples of quasi-2D micropatterning of LC films in the columnar phase and the first micropatterning of lyotropic LC films in general, as well as demonstrating alignment and configuration switching of typically difficult-to-align LCLC films via bulk elastic properties.

Controlling orientational order in block copolymers using low-intensity magnetic fields

PubMed Central

Choo, Youngwoo; Kawabata, Kohsuke; Kaufman, Gilad; Feng, Xunda; Di, Xiaojun; Rokhlenko, Yekaterina; Mahajan, Lalit H.; Ndaya, Dennis; Kasi, Rajeswari M.

2017-01-01

The interaction of fields with condensed matter during phase transitions produces a rich variety of physical phenomena. Self-assembly of liquid crystalline block copolymers (LC BCPs) in the presence of a magnetic field, for example, can result in highly oriented microstructures due to the LC BCP’s anisotropic magnetic susceptibility. We show that such oriented mesophases can be produced using low-intensity fields (<0.5 T) that are accessible using permanent magnets, in contrast to the high fields (>4 T) and superconducting magnets required to date. Low-intensity field alignment is enabled by the addition of labile mesogens that coassemble with the system’s nematic and smectic A mesophases. The alignment saturation field strength and alignment kinetics have pronounced dependences on the free mesogen concentration. Highly aligned states with orientation distribution coefficients close to unity were obtained at fields as small as 0.2 T. This remarkable field response originates in an enhancement of alignment kinetics due to a reduction in viscosity, and increased magnetostatic energy due to increases in grain size, in the presence of labile mesogens. These developments provide routes for controlling structural order in BCPs, including the possibility of producing nontrivial textures and patterns of alignment by locally screening fields using magnetic nanoparticles. PMID:29078379

Localization of ultra-low frequency waves in multi-ion plasmas of the planetary magnetosphere

DOE PAGES

Kim, Eun -Hwa; Johnson, Jay R.; Lee, Dong -Hun

2015-01-01

By adopting a 2D time-dependent wave code, we investigate how mode-converted waves at the Ion-Ion Hybrid (IIH) resonance and compressional waves propagate in 2D density structures with a wide range of field-aligned wavenumbers to background magnetic fields. The simulation results show that the mode-converted waves have continuous bands across the field line consistent with previous numerical studies. These waves also have harmonic structures in frequency domain and are localized in the field-aligned heavy ion density well. Lastly, our results thus emphasize the importance of a field-aligned heavy ion density structure for ultra-low frequency wave propagation, and suggest that IIH wavesmore » can be localized in different locations along the field line.« less

VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

Fast and accurate phylogeny reconstruction using filtered spaced-word matches

PubMed Central

Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-01-01

Abstract Motivation: Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. Availability and Implementation: The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/ Contact: chris.leimeister@stud.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28073754

CuPc/Au(1 1 0): Determination of the azimuthal alignment by a combination of angle-resolved photoemission and density functional theory

PubMed Central

Lüftner, Daniel; Milko, Matus; Huppmann, Sophia; Scholz, Markus; Ngyuen, Nam; Wießner, Michael; Schöll, Achim; Reinert, Friedrich; Puschnig, Peter

2014-01-01

Here we report on a combined experimental and theoretical study on the structural and electronic properties of a monolayer of Copper-Phthalocyanine (CuPc) on the Au(1 1 0) surface. Low-energy electron diffraction reveals a commensurate overlayer unit cell containing one adsorbate species. The azimuthal alignment of the CuPc molecule is revealed by comparing experimental constant binding energy (kxky)-maps using angle-resolved photoelectron spectroscopy with theoretical momentum maps of the free molecule's highest occupied molecular orbital (HOMO). This structural information is confirmed by total energy calculations within the framework of van-der-Waals corrected density functional theory. The electronic structure is further analyzed by computing the molecule-projected density of states, using both a semi-local and a hybrid exchange-correlation functional. In agreement with experiment, the HOMO is located about 1.2 eV below the Fermi-level, while there is no significant charge transfer into the molecule and the CuPc LUMO remains unoccupied on the Au(1 1 0) surface. PMID:25284953

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-07-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

GOSSIP: a method for fast and accurate global alignment of protein structures.

PubMed

Kifer, I; Nussinov, R; Wolfson, H J

2011-04-01

The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

Structure-rheology relationship in a sheared lamellar fluid.

PubMed

Jaju, S J; Kumaran, V

2016-03-01

The structure-rheology relationship in the shear alignment of a lamellar fluid is studied using a mesoscale model which provides access to the lamellar configurations and the rheology. Based on the equations and free energy functional, the complete set of dimensionless groups that characterize the system are the Reynolds number (ργL(2)/μ), the Schmidt number (μ/ρD), the Ericksen number (μγ/B), the interface sharpness parameter r, the ratio of the viscosities of the hydrophilic and hydrophobic parts μ(r), and the ratio of the system size and layer spacing (L/λ). Here, ρ and μ are the fluid density and average viscosity, γ is the applied strain rate, D is the coefficient of diffusion, B is the compression modulus, μ(r) is the maximum difference in the viscosity of the hydrophilic and hydrophobic parts divided by the average viscosity, and L is the system size in the cross-stream direction. The lattice Boltzmann method is used to solve the concentration and momentum equations for a two dimensional system of moderate size (L/λ=32) and for a low Reynolds number, and the other parameters are systematically varied to examine the qualitative features of the structure and viscosity evolution in different regimes. At low Schmidt numbers where mass diffusion is faster than momentum diffusion, there is fast local formation of randomly aligned domains with "grain boundaries," which are rotated by the shear flow to align along the extensional axis as time increases. This configuration offers a high resistance to flow, and the layers do not align in the flow direction even after 1000 strain units, resulting in a viscosity higher than that for an aligned lamellar phase. At high Schmidt numbers where momentum diffusion is fast, the shear flow disrupts layers before they are fully formed by diffusion, and alignment takes place by the breakage and reformation of layers by shear, resulting in defects (edge dislocations) embedded in a background of nearly aligned layers. At high Ericksen number where the viscous forces are large compared to the restoring forces due to layer compression and bending, shear tends to homogenize the concentration field, and the viscosity decreases significantly. At very high Ericksen number, shear even disrupts the layering of the lamellar phase. At low Ericksen number, shear results in the formation of well aligned layers with edge dislocations. However, these edge dislocations take a long time to anneal; the relatively small misalignment due to the defects results in a large increase in viscosity due to high layer stiffness and due to shear localization, because the layers between defects get pinned and move as a plug with no shear. An increase in the viscosity contrast between the hydrophilic and hydrophobic parts does not alter the structural characteristics during alignment. However, there is a significant increase in the viscosity, due to pinning of the layers between defects, which results in a plug flow between defects and a localization of the shear to a part of the domain.

The structure and statistics of interstellar turbulence

NASA Astrophysics Data System (ADS)

Kritsuk, A. G.; Ustyugov, S. D.; Norman, M. L.

2017-06-01

We explore the structure and statistics of multiphase, magnetized ISM turbulence in the local Milky Way by means of driven periodic box numerical MHD simulations. Using the higher order-accurate piecewise-parabolic method on a local stencil (PPML), we carry out a small parameter survey varying the mean magnetic field strength and density while fixing the rms velocity to observed values. We quantify numerous characteristics of the transient and steady-state turbulence, including its thermodynamics and phase structure, kinetic and magnetic energy power spectra, structure functions, and distribution functions of density, column density, pressure, and magnetic field strength. The simulations reproduce many observables of the local ISM, including molecular clouds, such as the ratio of turbulent to mean magnetic field at 100 pc scale, the mass and volume fractions of thermally stable Hi, the lognormal distribution of column densities, the mass-weighted distribution of thermal pressure, and the linewidth-size relationship for molecular clouds. Our models predict the shape of magnetic field probability density functions (PDFs), which are strongly non-Gaussian, and the relative alignment of magnetic field and density structures. Finally, our models show how the observed low rates of star formation per free-fall time are controlled by the multiphase thermodynamics and large-scale turbulence.

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

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

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

Solution structural ensembles of substrate-free cytochrome P450(cam).

PubMed

Asciutto, Eliana K; Young, Matthew J; Madura, Jeffry; Pochapsky, Susan Sondej; Pochapsky, Thomas C

2012-04-24

Removal of substrate (+)-camphor from the active site of cytochrome P450(cam) (CYP101A1) results in nuclear magnetic resonance-detected perturbations in multiple regions of the enzyme. The (1)H-(15)N correlation map of substrate-free diamagnetic Fe(II) CO-bound CYP101A permits these perturbations to be mapped onto the solution structure of the enzyme. Residual dipolar couplings (RDCs) were measured for (15)N-(1)H amide pairs in two independent alignment media for the substrate-free enzyme and used as restraints in solvated molecular dynamics (MD) simulations to generate an ensemble of best-fit structures of the substrate-free enzyme in solution. Nuclear magnetic resonance-detected chemical shift perturbations reflect changes in the electronic environment of the NH pairs, such as hydrogen bonding and ring current shifts, and are observed for residues in the active site as well as in hinge regions between secondary structural features. RDCs provide information about relative orientations of secondary structures, and RDC-restrained MD simulations indicate that portions of a β-rich region adjacent to the active site shift so as to partially occupy the vacancy left by removal of the substrate. The accessible volume of the active site is reduced in the substrate-free enzyme relative to the substrate-bound structure calculated using the same methods. Both symmetric and asymmetric broadening of multiple resonances observed upon substrate removal as well as localized increased errors in RDC fits suggest that an ensemble of enzyme conformations are present in the substrate-free form.

Fusion bonding and alignment fixture

DOEpatents

Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

2000-01-01

An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all the components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

Template-Based Modeling of Protein-RNA Interactions.

PubMed

Zheng, Jinfang; Kundrotas, Petras J; Vakser, Ilya A; Liu, Shiyong

2016-09-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

Bayesian comparison of protein structures using partial Procrustes distance.

PubMed

Ejlali, Nasim; Faghihi, Mohammad Reza; Sadeghi, Mehdi

2017-09-26

An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

Self-diffusion Coefficient and Structure of Binary n-Alkane Mixtures at the Liquid-Vapor Interfaces.

PubMed

Chilukoti, Hari Krishna; Kikugawa, Gota; Ohara, Taku

2015-10-15

The self-diffusion coefficient and molecular-scale structure of several binary n-alkane liquid mixtures in the liquid-vapor interface regions have been examined using molecular dynamics simulations. It was observed that in hexane-tetracosane mixture hexane molecules are accumulated in the liquid-vapor interface region and the accumulation intensity decreases with increase in a molar fraction of hexane in the examined range. Molecular alignment and configuration in the interface region of the liquid mixture change with a molar fraction of hexane. The self-diffusion coefficient in the direction parallel to the interface of both tetracosane and hexane in their binary mixture increases in the interface region. It was found that the self-diffusion coefficient of both tetracosane and hexane in their binary mixture is considerably higher in the vapor side of the interface region as the molar fraction of hexane goes lower, which is mostly due to the increase in local free volume caused by the local structure of the liquid in the interface region.

iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.

PubMed

Yang, Chung-Han; Shih, Cheng-Ting; Chen, Kun-Tze; Lee, Po-Han; Tsai, Ping-Han; Lin, Jian-Cheng; Yen, Ching-Yu; Lin, Tiao-Yin; Lu, Chin Lung

2016-07-08

Since its first release in 2010, iPARTS has become a valuable tool for globally or locally aligning two RNA 3D structures. It was implemented by a structural alphabet (SA)-based approach, which uses an SA of 23 letters to reduce RNA 3D structures into 1D sequences of SA letters and applies traditional sequence alignment to these SA-encoded sequences for determining their global or local similarity. In this version, we have re-implemented iPARTS into a new web server iPARTS2 by constructing a totally new SA, which consists of 92 elements with each carrying both information of base and backbone geometry for a representative nucleotide. This SA is significantly different from the one used in iPARTS, because the latter consists of only 23 elements with each carrying only the backbone geometry information of a representative nucleotide. Our experimental results have shown that iPARTS2 outperforms its previous version iPARTS and also achieves better accuracy than other popular tools, such as SARA, SETTER and RASS, in RNA alignment quality and function prediction. iPARTS2 takes as input two RNA 3D structures in the PDB format and outputs their global or local alignments with graphical display. iPARTS2 is now available online at http://genome.cs.nthu.edu.tw/iPARTS2/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

PubMed

Lee, Hui Sun; Im, Wonpil

2016-04-01

Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. © 2016 The Protein Society.

Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics

PubMed Central

Lee, Byoungkoo; Konen, Jessica; Wilkinson, Scott; Marcus, Adam I.; Jiang, Yi

2017-01-01

Invasive cancer cells interact with the surrounding extracellular matrix (ECM), remodeling ECM fiber network structure by condensing, degrading, and aligning these fibers. We developed a novel local alignment vector analysis method to quantitatively measure collagen fiber alignment as a vector field using Circular Statistics. This method was applied to human non-small cell lung carcinoma (NSCLC) cell lines, embedded as spheroids in a collagen gel. Collagen remodeling was monitored using second harmonic generation imaging under normal conditions and when the LKB1-MARK1 pathway was disrupted through RNAi-based approaches. The results showed that inhibiting LKB1 or MARK1 in NSCLC increases the collagen fiber alignment and captures outward alignment vectors from the tumor spheroid, corresponding to high invasiveness of LKB1 mutant cancer cells. With time-lapse imaging of ECM micro-fiber morphology, the local alignment vector can measure the dynamic signature of invasive cancer cell activity and cell-migration-induced ECM and collagen remodeling and realigning dynamics. PMID:28045069

SPIN ALIGNMENTS OF SPIRAL GALAXIES WITHIN THE LARGE-SCALE STRUCTURE FROM SDSS DR7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Youcai; Yang, Xiaohu; Luo, Wentao

Using a sample of spiral galaxies selected from the Sloan Digital Sky Survey Data Release 7 and Galaxy Zoo 2, we investigate the alignment of spin axes of spiral galaxies with their surrounding large-scale structure, which is characterized by the large-scale tidal field reconstructed from the data using galaxy groups above a certain mass threshold. We find that the spin axes only have weak tendencies to be aligned with (or perpendicular to) the intermediate (or minor) axis of the local tidal tensor. The signal is the strongest in a cluster environment where all three eigenvalues of the local tidal tensor aremore » positive. Compared to the alignments between halo spins and the local tidal field obtained in N-body simulations, the above observational results are in best agreement with those for the spins of inner regions of halos, suggesting that the disk material traces the angular momentum of dark matter halos in the inner regions.« less

Template-Based Modeling of Protein-RNA Interactions

PubMed Central

Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.

2016-01-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. PMID:27662342

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

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

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

A three-dimensional modelling of the layered structure of comet 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Penasa, L.; Massironi, M.; Naletto, G.; Simioni, E.; Ferrari, S.; Pajola, M.; Lucchetti, A.; Preusker, F.; Scholten, F.; Jorda, L.; Gaskell, R.; Ferri, F.; Marzari, F.; Davidsson, B.; Mottola, S.; Sierks, H.; Barbieri, C.; Lamy, P. L.; Rodrigo, R.; Koschny, D.; Rickman, H.; Keller, H. U.; Agarwal, J.; A'Hearn, M. F.; Barucci, M. A.; Bertaux, J. L.; Bertini, I.; Cremonese, G.; Da Deppo, V.; Debei, S.; De Cecco, M.; Deller, J.; Feller, C.; Fornasier, S.; Frattin, E.; Fulle, M.; Groussin, O.; Gutierrez, P. J.; Güttler, C.; Hofmann, M.; Hviid, S. F.; Ip, W. H.; Knollenberg, J.; Kramm, J. R.; Kührt, E.; Küppers, M.; La Forgia, F.; Lara, L. M.; Lazzarin, M.; Lee, J.-C.; Lopez Moreno, J. J.; Oklay, N.; Shi, X.; Thomas, N.; Tubiana, C.; Vincent, J. B.

2017-07-01

We provide a three-dimensional model of the inner layered structure of comet 67P based on the hypothesis of an extended layering independently wrapping each lobe. A large set of terrace orientations was collected on the latest shape model and then used as a proxy for the local orientation of the surfaces of discontinuity which defines the layers. We modelled the terraces as a family of concentric ellipsoidal shells with fixed axis ratios, producing a model that is completely defined by just eight free parameters. Each lobe of 67P has been modelled independently, and the two sets of parameters have been estimated by means of non-linear optimization of the measured terrace orientations. The proposed model is able to predict the orientation of terraces, the elongation of cliffs, the linear traces observed in the Wosret and Hathor regions and the peculiar alignment of boulder-like features which has been observed in the Hapi region, which appears to be related to the inner layering of the big lobe. Our analysis allowed us to identify a plane of junction between the two lobes, further confirming the independent nature of the lobes. Our layering models differ from the best-fitting topographic ellipsoids of the surface, demonstrating that the terraces are aligned to an internal structure of discontinuities, which is unevenly exposed on the surface, suggesting a complex history of localized material removal from the nucleus.

Structure determination of molecules in an alignment laser field by femtosecond photoelectron diffraction using an X-ray free-electron laser

PubMed Central

Minemoto, Shinichirou; Teramoto, Takahiro; Akagi, Hiroshi; Fujikawa, Takashi; Majima, Takuya; Nakajima, Kyo; Niki, Kaori; Owada, Shigeki; Sakai, Hirofumi; Togashi, Tadashi; Tono, Kensuke; Tsuru, Shota; Wada, Ken; Yabashi, Makina; Yoshida, Shintaro; Yagishita, Akira

2016-01-01

We have successfully determined the internuclear distance of I2 molecules in an alignment laser field by applying our molecular structure determination methodology to an I 2p X-ray photoelectron diffraction profile observed with femtosecond X-ray free electron laser pulses. Using this methodology, we have found that the internuclear distance of the sample I2 molecules in an alignment Nd:YAG laser field of 6 × 1011 W/cm2 is elongated by from 0.18 to 0.30 Å “in average” relatively to the equilibrium internuclear distance of 2.666 Å. Thus, the present experiment constitutes a critical step towards the goal of femtosecond imaging of chemical reactions and opens a new direction for the study of ultrafast chemical reaction in the gas phase. PMID:27934891

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

PubMed Central

2016-01-01

Abstract Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G‐LoSA. G‐LoSA aligns protein local structures in a sequence order independent way and provides a GA‐score, a chemical feature‐based and size‐independent structure similarity score. Our benchmark validation shows the robust performance of G‐LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure‐centric comparative biology studies. In particular, G‐LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G‐LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer‐aided drug design. We hope that G‐LoSA can be a useful computational method for exploring interesting biological problems through large‐scale comparison of protein local structures and facilitating drug discovery research and development. G‐LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. PMID:26813336

A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.

PubMed

Luczak, Brian B; James, Benjamin T; Girgis, Hani Z

2017-12-06

Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares. These statistics are calculated on two k-mer histograms representing two sequences. Our evaluations using global alignment scores revealed that the majority of the statistics are sensitive and capable of finding similar sequences to a query sequence. Therefore, any of these statistics can filter out dissimilar sequences quickly. Further, we observed that multiplicative combinations of the statistics are highly correlated with the identity score. Furthermore, combinations involving sequence length difference or Earth Mover's distance, which takes the length difference into account, are always among the highest correlated paired statistics with identity scores. Similarly, paired statistics including length difference or Earth Mover's distance are among the best performers in finding the K-closest sequences. Interestingly, similar performance can be obtained using histograms of shorter words, resulting in reducing the memory requirement and increasing the speed remarkably. Moreover, we found that simple single statistics are sufficient for processing next-generation sequencing reads and for applications relying on local alignment. Finally, we measured the time requirement of each statistic. The survey and the evaluations will help scientists with identifying efficient alternatives to the costly alignment algorithm, saving thousands of computational hours. The source code of the benchmarking tool is available as Supplementary Materials. © The Author 2017. Published by Oxford University Press.

Method for vacuum fusion bonding

DOEpatents

Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

2001-01-01

An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

PubMed

Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-03-10

Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

Self aligned hysteresis free carbon nanotube field-effect transistors

NASA Astrophysics Data System (ADS)

Shlafman, M.; Tabachnik, T.; Shtempluk, O.; Razin, A.; Kochetkov, V.; Yaish, Y. E.

2016-04-01

Hysteresis phenomenon in the transfer characteristics of carbon nanotube field effect transistor (CNT FET) is being considered as the main obstacle for successful realization of electronic devices based on CNTs. In this study, we prepare four kinds of CNTFETs and explore their hysteretic behavior. Two kinds of devices comprise on-surface CNTs (type I) and suspended CNTs (type II) with thin insulating layer underneath and a single global gate which modulates the CNT conductance. The third and fourth types (types III and IV) consist of suspended CNT over a metallic local gate underneath, where for type IV the local gate was patterned self aligned with the source and drain electrodes. The first two types of devices, i.e., type I and II, exhibit substantial hysteresis which increases with scanning range and sweeping time. Under high vacuum conditions and moderate electric fields ( |E |>4 ×106 V /cm ), the hysteresis for on-surface devices cannot be eliminated, as opposed to suspended devices. Interestingly, type IV devices exhibit no hysteresis at all at ambient conditions, and from the different roles which the global and local gates play for the four types of devices, we could learn about the hysteresis mechanism of this system. We believe that these self aligned hysteresis free FETs will enable the realization of different electronic devices and sensors based on CNTs.

Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

DOE PAGES

Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; ...

2017-02-21

The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. Here, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by constructionmore » captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. This approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.« less

Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

NASA Astrophysics Data System (ADS)

Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; Kronik, Leeor; Neaton, Jeffrey B.

2017-03-01

The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. In this work, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by construction captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. Our approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.

fRMSDPred: Predicting Local RMSD Between Structural Fragments Using Sequence Information

DTIC Science & Technology

2007-04-04

machine learning approaches for estimating the RMSD value of a pair of protein fragments. These estimated fragment-level RMSD values can be used to construct the alignment, assess the quality of an alignment, and identify high-quality alignment segments. We present algorithms to solve this fragment-level RMSD prediction problem using a supervised learning framework based on support vector regression and classification that incorporates protein profiles, predicted secondary structure, effective information encoding schemes, and novel second-order pairwise exponential kernel

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

XUV ionization of aligned molecules

NASA Astrophysics Data System (ADS)

Kelkensberg, F.; Rouzée, A.; Siu, W.; Gademann, G.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.; Vrakking, M. J. J.

2011-11-01

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 CO2 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.

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

PubMed Central

2007-01-01

Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for pairwise RNA structure prediction methods in a principled fashion. These constraints can reduce the computational and memory requirements of these methods while maintaining or improving their accuracy of structural prediction. This extends the practical reach of these methods to longer length sequences. The revised Dynalign code is freely available for download. PMID:17445273

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology.

Achievable flatness in a large microwave power transmitting antenna

NASA Technical Reports Server (NTRS)

Ried, R. C.

1980-01-01

A dual reference SPS system with pseudoisotropic graphite composite as a representative dimensionally stable composite was studied. The loads, accelerations, thermal environments, temperatures and distortions were calculated for a variety of operational SPS conditions along with statistical considerations of material properties, manufacturing tolerances, measurement accuracy and the resulting loss of sight (LOS) and local slope distributions. A LOS error and a subarray rms slope error of two arc minutes can be achieved with a passive system. Results show that existing materials measurement, manufacturing, assembly and alignment techniques can be used to build the microwave power transmission system antenna structure. Manufacturing tolerance can be critical to rms slope error. The slope error budget can be met with a passive system. Structural joints without free play are essential in the assembly of the large truss structure. Variations in material properties, particularly for coefficient of thermal expansion from part to part, is more significant than actual value.

Characterising RNA secondary structure space using information entropy

PubMed Central

2013-01-01

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/. PMID:23368905

Purification process for vertically aligned carbon nanofibers

NASA Technical Reports Server (NTRS)

Nguyen, Cattien V.; Delziet, Lance; Matthews, Kristopher; Chen, Bin; Meyyappan, M.

2003-01-01

Individual, free-standing, vertically aligned multiwall carbon nanotubes or nanofibers are ideal for sensor and electrode applications. Our plasma-enhanced chemical vapor deposition techniques for producing free-standing and vertically aligned carbon nanofibers use catalyst particles at the tip of the fiber. Here we present a simple purification process for the removal of iron catalyst particles at the tip of vertically aligned carbon nanofibers derived by plasma-enhanced chemical vapor deposition. The first step involves thermal oxidation in air, at temperatures of 200-400 degrees C, resulting in the physical swelling of the iron particles from the formation of iron oxide. Subsequently, the complete removal of the iron oxide particles is achieved with diluted acid (12% HCl). The purification process appears to be very efficient at removing all of the iron catalyst particles. Electron microscopy images and Raman spectroscopy data indicate that the purification process does not damage the graphitic structure of the nanotubes.

Intradomain phase transitions in flexible block copolymers with self-aligning segments.

PubMed

Burke, Christopher J; Grason, Gregory M

2018-05-07

We study a model of flexible block copolymers (BCPs) in which there is an enlthalpic preference for orientational order, or local alignment, among like-block segments. We describe a generalization of the self-consistent field theory of flexible BCPs to include inter-segment orientational interactions via a Landau-de Gennes free energy associated with a polar or nematic order parameter for segments of one component of a diblock copolymer. We study the equilibrium states of this model numerically, using a pseudo-spectral approach to solve for chain conformation statistics in the presence of a self-consistent torque generated by inter-segment alignment forces. Applying this theory to the structure of lamellar domains composed of symmetric diblocks possessing a single block of "self-aligning" polar segments, we show the emergence of spatially complex segment order parameters (segment director fields) within a given lamellar domain. Because BCP phase separation gives rise to spatially inhomogeneous orientation order of segments even in the absence of explicit intra-segment aligning forces, the director fields of BCPs, as well as thermodynamics of lamellar domain formation, exhibit a highly non-linear dependence on both the inter-block segregation (χN) and the enthalpy of alignment (ε). Specifically, we predict the stability of new phases of lamellar order in which distinct regions of alignment coexist within the single mesodomain and spontaneously break the symmetries of the lamella (or smectic) pattern of composition in the melt via in-plane tilt of the director in the centers of the like-composition domains. We further show that, in analogy to Freedericksz transition confined nematics, the elastic costs to reorient segments within the domain, as described by the Frank elasticity of the director, increase the threshold value ε needed to induce this intra-domain phase transition.

Intradomain phase transitions in flexible block copolymers with self-aligning segments

NASA Astrophysics Data System (ADS)

Burke, Christopher J.; Grason, Gregory M.

2018-05-01

We study a model of flexible block copolymers (BCPs) in which there is an enlthalpic preference for orientational order, or local alignment, among like-block segments. We describe a generalization of the self-consistent field theory of flexible BCPs to include inter-segment orientational interactions via a Landau-de Gennes free energy associated with a polar or nematic order parameter for segments of one component of a diblock copolymer. We study the equilibrium states of this model numerically, using a pseudo-spectral approach to solve for chain conformation statistics in the presence of a self-consistent torque generated by inter-segment alignment forces. Applying this theory to the structure of lamellar domains composed of symmetric diblocks possessing a single block of "self-aligning" polar segments, we show the emergence of spatially complex segment order parameters (segment director fields) within a given lamellar domain. Because BCP phase separation gives rise to spatially inhomogeneous orientation order of segments even in the absence of explicit intra-segment aligning forces, the director fields of BCPs, as well as thermodynamics of lamellar domain formation, exhibit a highly non-linear dependence on both the inter-block segregation (χN) and the enthalpy of alignment (ɛ). Specifically, we predict the stability of new phases of lamellar order in which distinct regions of alignment coexist within the single mesodomain and spontaneously break the symmetries of the lamella (or smectic) pattern of composition in the melt via in-plane tilt of the director in the centers of the like-composition domains. We further show that, in analogy to Freedericksz transition confined nematics, the elastic costs to reorient segments within the domain, as described by the Frank elasticity of the director, increase the threshold value ɛ needed to induce this intra-domain phase transition.

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

NASA Astrophysics Data System (ADS)

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. Hybertsen. It made use of resources at the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Lab.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

XUV ionization of aligned molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelkensberg, F.; Siu, W.; Gademann, G.

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.

Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser

DOE PAGES

Popp, David; Loh, N. Duane; Zorgati, Habiba; ...

2017-06-02

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments ( Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determinemore » that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.« less

Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popp, David; Loh, N. Duane; Zorgati, Habiba

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments ( Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determinemore » that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.« less

Dali server update.

PubMed

Holm, Liisa; Laakso, Laura M

2016-07-08

The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multi-subject Manifold Alignment of Functional Network Structures via Joint Diagonalization.

PubMed

Nenning, Karl-Heinz; Kollndorfer, Kathrin; Schöpf, Veronika; Prayer, Daniela; Langs, Georg

2015-01-01

Functional magnetic resonance imaging group studies rely on the ability to establish correspondence across individuals. This enables location specific comparison of functional brain characteristics. Registration is often based on morphology and does not take variability of functional localization into account. This can lead to a loss of specificity, or confounds when studying diseases. In this paper we propose multi-subject functional registration by manifold alignment via coupled joint diagonalization. The functional network structure of each subject is encoded in a diffusion map, where functional relationships are decoupled from spatial position. Two-step manifold alignment estimates initial correspondences between functionally equivalent regions. Then, coupled joint diagonalization establishes common eigenbases across all individuals, and refines the functional correspondences. We evaluate our approach on fMRI data acquired during a language paradigm. Experiments demonstrate the benefits in matching accuracy achieved by coupled joint diagonalization compared to previously proposed functional alignment approaches, or alignment based on structural correspondences.

Dynamical formation of spatially localized arrays of aligned nanowires in plastic films with magnetic anisotropy.

PubMed

Fragouli, Despina; Buonsanti, Raffaella; Bertoni, Giovanni; Sangregorio, Claudio; Innocenti, Claudia; Falqui, Andrea; Gatteschi, Dante; Cozzoli, Pantaleo Davide; Athanassiou, Athanassia; Cingolani, Roberto

2010-04-27

We present a simple technique for magnetic-field-induced formation, assembling, and positioning of magnetic nanowires in a polymer film. Starting from a polymer/iron oxide nanoparticle casted solution that is allowed to dry along with the application of a weak magnetic field, nanocomposite films incorporating aligned nanocrystal-built nanowire arrays are obtained. The control of the dimensions of the nanowires and of their localization across the polymer matrix is achieved by varying the duration of the applied magnetic field, in combination with the evaporation dynamics. These multifunctional anisotropic free-standing nanocomposite films, which demonstrate high magnetic anisotropy, can be used in a wide field of technological applications, ranging from sensors to microfluidics and magnetic devices.

Predicted electric-field-induced hexatic structure in an ionomer membrane

NASA Astrophysics Data System (ADS)

Allahyarov, Elshad; Taylor, Philip L.

2009-08-01

Coarse-grained molecular-dynamics simulations were used to study the morphological changes induced in a Nafion®-like ionomer by the imposition of a strong electric field. We observe the formation of structures aligned along the direction of the applied field. The polar head groups of the ionomer sidechains aggregate into clusters, which then form rodlike formations which assemble into a hexatic array aligned with the direction of the field. Occasionally these lines of sulfonates and protons form a helical structure. Upon removal of the electric field, the hexatic array of rodlike structures persists and has a lower calculated free energy than the original isotropic morphology.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

Orientation of cosmic web filaments with respect to the underlying velocity field

NASA Astrophysics Data System (ADS)

Tempel, E.; Libeskind, N. I.; Hoffman, Y.; Liivamägi, L. J.; Tamm, A.

2014-01-01

The large-scale structure of the Universe is characterized by a web-like structure made of voids, sheets, filaments and knots. The structure of this so-called cosmic web is dictated by the local velocity shear tensor. In particular, the local direction of a filament should be strongly aligned with hat{e}_3, the eigenvector associated with the smallest eigenvalue of the tensor. That conjecture is tested here on the basis of a cosmological simulation. The cosmic web delineated by the halo distribution is probed by a marked point process with interactions (the Bisous model), detecting filaments directly from the halo distribution (P-web). The detected P-web filaments are found to be strongly aligned with the local hat{e}_3: the alignment is within 30° for ˜80 per cent of the elements. This indicates that large-scale filaments defined purely from the distribution of haloes carry more than just morphological information, although the Bisous model does not make any prior assumption on the underlying shear tensor. The P-web filaments are also compared to the structure revealed from the velocity shear tensor itself (V-web). In the densest regions, the P- and V-web filaments overlap well (90 per cent), whereas in lower density regions, the P-web filaments preferentially mark sheets in the V-web.

MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

PubMed

Andreini, Claudia; Cavallaro, Gabriele; Rosato, Antonio; Valasatava, Yana

2013-11-25

We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).

Infrastructure-Free Mapping and Localization for Tunnel-Based Rail Applications Using 2D Lidar

NASA Astrophysics Data System (ADS)

Daoust, Tyler

This thesis presents an infrastructure-free mapping and localization framework for rail vehicles using only a lidar sensor. The method was designed to handle modern underground tunnels: narrow, parallel, and relatively smooth concrete walls. A sliding-window algorithm was developed to estimate the train's motion, using a Renyi's Quadratic Entropy (RQE)-based point-cloud alignment system. The method was tested with datasets gathered on a subway train travelling at high speeds, with 75 km of data across 14 runs, simulating 500 km of localization. The system was capable of mapping with an average error of less than 0.6 % by distance. It was capable of continuously localizing, relative to the map, to within 10 cm in stations and at crossovers, and 2.3 m in pathological sections of tunnel. This work has the potential to improve train localization in a tunnel, which can be used to increase capacity and for automation purposes.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

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

PubMed

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

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

Dipolar correlations and the dielectric permittivity of water.

PubMed

Sharma, Manu; Resta, Raffaele; Car, Roberto

2007-06-15

The static dielectric properties of liquid and solid water are investigated within linear response theory in the context of ab initio molecular dynamics. Using maximally localized Wannier functions to treat the macroscopic polarization we formulate a first-principles, parameter-free, generalization of Kirkwood's phenomenological theory. Our calculated static permittivity is in good agreement with experiment. Two effects of the hydrogen bonds, i.e., a significant increase of the average local moment and a local alignment of the molecular dipoles, contribute in almost equal measure to the unusually large dielectric constant of water.

"In the driver's seat": the Health Sector Strategic Master Plan as an instrument for aid coordination in Mongolia.

PubMed

Ulikpan, Anar; Narula, Indermohan; Malik, Asmat; Hill, Peter

2014-04-03

In 2005, the Ministry of Health (MoH) in Mongolia initiated the process of developing its Health Sector Strategic Master Plan (HSSMP), using a wide-ranging consultative process, driven by the MoH, and requiring participation from all levels of health facilities, other ministries, donor agencies and NGOs. Among other objectives, the MoH sought to coordinate the disparate inputs from key donors through the HSSMP, aligning them with the Plan's structure. This research explores the extent to which the HSSMP process served as a mechanism for effective aid coordination while promoting ownership and capacity building and the lessons learned for the wider international development community. The study is based on document review, key-informant interviews and authors' experience and participation in the MoH planning processes. The HSSMP process improved alignment and harmonisation. It enabled a better local understanding of the benefits of aid coordination, and the recognition that aid coordination as not only a mere administrative task, but a strategic step towards comprehensive management of both domestic and external resources. The process was not challenge free; the fractious political environment, the frequent turnover of key MoH staff, the resistance of some donors towards MoH scrutiny over their programmes and the dismantling of the central coordination and return of seconded staff following completion of the HSSMP, has slowed the pace of reform. Despite the challenges, the approach resulted in positive outcomes in the areas of ownership and better aid coordination, with HSSMP development emphasising ownership and capacity building. This contrasted with the usual outcomes focus, and neglect of the capacity building learning processes and structural and policy changes needed to ensure sustainable change. The largest and most influential programmes in the health sector are now largely aligned with HSSMP strategies, enabling the MoH to utilize these opportunities to optimise the HSSMP outcomes. The lessons for Ministries of Health in similar Post-Soviet countries--or other emerging economies where government capacity and local policy processes are relatively strong--are clear: the development of solid governance and technical infrastructure in terms of planning and evaluation provide a solid structure for donor coordination and insure against local political change.

“In the driver’s seat”: The Health Sector Strategic Master Plan as an instrument for aid coordination in Mongolia

PubMed Central

2014-01-01

In 2005, the Ministry of Health (MoH) in Mongolia initiated the process of developing its Health Sector Strategic Master Plan (HSSMP), using a wide-ranging consultative process, driven by the MoH, and requiring participation from all levels of health facilities, other ministries, donor agencies and NGOs. Among other objectives, the MoH sought to coordinate the disparate inputs from key donors through the HSSMP, aligning them with the Plan’s structure. This research explores the extent to which the HSSMP process served as a mechanism for effective aid coordination while promoting ownership and capacity building and the lessons learned for the wider international development community. The study is based on document review, key-informant interviews and authors’ experience and participation in the MoH planning processes. The HSSMP process improved alignment and harmonisation. It enabled a better local understanding of the benefits of aid coordination, and the recognition that aid coordination as not only a mere administrative task, but a strategic step towards comprehensive management of both domestic and external resources. The process was not challenge free; the fractious political environment, the frequent turnover of key MoH staff, the resistance of some donors towards MoH scrutiny over their programmes and the dismantling of the central coordination and return of seconded staff following completion of the HSSMP, has slowed the pace of reform. Despite the challenges, the approach resulted in positive outcomes in the areas of ownership and better aid coordination, with HSSMP development emphasising ownership and capacity building. This contrasted with the usual outcomes focus, and neglect of the capacity building learning processes and structural and policy changes needed to ensure sustainable change. The largest and most influential programmes in the health sector are now largely aligned with HSSMP strategies, enabling the MoH to utilize these opportunities to optimise the HSSMP outcomes. The lessons for Ministries of Health in similar Post-Soviet countries--or other emerging economies where government capacity and local policy processes are relatively strong--are clear: the development of solid governance and technical infrastructure in terms of planning and evaluation provide a solid structure for donor coordination and insure against local political change. PMID:24708860

Optimal design of an alignment-free two-DOF rehabilitation robot for the shoulder complex.

PubMed

Galinski, Daniel; Sapin, Julien; Dehez, Bruno

2013-06-01

This paper presents the optimal design of an alignment-free exoskeleton for the rehabilitation of the shoulder complex. This robot structure is constituted of two actuated joints and is linked to the arm through passive degrees of freedom (DOFs) to drive the flexion-extension and abduction-adduction movements of the upper arm. The optimal design of this structure is performed through two steps. The first step is a multi-objective optimization process aiming to find the best parameters characterizing the robot and its position relative to the patient. The second step is a comparison process aiming to select the best solution from the optimization results on the basis of several criteria related to practical considerations. The optimal design process leads to a solution outperforming an existing solution on aspects as kinematics or ergonomics while being more simple.

Genome alignment with graph data structures: a comparison

PubMed Central

2014-01-01

Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

PubMed Central

Little, Damon P.

2011-01-01

For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple–sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple–sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are unable to accurately differentiate between highly similar sequences and are not designed to cope with hierarchic phylogenetic relationships or within taxon variability. Here, I present a novel alignment–free sequence identification algorithm–BRONX–that accounts for observed within taxon variability and hierarchic relationships among taxa. BRONX identifies short variable segments and corresponding invariant flanking regions in reference sequences. These flanking regions are used to score variable regions in the query sequence without the production of a global multiple–sequence alignment. By incorporating observed within taxon variability into the scoring procedure, misidentifications arising from shared alleles/haplotypes are minimized. An explicit treatment of more inclusive terminals allows for separate identifications to be made for each taxonomic level and/or for user–defined terminals. BRONX performs better than all other methods when there is imperfect overlap between query and reference sequences (e.g. mini–barcode queries against a full–length barcode database). BRONX consistently produced better identifications at the genus–level for all query types. PMID:21857897

Representing and comparing protein structures as paths in three-dimensional space

PubMed Central

Zhi, Degui; Krishna, S Sri; Cao, Haibo; Pevzner, Pavel; Godzik, Adam

2006-01-01

Background Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction. Results We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure. Conclusion Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver. PMID:17052359

Mechanoresponsive, omni-directional and local matrix-degrading actin protrusions in human mesenchymal stem cells microencapsulated in a 3D collagen matrix.

PubMed

Ho, Fu Chak; Zhang, Wei; Li, Yuk Yin; Chan, Barbara Pui

2015-01-01

Cells are known to respond to multiple niche signals including extracellular matrix and mechanical loading. In others and our own studies, mechanical loading has been shown to induce the formation of cell alignment in 3D collagen matrix with random meshwork, challenging our traditional understanding on the necessity of having aligned substrates as the prerequisite of alignment formation. This motivates our adventure in deciphering the mechanism of loading-induced cell alignment and hence the discovery of the novel protrusive functional structure at the cell-matrix interface. Here we report the formation of mechanoresponsive, omni-directional and local matrix-degrading actin protrusions in human mesenchymal stem cells (hMSCs) microencapsulated in collagen following a shifted actin assembly/disassembly balance. These actin protrusive structures exhibit morphological and compositional similarity to filopodia and invadopodia but differ from them in stability, abundance, signaling and function. Without ruling out the possibility that these structures may comprise special subsets of filopodia and invadopodia, we propose to name them as mechanopodia so as to reveal their mechano-inductive mechanism. We also suggest that more intensive investigations are needed to delineate the functional significance and physiological relevance of these structures. This work identifies a brand new target for cell-matrix interaction and mechanoregulation studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed

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

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.

Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene.

PubMed

Seuring, Carolin; Ayyer, Kartik; Filippaki, Eleftheria; Barthelmess, Miriam; Longchamp, Jean-Nicolas; Ringler, Philippe; Pardini, Tommaso; Wojtas, David H; Coleman, Matthew A; Dörner, Katerina; Fuglerud, Silje; Hammarin, Greger; Habenstein, Birgit; Langkilde, Annette E; Loquet, Antoine; Meents, Alke; Riek, Roland; Stahlberg, Henning; Boutet, Sébastien; Hunter, Mark S; Koglin, Jason; Liang, Mengning; Ginn, Helen M; Millane, Rick P; Frank, Matthias; Barty, Anton; Chapman, Henry N

2018-05-09

Here we present a new approach to diffraction imaging of amyloid fibrils, combining a free-standing graphene support and single nanofocused X-ray pulses of femtosecond duration from an X-ray free-electron laser. Due to the very low background scattering from the graphene support and mutual alignment of filaments, diffraction from tobacco mosaic virus (TMV) filaments and amyloid protofibrils is obtained to 2.7 Å and 2.4 Å resolution in single diffraction patterns, respectively. Some TMV diffraction patterns exhibit asymmetry that indicates the presence of a limited number of axial rotations in the XFEL focus. Signal-to-noise levels from individual diffraction patterns are enhanced using computational alignment and merging, giving patterns that are superior to those obtainable from synchrotron radiation sources. We anticipate that our approach will be a starting point for further investigations into unsolved structures of filaments and other weakly scattering objects.

Unsupervised image matching based on manifold alignment.

PubMed

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

2012-08-01

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

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

PubMed

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

PubMed Central

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit PMID:25816325

Self-aligned nanoforest in silicon nanowire for sensitive conductance modulation.

PubMed

Seol, Myeong-Lok; Ahn, Jae-Hyuk; Choi, Ji-Min; Choi, Sung-Jin; Choi, Yang-Kyu

2012-11-14

A self-aligned and localized nanoforest structure is constructed in a top-down fabricated silicon nanowire (SiNW). The surface-to-volume ratio (SVR) of the SiNW is enhanced due to the local nanoforest formation. The conductance modulation property of the SiNWs, which is an important characteristic in sensor and charge transfer based applications, can be largely enhanced. For the selective modification of the channel region, localized Joule-heating and subsequent metal-assisted chemical etching (mac-etch) are employed. The nanoforest is formed only in the channel region without misalignment due to the self-aligned process of Joule-heating. The modified SiNW is applied to a porphyrin-silicon hybrid device to verify the enhanced conductance modulation. The charge transfer efficiency between the porphyrin and the SiNW, which is caused by external optical excitation, is clearly increased compared to the initial SiNW. The effect of the local nanoforest formation is enhanced when longer etching times and larger widths are used.

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

PubMed Central

Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

2016-01-01

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

PubMed Central

Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

2007-01-01

The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

Molecular crowding of collagen: a pathway to produce highly-organized collagenous structures.

PubMed

Saeidi, Nima; Karmelek, Kathryn P; Paten, Jeffrey A; Zareian, Ramin; DiMasi, Elaine; Ruberti, Jeffrey W

2012-10-01

Collagen in vertebrate animals is often arranged in alternating lamellae or in bundles of aligned fibrils which are designed to withstand in vivo mechanical loads. The formation of these organized structures is thought to result from a complex, large-area integration of individual cell motion and locally-controlled synthesis of fibrillar arrays via cell-surface fibripositors (direct matrix printing). The difficulty of reproducing such a process in vitro has prevented tissue engineers from constructing clinically useful load-bearing connective tissue directly from collagen. However, we and others have taken the view that long-range organizational information is potentially encoded into the structure of the collagen molecule itself, allowing the control of fibril organization to extend far from cell (or bounding) surfaces. We here demonstrate a simple, fast, cell-free method capable of producing highly-organized, anistropic collagen fibrillar lamellae de novo which persist over relatively long-distances (tens to hundreds of microns). Our approach to nanoscale organizational control takes advantage of the intrinsic physiochemical properties of collagen molecules by inducing collagen association through molecular crowding and geometric confinement. To mimic biological tissues which comprise planar, aligned collagen lamellae (e.g. cornea, lamellar bone or annulus fibrosus), type I collagen was confined to a thin, planar geometry, concentrated through molecular crowding and polymerized. The resulting fibrillar lamellae show a striking resemblance to native load-bearing lamellae in that the fibrils are small, generally aligned in the plane of the confining space and change direction en masse throughout the thickness of the construct. The process of organizational control is consistent with embryonic development where the bounded planar cell sheets produced by fibroblasts suggest a similar confinement/concentration strategy. Such a simple approach to nanoscale organizational control of structure not only makes de novo tissue engineering a possibility, but also suggests a clearer pathway to organization for fibroblasts than direct matrix printing. Copyright © 2012 Elsevier Ltd. All rights reserved.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemla, A; Lang, D; Kostova, T

2010-11-29

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitatemore » the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position.« less

Fast alignment-free sequence comparison using spaced-word frequencies.

PubMed

Leimeister, Chris-Andre; Boden, Marcus; Horwege, Sebastian; Lindner, Sebastian; Morgenstern, Burkhard

2014-07-15

Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free approaches work by comparing the word composition of sequences. A well-known problem with these methods is that neighbouring word matches are far from independent. To reduce the statistical dependency between adjacent word matches, we propose to use 'spaced words', defined by patterns of 'match' and 'don't care' positions, for alignment-free sequence comparison. We describe a fast implementation of this approach using recursive hashing and bit operations, and we show that further improvements can be achieved by using multiple patterns instead of single patterns. To evaluate our approach, we use spaced-word frequencies as a basis for fast phylogeny reconstruction. Using real-world and simulated sequence data, we demonstrate that our multiple-pattern approach produces better phylogenies than approaches relying on contiguous words. Our program is freely available at http://spaced.gobics.de/. © The Author 2014. Published by Oxford University Press.

The role of disclinations on the organization and conductivity in liquid crystal nanocomposites

NASA Astrophysics Data System (ADS)

Martinez-Miranda, Luz J.; Romero-Hasler, P.; Meneses-Franco, A.; Soto-Bustamante, E. A.

The structure of TiO2 nanoparticles in a liquid crystal nanocomposite was found to be an oblique structure due to the alignment of the TiO2 with respect to the liquid crystals. This order is anisotropic due to the ordering of the liquid crystals. The particles are highly localized in the nanocomposite, which has consequences in the electrical percolation. We want to obtain an understanding of how the nanoparticles organize in this highly localized fashion. The nanoparticles and the liquid crystals phase separate, with the nanoparticles accumulating in the defects exhibited by the liquid crystal even after being sonicated initially. The liquid crystal is polymerized by the process of electropolymerization that takes place in the isotropic phase of the monomers. The nanoparticles are free to move away from the defects where they phase separate since the defects disappear in the isotropic. We believe the polymerization imposes a limitation in the movement of the nanoparticles. The combination of the accumulation in the disclinations, the polymerization in the isotropic and the formation of the liquid crystal unit side chains can affect the conductivity of the nanocomposite. NSF-OISE-1157589; Fondecyt Project 1130187; CONICYT scholarships 21130413 and 21090713.

An extensive assessment of network alignment algorithms for comparison of brain connectomes.

PubMed

Milano, Marianna; Guzzi, Pietro Hiram; Tymofieva, Olga; Xu, Duan; Hess, Christofer; Veltri, Pierangelo; Cannataro, Mario

2017-06-06

Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area. Here we focus on the representation of connectomes by using graph theory formalisms. Macroscopic human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. The atlas-based parcellations present some known limitations in cases of early brain development and abnormal anatomy. Consequently, it has been recently proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space, as a way to deal with the unknown correspondences of the parcels. Such process requires modeling of the brain using graph theory and the subsequent comparison of the structure of graphs. The latter step may be modeled as a network alignment (NA) problem. In this work, we first define the problem formally, then we test six existing state of the art of network aligners on diffusion MRI-derived brain networks. We compare the performances of algorithms by assessing six topological measures. We also evaluated the robustness of algorithms to alterations of the dataset. The results confirm that NA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes. The analysis shows MAGNA++ is the best global alignment algorithm. The paper presented a new analysis methodology that uses network alignment for validating atlas-free parcellation brain connectomes. The methodology has been experimented on several brain datasets.

Label-Free Alignment of Nonmagnetic Particles in a Small Uniform Magnetic Field.

PubMed

Wang, Zhaomeng; Wang, Ying; Wu, Rui Ge; Wang, Z P; Ramanujan, R V

2018-01-01

Label-free manipulation of biological entities can minimize damage, increase viability and improve efficiency of subsequent analysis. Understanding the mechanism of interaction between magnetic and nonmagnetic particles in an inverse ferrofluid can provide a mechanism of label-free manipulation of such entities in a uniform magnetic field. The magnetic force, induced by relative magnetic susceptibility difference between nonmagnetic particles and surrounding magnetic particles as well as particle-particle interaction were studied. Label-free alignment of nonmagnetic particles can be achieved by higher magnetic field strength (Ba), smaller particle spacing (R), larger particle size (rp1), and higher relative magnetic permeability difference between particle and the surrounding fluid (Rμr). Rμr can be used to predict the direction of the magnetic force between both magnetic and nonmagnetic particles. A sandwich structure, containing alternate layers of magnetic and nonmagnetic particle chains, was studied. This work can be used for manipulation of nonmagnetic particles in lab-on-a-chip applications.

Is multiple-sequence alignment required for accurate inference of phylogeny?

PubMed

Höhl, Michael; Ragan, Mark A

2007-04-01

The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from http://www.bioinformatics.org.au (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from k-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length k of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

PubMed

Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

2016-05-15

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. Copyright © 2016 Elsevier Inc. All rights reserved.

Innovative method to suppress local geometry distortions for fabrication of interdigitated electrode arrays with nano gaps

NASA Astrophysics Data System (ADS)

Partel, S.; Urban, G.

2016-03-01

In this paper we present a method to optimize the lithography process for the fabrication of interdigitated electrode arrays (IDA) for a lift-off free electrochemical biosensor. The biosensor is based on amperometric method to allow a signal amplification by redox cycling. We already demonstrated a method to fabricate IDAs with nano gaps with conventional mask aligner lithography and two subsequent deposition processes. By decreasing the distance down to the nanometer range the linewidth variation is becoming the most critical factor and can result in a short circuit of the electrodes. Therefore, the light propagation and the resist pattern of the mask aligner lithography process are simulated to optimize the lithography process. To optimize the outer finger structure assistant features (AsFe) were introduced. The AsFe allow an optimization of the intensity distribution at the electrode fingers. Hence, the periodicity is expanded and the outer structure of the IDA is practically a part of the periodic array. The better CD uniformity can be obtained by adding three assistant features which generate an equal intensity distributions for the complete finger pattern. Considering a mask optimization of the outer structures would also be feasible. However, due to the strong impact of the gap between mask and wafer at contact lithography it is not practicable. The better choice is to create the same intensity distribution for all finger structures. With the introduction of the assistant features large areas with electrode gap sizes in the sub 100 nm region are demonstrated.

MSuPDA: A Memory Efficient Algorithm for Sequence Alignment.

PubMed

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

2016-03-01

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

Octahedral Tin Dioxide Nanocrystals Anchored on Vertically Aligned Carbon Aerogels as High Capacity Anode Materials for Lithium-Ion Batteries.

PubMed

Liu, Mingkai; Liu, Yuqing; Zhang, Yuting; Li, Yiliao; Zhang, Peng; Yan, Yan; Liu, Tianxi

2016-08-11

A novel binder-free graphene - carbon nanotubes - SnO2 (GCNT-SnO2) aerogel with vertically aligned pores was prepared via a simple and efficient directional freezing method. SnO2 octahedrons exposed of {221} high energy facets were uniformly distributed and tightly anchored on multidimensional graphene/carbon nanotube (GCNT) composites. Vertically aligned pores can effectively prevent the emersion of "closed" pores which cannot load the active SnO2 nanoparticles, further ensure quick immersion of electrolyte throughout the aerogel, and can largely shorten the transport distance between lithium ions and active sites of SnO2. Especially, excellent electrical conductivity of GCNT-SnO2 aerogel was achieved as a result of good interconnected networks of graphene and CNTs. Furthermore, meso- and macroporous structures with large surface area created by the vertically aligned pores can provide great benefit to the favorable transport kinetics for both lithium ion and electrons and afford sufficient space for volume expansion of SnO2. Due to the well-designed architecture of GCNT-SnO2 aerogel, a high specific capacity of 1190 mAh/g with good long-term cycling stability up to 1000 times was achieved. This work provides a promising strategy for preparing free-standing and binder-free active electrode materials with high performance for lithium ion batteries and other energy storage devices.

Octahedral Tin Dioxide Nanocrystals Anchored on Vertically Aligned Carbon Aerogels as High Capacity Anode Materials for Lithium-Ion Batteries

NASA Astrophysics Data System (ADS)

Liu, Mingkai; Liu, Yuqing; Zhang, Yuting; Li, Yiliao; Zhang, Peng; Yan, Yan; Liu, Tianxi

2016-08-01

A novel binder-free graphene - carbon nanotubes - SnO2 (GCNT-SnO2) aerogel with vertically aligned pores was prepared via a simple and efficient directional freezing method. SnO2 octahedrons exposed of {221} high energy facets were uniformly distributed and tightly anchored on multidimensional graphene/carbon nanotube (GCNT) composites. Vertically aligned pores can effectively prevent the emersion of “closed” pores which cannot load the active SnO2 nanoparticles, further ensure quick immersion of electrolyte throughout the aerogel, and can largely shorten the transport distance between lithium ions and active sites of SnO2. Especially, excellent electrical conductivity of GCNT-SnO2 aerogel was achieved as a result of good interconnected networks of graphene and CNTs. Furthermore, meso- and macroporous structures with large surface area created by the vertically aligned pores can provide great benefit to the favorable transport kinetics for both lithium ion and electrons and afford sufficient space for volume expansion of SnO2. Due to the well-designed architecture of GCNT-SnO2 aerogel, a high specific capacity of 1190 mAh/g with good long-term cycling stability up to 1000 times was achieved. This work provides a promising strategy for preparing free-standing and binder-free active electrode materials with high performance for lithium ion batteries and other energy storage devices.

Measurement of untruncated nuclear spin interactions via zero- to ultralow-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Blanchard, J. W.; Sjolander, T. F.; King, J. P.; Ledbetter, M. P.; Levine, E. H.; Bajaj, V. S.; Budker, D.; Pines, A.

2015-12-01

Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) provides a new regime for the measurement of nuclear spin-spin interactions free from the effects of large magnetic fields, such as truncation of terms that do not commute with the Zeeman Hamiltonian. One such interaction, the magnetic dipole-dipole coupling, is a valuable source of spatial information in NMR, though many terms are unobservable in high-field NMR, and the coupling averages to zero under isotropic molecular tumbling. Under partial alignment, this information is retained in the form of so-called residual dipolar couplings. We report zero- to ultralow-field NMR measurements of residual dipolar couplings in acetonitrile-2-13C aligned in stretched polyvinyl acetate gels. This permits the investigation of dipolar couplings as a perturbation on the indirect spin-spin J coupling in the absence of an applied magnetic field. As a consequence of working at zero magnetic field, we observe terms of the dipole-dipole coupling Hamiltonian that are invisible in conventional high-field NMR. This technique expands the capabilities of zero- to ultralow-field NMR and has potential applications in precision measurement of subtle physical interactions, chemical analysis, and characterization of local mesoscale structure in materials.

The sagittal stem alignment and the stem version clearly influence the impingement-free range of motion in total hip arthroplasty: a computer model-based analysis.

PubMed

Müller, Michael; Duda, Georg; Perka, Carsten; Tohtz, Stephan

2016-03-01

The component alignment in total hip arthroplasty influences the impingement-free range of motion (ROM). While substantiated data is available for the cup positioning, little is known about the stem alignment. Especially stem rotation and the sagittal alignment influence the position of the cone in relation to the edge of the socket and thus the impingement-free functioning. Hence, the question arises as to what influence do these parameters have on the impingement-free ROM? With the help of a computer model the influence of the sagittal stem alignment and rotation on the impingement-free ROM were investigated. The computer model was based on the CT dataset of a patient with a non-cemented THA. In the model the stem version was set at 10°/0°/-10° and the sagittal alignment at 5°/0°/-5°, which resulted in nine alternative stem positions. For each position, the maximum impingement-free ROM was investigated. Both stem version and sagittal stem alignment have a relevant influence on the impingement-free ROM. In particular, flexion and extension as well as internal and external rotation capability present evident differences. In the position intervals of 10° sagittal stem alignment and 20° stem version a difference was found of about 80° in the flexion and 50° in the extension capability. Likewise, differences were evidenced of up to 72° in the internal and up to 36° in the external rotation. The sagittal stem alignment and the stem torsion have a relevant influence on the impingement-free ROM. To clarify the causes of an impingement or accompanying problems, both parameters should be examined and, if possible, a combined assessment of these factors should be made.

Mapping local orientation of aligned fibrous scatterers for cancerous tissues using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Liu, Shaoxiong; Guo, Yihong; Wu, Jian; He, Yonghong; Ma, Hui

2014-10-01

Polarization measurements are sensitive to the microstructure of tissues and can be used to detect pathological changes. Many tissues contain anisotropic fibrous structures. We obtain the local orientation of aligned fibrous scatterers using different groups of the backscattering Mueller matrix elements. Experiments on concentrically well-aligned silk fibers and unstained human papillary thyroid carcinoma tissues show that the m22, m33, m23, and m32 elements have better contrast but higher degeneracy for the extraction of orientation angles. The m12 and m13 elements show lower contrast, but allow us to determine the orientation angle for the fibrous scatterers along all directions. Moreover, Monte Carlo simulations based on the sphere-cylinder scattering model indicate that the oblique incidence of the illumination beam introduces some errors in the orientation angles obtained by both methods. Mapping the local orientation of anisotropic tissues may not only provide information on pathological changes, but can also give new leads to reduce the orientation dependence of polarization measurements.

Tuning the Spin-Alignment of Interstitial Electrons in Two-Dimensional Y2C Electride via Chemical Pressure.

PubMed

Park, Jongho; Hwang, Jae-Yeol; Lee, Kyu Hyoung; Kim, Seong-Gon; Lee, Kimoon; Kim, Sung Wng

2017-12-06

We report that the spin-alignment of interstitial anionic electrons (IAEs) in two-dimensional (2D) interlayer spacing can be tuned by chemical pressure that controls the magnetic properties of 2D electrides. It was clarified from the isovalent Sc substitution on the Y site in the 2D Y 2 C electride that the localization degree of IAEs at the interlayer becomes stronger as the unit cell volume and c-axis lattice parameter were systematically reduced by increasing the Sc contents, thus eventually enhancing superparamagnetic behavior originated from the increase in ferromagnetic particle concentration. It was also found that the spin-aligned localized IAEs dominated the electrical conduction of heavily Sc-substituted Y 2 C electride. These results indicate that the physcial properties of 2D electrides can be tailored by adjusting the localization of IAEs at interlayer spacing via structural modification that controls the spin instability as found in three-dimensional elemental electrides of pressurized potassium metals.

NoFold: RNA structure clustering without folding or alignment.

PubMed

Middleton, Sarah A; Kim, Junhyong

2014-11-01

Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Time-Resolved Small-Angle X-ray Scattering Reveals Millisecond Transitions of a DNA Origami Switch.

PubMed

Bruetzel, Linda K; Walker, Philipp U; Gerling, Thomas; Dietz, Hendrik; Lipfert, Jan

2018-04-11

Self-assembled DNA structures enable creation of specific shapes at the nanometer-micrometer scale with molecular resolution. The construction of functional DNA assemblies will likely require dynamic structures that can undergo controllable conformational changes. DNA devices based on shape complementary stacking interactions have been demonstrated to undergo reversible conformational changes triggered by changes in ionic environment or temperature. An experimentally unexplored aspect is how quickly conformational transitions of large synthetic DNA origami structures can actually occur. Here, we use time-resolved small-angle X-ray scattering to monitor large-scale conformational transitions of a two-state DNA origami switch in free solution. We show that the DNA device switches from its open to its closed conformation upon addition of MgCl 2 in milliseconds, which is close to the theoretical diffusive speed limit. In contrast, measurements of the dimerization of DNA origami bricks reveal much slower and concentration-dependent assembly kinetics. DNA brick dimerization occurs on a time scale of minutes to hours suggesting that the kinetics depend on local concentration and molecular alignment.

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

PubMed

Zhang, Gaihua; Su, Zhen

2012-01-01

Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/β-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Domain alignment within ferroelectric/dielectric PbTiO 3 /SrTiO 3 superlattice nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Joonkyu; Mangeri, John; Zhang, Qingteng

The ferroelectric domain pattern within lithographically defined PbTiO 3/SrTiO 3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau–Ginzburg–Devonshire model show that the preferred direction of the alignment resultsmore » from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Thus, our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.« less

Domain alignment within ferroelectric/dielectric PbTiO 3 /SrTiO 3 superlattice nanostructures

DOE PAGES

Park, Joonkyu; Mangeri, John; Zhang, Qingteng; ...

2018-01-22

The ferroelectric domain pattern within lithographically defined PbTiO 3/SrTiO 3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau–Ginzburg–Devonshire model show that the preferred direction of the alignment resultsmore » from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Thus, our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.« less

Model of myosin node aggregation into a contractile ring: the effect of local alignment

NASA Astrophysics Data System (ADS)

Ojkic, Nikola; Wu, Jian-Qiu; Vavylonis, Dimitrios

2011-09-01

Actomyosin bundles frequently form through aggregation of membrane-bound myosin clusters. One such example is the formation of the contractile ring in fission yeast from a broad band of cortical nodes. Nodes are macromolecular complexes containing several dozens of myosin-II molecules and a few formin dimers. The condensation of a broad band of nodes into the contractile ring has been previously described by a search, capture, pull and release (SCPR) model. In SCPR, a random search process mediated by actin filaments nucleated by formins leads to transient actomyosin connections among nodes that pull one another into a ring. The SCPR model reproduces the transport of nodes over long distances and predicts observed clump-formation instabilities in mutants. However, the model does not generate transient linear elements and meshwork structures as observed in some wild-type and mutant cells during ring assembly. As a minimal model of node alignment, we added short-range aligning forces to the SCPR model representing currently unresolved mechanisms that may involve structural components, cross-linking and bundling proteins. We studied the effect of the local node alignment mechanism on ring formation numerically. We varied the new parameters and found viable rings for a realistic range of values. Morphologically, transient structures that form during ring assembly resemble those observed in experiments with wild-type and cdc25-22 cells. Our work supports a hierarchical process of ring self-organization involving components drawn together from distant parts of the cell followed by progressive stabilization.

STELLAR: fast and exact local alignments

PubMed Central

2011-01-01

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. PMID:22151882

MSuPDA: A memory efficient algorithm for sequence alignment.

PubMed

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

2015-01-16

Space complexity is a million dollar question in DNA sequence alignments. In this regards, MSuPDA (Memory Saving under Pushdown Automata) can help to reduce the occupied spaces in computer memory. Our proposed process is that Anchor Seed (AS) will be selected from given data set of Nucleotides base pairs for local sequence alignment. Quick Splitting (QS) techniques will separate the Anchor Seed from all the DNA genome segments. Selected Anchor Seed will be placed to pushdown Automata's (PDA) input unit. Whole DNA genome segments will be placed into PDA's stack. Anchor Seed from input unit will be matched with the DNA genome segments from stack of PDA. Whatever matches, mismatches or Indel, of Nucleotides will be POP from the stack under the control of control unit of Pushdown Automata. During the POP operation on stack it will free the memory cell occupied by the Nucleotide base pair.

CAFE: aCcelerated Alignment-FrEe sequence analysis.

PubMed

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

2017-07-03

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

PubMed Central

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-01-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

NASA Astrophysics Data System (ADS)

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-03-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.

LPV Modeling of a Flexible Wing Aircraft Using Modal Alignment and Adaptive Gridding Methods

NASA Technical Reports Server (NTRS)

Al-Jiboory, Ali Khudhair; Zhu, Guoming; Swei, Sean Shan-Min; Su, Weihua; Nguyen, Nhan T.

2017-01-01

One of the earliest approaches in gain-scheduling control is the gridding based approach, in which a set of local linear time-invariant models are obtained at various gridded points corresponding to the varying parameters within the flight envelop. In order to ensure smooth and effective Linear Parameter-Varying control, aligning all the flexible modes within each local model and maintaining small number of representative local models over the gridded parameter space are crucial. In addition, since the flexible structural models tend to have large dimensions, a tractable model reduction process is necessary. In this paper, the notion of s-shifted H2- and H Infinity-norm are introduced and used as a metric to measure the model mismatch. A new modal alignment algorithm is developed which utilizes the defined metric for aligning all the local models over the entire gridded parameter space. Furthermore, an Adaptive Grid Step Size Determination algorithm is developed to minimize the number of local models required to represent the gridded parameter space. For model reduction, we propose to utilize the concept of Composite Modal Cost Analysis, through which the collective contribution of each flexible mode is computed and ranked. Therefore, a reduced-order model is constructed by retaining only those modes with significant contribution. The NASA Generic Transport Model operating at various flight speeds is studied for verification purpose, and the analysis and simulation results demonstrate the effectiveness of the proposed modeling approach.

Global universe anisotropy probed by the alignment of structures in the cosmic microwave background.

PubMed

Wiaux, Y; Vielva, P; Martínez-González, E; Vandergheynst, P

2006-04-21

We question the global universe isotropy by probing the alignment of local structures in the cosmic microwave background (CMB) radiation. The original method proposed relies on a steerable wavelet decomposition of the CMB signal on the sphere. The analysis of the first-year Wilkinson Microwave Anisotropy Probe data identifies a mean preferred plane with a normal direction close to the CMB dipole axis, and a mean preferred direction in this plane, very close to the ecliptic poles axis. Previous statistical anisotropy results are thereby synthesized, but further analyses are still required to establish their origin.

What difference reveals about similarity.

PubMed

Sagi, Eyal; Gentner, Dedre; Lovett, Andrew

2012-08-01

Detecting that two images are different is faster for highly dissimilar images than for highly similar images. Paradoxically, we showed that the reverse occurs when people are asked to describe how two images differ--that is, to state a difference between two images. Following structure-mapping theory, we propose that this disassociation arises from the multistage nature of the comparison process. Detecting that two images are different can be done in the initial (local-matching) stage, but only for pairs with low overlap; thus, "different" responses are faster for low-similarity than for high-similarity pairs. In contrast, identifying a specific difference generally requires a full structural alignment of the two images, and this alignment process is faster for high-similarity pairs. We described four experiments that demonstrate this dissociation and show that the results can be simulated using the Structure-Mapping Engine. These results pose a significant challenge for nonstructural accounts of similarity comparison and suggest that structural alignment processes play a significant role in visual comparison. Copyright © 2012 Cognitive Science Society, Inc.

Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.

PubMed

Tang, Kujin; Lu, Yang Young; Sun, Fengzhu

2018-01-01

Horizontal gene transfer (HGT) plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and [Formula: see text] that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evolutionary distance between host and donor sequences, size of sliding window, and host genome composition on the performances of alignment-free methods to detect HGT. Our study showed that alignment-free methods can predict HGT accurately when host and donor genomes are in different order levels. Among all methods, CVTree with word length of 3, [Formula: see text] with word length 3, Markov order 1 and [Formula: see text] with word length 4, Markov order 1 outperform others in terms of their highest F 1 -score and their robustness under the influence of different factors.

Dissipation dynamics of field-free molecular alignment for symmetric-top molecules: Ethane (C2H6)

NASA Astrophysics Data System (ADS)

Zhang, H.; Billard, F.; Yu, X.; Faucher, O.; Lavorel, B.

2018-03-01

The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure. It is observed that the permanent alignment always decays slower compared to the transient alignment within the measured pressure range. This demonstrates that the propensity of molecules to conserve the orientation of angular momentum during collisions, previously observed for linear species, is also applicable to symmetric-top molecules. The results of this work provide valuable information for further theoretical understanding of collisional relaxation within nonlinear polyatomic molecules, which are expected to present interesting and nontrivial features due to an extra rotational degree of freedom.

Clustering of reads with alignment-free measures and quality values.

PubMed

Comin, Matteo; Leoni, Andrea; Schimd, Michele

2015-01-01

The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

Dynamic Tensile Loading Improves the Functional Properties of Mesenchymal Stem Cell-Laden Nanofiber-Based Fibrocartilage

PubMed Central

Baker, Brendon M.; Shah, Roshan P.; Huang, Alice H.

2011-01-01

Fibrocartilaginous tissues such as the meniscus serve critical load-bearing roles, relying on arrays of collagen fibers to resist tensile loads experienced with normal activity. As these structures are frequently injured and possess limited healing capacity, there exists great demand for tissue-engineered replacements. Toward recreating the structural features of these anisotropic tissues in vitro, we employ scaffolds composed of co-aligned nanofibers that direct mesenchymal stem cell (MSC) orientation and the formation of organized extracellular matrix (ECM). Concomitant with ECM synthesis, the mechanical properties of constructs increase with free-swelling culture, but ultimately failed to achieve equivalence with meniscal fibrocartilage. As mechanical forces are essential to the development and maintenance of musculoskeletal tissues, this work examined the effect of cyclic tensile loading on MSC-laden nanofibrous constructs. We hypothesized that loading would modulate the transcriptional behavior of MSCs, spur the deposition of ECM, and lead to enhancements in construct mechanical properties compared to free-swelling controls. Fiber-aligned scaffolds were seeded with MSCs and dynamically loaded daily in tension or maintained as nonloaded controls for 4 weeks. With mechanical stimulation, fibrous gene expression increased, collagen deposition increased, and the tensile modulus increased by 16% relative to controls. These results show that dynamic tensile loading enhances the maturation of MSC-laden aligned nanofibrous constructs, suggesting that recapitulation of the structural and mechanical environment of load-bearing tissues results in increases in functional properties that can be exploited for tissue engineering applications. PMID:21247342

Dynamic tensile loading improves the functional properties of mesenchymal stem cell-laden nanofiber-based fibrocartilage.

PubMed

Baker, Brendon M; Shah, Roshan P; Huang, Alice H; Mauck, Robert L

2011-05-01

Fibrocartilaginous tissues such as the meniscus serve critical load-bearing roles, relying on arrays of collagen fibers to resist tensile loads experienced with normal activity. As these structures are frequently injured and possess limited healing capacity, there exists great demand for tissue-engineered replacements. Toward recreating the structural features of these anisotropic tissues in vitro, we employ scaffolds composed of co-aligned nanofibers that direct mesenchymal stem cell (MSC) orientation and the formation of organized extracellular matrix (ECM). Concomitant with ECM synthesis, the mechanical properties of constructs increase with free-swelling culture, but ultimately failed to achieve equivalence with meniscal fibrocartilage. As mechanical forces are essential to the development and maintenance of musculoskeletal tissues, this work examined the effect of cyclic tensile loading on MSC-laden nanofibrous constructs. We hypothesized that loading would modulate the transcriptional behavior of MSCs, spur the deposition of ECM, and lead to enhancements in construct mechanical properties compared to free-swelling controls. Fiber-aligned scaffolds were seeded with MSCs and dynamically loaded daily in tension or maintained as nonloaded controls for 4 weeks. With mechanical stimulation, fibrous gene expression increased, collagen deposition increased, and the tensile modulus increased by 16% relative to controls. These results show that dynamic tensile loading enhances the maturation of MSC-laden aligned nanofibrous constructs, suggesting that recapitulation of the structural and mechanical environment of load-bearing tissues results in increases in functional properties that can be exploited for tissue engineering applications.

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

PubMed

Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

Generation of Alfvenic Double Layers, Formation of Auroral Arcs, and Their Impact on Energy and Momentum Transfer in M-I Coupling System

NASA Astrophysics Data System (ADS)

Song, Y.; Lysak, R. L.

2017-12-01

Parallel electrostatic electric fields provide a powerful mechanism to accelerate auroral particles to high energy in the auroral acceleration region (AAR), creating both quasi-static and Alfvenic discrete aurorae. The total field-aligned current can be written as J||total=J||+J||D, where the displacement current is denoted as J||D=(1/4π)(∂E||/∂t), which describes the E||-generation (Song and Lysak, 2006). The generation of the total field-aligned current is related to spatial gradients of the parallel vorticity caused by the axial torque acting on field-aligned flux tubes in M-I coupling system. It should be noticed that parallel electric fields are not produced by the field-aligned current. In fact, the E||-generation is caused by Alfvenic interaction in the M-I coupling system, and is favored by a low plasma density and the enhanced localized azimuthal magnetic flux. We suggest that the nonlinear interaction of incident and reflected Alfven wave packets in the AAR can create reactive stress concentration, and therefore can generate the parallel electrostatic electric fields together with a seed low density cavity. The generated electric fields will quickly deepen the seed low density cavity, which can effectively create even stronger electrostatic electric fields. The electrostatic electric fields nested in a low density cavity and surrounded by enhanced azimuthal magnetic flux constitute Alfvenic electromagnetic plasma structures, such as Alfvenic Double Layers (DLs). The Poynting flux carried by Alfven waves can continuously supply energy from the generator region to the auroral acceleration region, supporting and sustaining Alfvenic DLs with long-lasting electrostatic electric fields which accelerate auroral particles to high energy. The generation of parallel electric fields and the formation of auroral arcs can redistribute perpendicular mechanical and magnetic stresses in auroral flux tubes, decoupling the magnetosphere from ionosphere drag locally. This may enhance the magnetotail earthward shear flows and rapidly buildup stronger parallel electric fields in the auroral acceleration region, leading to a sudden and violent tail energy release, if there is accumulated free magnetic energy in the tail.

Investigations of the local environment and macroscopic alignment behavior of novel polymerizeable lyotropic liquid crystals using nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Juang, Elizabeth

In this dissertation, a variety of NMR techniques were used to explore the local environment of novel polymerizeable lyotropic liquid crystals (LLC). The LLC monomers examined in this study self-assemble in the presence of a small amount of water to form uniform, nanometer-scale tubes with aqueous interiors. The phase architecture is retained upon photopolymerization to yield the resulting nanoporous material. By dissolving reactive precursors into the aqueous phase, well- structured nancomposite materials have also been formed. Proposed uses for these novel polymerizeable LLCs are as porous water filtration membranes, as heterogeneous organic catalysts, and as nanocomposite materials for load bearing and optical applications. In order to better exploit these polymerizeable LLCs for materials development, the local environment must be examined. In addition, the macroscopic orientation of these materials remains an important step in their advancement. Various NMR studies were conducted on these novel LLCs. NMR T1 relaxation measurements were conducted to elucidate the local environment and dynamics of the 23Na counterions located inside the aqueous channels. 2H NMR line shape analyses were used to characterize the local structure and dynamics near the hydrophilic headgroup. 29 Si NMR studies were performed on silica nanocomposites formed with these LLC structures. Finally, the macroscopic alignment behavior of these novel LLCs using shear and magnetic fields was examined.

Seed/catalyst-free growth of zinc oxide nanostructures on multilayer graphene by thermal evaporation

PubMed Central

2014-01-01

We report the seed/catalyst-free growth of ZnO on multilayer graphene by thermal evaporation of Zn in the presence of O2 gas. The effects of substrate temperatures were studied. The changes of morphologies were very significant where the grown ZnO structures show three different structures, i.e., nanoclusters, nanorods, and thin films at 600°C, 800°C, and 1,000°C, respectively. High-density vertically aligned ZnO nanorods comparable to other methods were obtained. A growth mechanism was proposed based on the obtained results. The ZnO/graphene hybrid structure provides several potential applications in electronics and optoelectronics. PMID:24533793

Mesohysteresis model for ferromagnetic materials by minimization of the micromagnetic free energy

NASA Astrophysics Data System (ADS)

van den Berg, A.; Dupré, L.; Van de Wiele, B.; Crevecoeur, G.

2009-04-01

To study the connection between macroscopic hysteretic behavior and the microstructural properties, this paper presents and validates a new material dependent three-dimensional mesoscopic magnetic hysteresis model. In the presented mesoscopic description, the different micromagnetic energy terms are reformulated on the space scale of the magnetic domains. The sample is discretized in cubic cells, each with a local stress state, local bcc crystallographic axes, etc. The magnetization is assumed to align with one of the three crystallographic axes, in positive or negative sense, defining six volume fractions within each cell. The micromagnetic Gibbs free energy is described in terms of these volume fractions. Hysteresis loops are computed by minimizing the mesoscopic Gibbs free energy using a modified gradient search for a sequence of external applied fields. To validate the mesohysteresis model, we studied the magnetic memory properties. Numerical experiments reveal that (1) minor hysteresis loops are indeed closed and (2) the closed minor loops are erased from the memory.

Biological intuition in alignment-free methods: response to Posada.

PubMed

Ragan, Mark A; Chan, Cheong Xin

2013-08-01

A recent editorial in Journal of Molecular Evolution highlights opportunities and challenges facing molecular evolution in the era of next-generation sequencing. Abundant sequence data should allow more-complex models to be fit at higher confidence, making phylogenetic inference more reliable and improving our understanding of evolution at the molecular level. However, concern that approaches based on multiple sequence alignment may be computationally infeasible for large datasets is driving the development of so-called alignment-free methods for sequence comparison and phylogenetic inference. The recent editorial characterized these approaches as model-free, not based on the concept of homology, and lacking in biological intuition. We argue here that alignment-free methods have not abandoned models or homology, and can be biologically intuitive.

Genetic algorithms for protein threading.

PubMed

Yadgari, J; Amir, A; Unger, R

1998-01-01

Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible. As a result, in the last few years researchers have started to address the "inverse folding problem": Identifying and aligning a sequence to the fold with which it is most compatible, a process known as "threading". In two meetings in which protein folding predictions were objectively evaluated, it became clear that threading as a concept promises a real breakthrough, but that much improvement is still needed in the technique itself. Threading is a NP-hard problem, and thus no general polynomial solution can be expected. Still a practical approach with demonstrated ability to find optimal solutions in many cases, and acceptable solutions in other cases, is needed. We applied the technique of Genetic Algorithms in order to significantly improve the ability of threading algorithms to find the optimal alignment of a sequence to a structure, i.e. the alignment with the minimum free energy. A major progress reported here is the design of a representation of the threading alignment as a string of fixed length. With this representation validation of alignments and genetic operators are effectively implemented. Appropriate data structure and parameters have been selected. It is shown that Genetic Algorithm threading is effective and is able to find the optimal alignment in a few test cases. Furthermore, the described algorithm is shown to perform well even without pre-definition of core elements. Existing threading methods are dependent on such constraints to make their calculations feasible. But the concept of core elements is inherently arbitrary and should be avoided if possible. While a rigorous proof is hard to submit yet an, we present indications that indeed Genetic Algorithm threading is capable of finding consistently good solutions of full alignments in search spaces of size up to 10(70).

Controlled epitaxial graphene growth within removable amorphous carbon corrals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmer, James; Hu, Yike; Hankinson, John

2014-07-14

We address the question of control of the silicon carbide (SiC) steps and terraces under epitaxial graphene on SiC and demonstrate amorphous carbon (aC) corrals as an ideal method to pin SiC surface steps. aC is compatible with graphene growth, structurally stable at high temperatures, and can be removed after graphene growth. For this, aC is first evaporated and patterned on SiC, then annealed in the graphene growth furnace. There at temperatures above 1200 °C, mobile SiC steps accumulate at the aC corral that provide effective step flow barriers. Aligned step free regions are thereby formed for subsequent graphene growth atmore » temperatures above 1330 °C. Atomic force microscopy imaging supports the formation of step-free terraces on SiC with the step morphology aligned to the aC corrals. Raman spectroscopy indicates the presence of good graphene sheets on the step-free terraces.« less

Misalignment corrections in optical interconnects

NASA Astrophysics Data System (ADS)

Song, Deqiang

Optical interconnects are considered a promising solution for long distance and high bitrate data transmissions, outperforming electrical interconnects in terms of loss and dispersion. Due to the bandwidth and distance advantage of optical interconnects, longer links have been implemented with optics. Recent studies show that optical interconnects have clear advantages even at very short distances---intra system interconnects. The biggest challenge for such optical interconnects is the alignment tolerance. Many free space optical components require very precise assembly and installation, and therefore the overall cost could be increased. This thesis studied the misalignment tolerance and possible alignment correction solutions for optical interconnects at backplane or board level. First the alignment tolerance for free space couplers was simulated and the result indicated the most critical alignments occur between the VCSEL, waveguide and microlens arrays. An in-situ microlens array fabrication method was designed and experimentally demonstrated, with no observable misalignment with the waveguide array. At the receiver side, conical lens arrays were proposed to replace simple microlens arrays for a larger angular alignment tolerance. Multilayer simulation models in CodeV were built to optimized the refractive index and shape profiles of the conical lens arrays. Conical lenses fabricated with micro injection molding machine and fiber etching were characterized. Active component VCSOA was used to correct misalignment in optical connectors between the board and backplane. The alignment correction capability were characterized for both DC and AC (1GHz) optical signal. The speed and bandwidth of the VCSOA was measured and compared with a same structure VCSEL. Based on the optical inverter being studied in our lab, an all-optical flip-flop was demonstrated using a pair of VCSOAs. This memory cell with random access ability can store one bit optical signal with set or reset beam. The operating conditions were studied to generate two stable states between the VCSOA pair. The entire functionality test was implemented with free space optical components.

Constitutive Modeling of Nanotube-Reinforced Polymer Composite Systems

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Harik, Vasyl M.; Wise, Kristopher E.; Gates, Thomas S.

2004-01-01

In this study, a technique has been proposed for developing constitutive models for polymer composite systems reinforced with single-walled carbon nanotubes (SWNT). Since the polymer molecules are on the same size scale as the nanotubes, the interaction at the polymer/nanotube interface is highly dependent on the local molecular structure and bonding. At these small length scales, the lattice structures of the nanotube and polymer chains cannot be considered continuous, and the bulk mechanical properties of the SWNT/polymer composites can no longer be determined through traditional micromechanical approaches that are formulated using continuum mechanics. It is proposed herein that the nanotube, the local polymer near the nanotube, and the nanotube/polymer interface can be modeled as an effective continuum fiber using an equivalent-continuum modeling method. The effective fiber retains the local molecular structure and bonding information and serves as a means for incorporating micromechanical analyses for the prediction of bulk mechanical properties of SWNT/polymer composites with various nanotube sizes and orientations. As an example, the proposed approach is used for the constitutive modeling of two SWNT/polyethylene composite systems, one with continuous and aligned SWNT and the other with discontinuous and randomly aligned nanotubes.

Constitutive Modeling of Nanotube-Reinforced Polymer Composite Systems

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Harik, Vasyl M.; Wise, Kristopher E.; Gates, Thomas S.

2001-01-01

In this study, a technique has been proposed for developing constitutive models for polymer composite systems reinforced with single-walled carbon nanotubes (SWNT). Since the polymer molecules are on the same size scale as the nanotubes, the interaction at the polymer/nanotube interface is highly dependent on the local molecular structure and bonding. At these small length scales, the lattice structures of the nanotube and polymer chains cannot be considered continuous, and the bulk mechanical properties of the SWNT/polymer composites can no longer be determined through traditional micromechanical approaches that are formulated using continuum mechanics. It is proposed herein that the nanotube, the local polymer near the nanotube, and the nanotube/polymer interface can be modeled as an effective continuum fiber using an equivalent-continuum modeling method. The effective fiber retains the local molecular structure and bonding information and serves as a means for incorporating micromechanical analyses for the prediction of bulk mechanical properties of SWNT/polymer composites with various nanotube sizes and orientations. As an example, the proposed approach is used for the constitutive modeling of two SWNT/polyethylene composite systems, one with continuous and aligned SWNT and the other with discontinuous and randomly aligned nanotubes.

The beaming of subhalo accretion

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.

2016-10-01

We examine the infall pattern of subhaloes onto hosts in the context of the large-scale structure. We find that the infall pattern is essentially driven by the shear tensor of the ambient velocity field. Dark matter subhaloes are preferentially accreted along the principal axis of the shear tensor which corresponds to the direction of weakest collapse. We examine the dependence of this preferential infall on subhalo mass, host halo mass and redshift. Although strongest for the most massive hosts and the most massive subhaloes at high redshift, the preferential infall of subhaloes is effectively universal in the sense that its always aligned with the axis of weakest collapse of the velocity shear tensor. It is the same shear tensor that dictates the structure of the cosmic web and hence the shear field emerges as the key factor that governs the local anisotropic pattern of structure formation. Since the small (sub-Mpc) scale is strongly correlated with the mid-range (~ 10 Mpc) scale - a scale accessible by current surveys of peculiar velocities - it follows that findings presented here open a new window into the relation between the observed large scale structure unveiled by current surveys of peculiar velocities and the preferential infall direction of the Local Group. This may shed light on the unexpected alignments of dwarf galaxies seen in the Local Group.

Multifunctional cell-culture platform for aligned cell sheet monitoring, transfer printing, and therapy.

PubMed

Kim, Seok Joo; Cho, Hye Rim; Cho, Kyoung Won; Qiao, Shutao; Rhim, Jung Soo; Soh, Min; Kim, Taeho; Choi, Moon Kee; Choi, Changsoon; Park, Inhyuk; Hwang, Nathaniel S; Hyeon, Taeghwan; Choi, Seung Hong; Lu, Nanshu; Kim, Dae-Hyeong

2015-03-24

While several functional platforms for cell culturing have been proposed for cell sheet engineering, a soft integrated system enabling in vitro physiological monitoring of aligned cells prior to their in vivo applications in tissue regeneration has not been reported. Here, we present a multifunctional, soft cell-culture platform equipped with ultrathin stretchable nanomembrane sensors and graphene-nanoribbon cell aligners, whose system modulus is matched with target tissues. This multifunctional platform is capable of aligning plated cells and in situ monitoring of cellular physiological characteristics during proliferation and differentiation. In addition, it is successfully applied as an in vitro muscle-on-a-chip testing platform. Finally, a simple but high-yield transfer printing mechanism is proposed to deliver cell sheets for scaffold-free, localized cell therapy in vivo. The muscle-mimicking stiffness of the platform allows the high-yield transfer printing of multiple cell sheets and results in successful therapies in diseased animal models. Expansion of current results to stem cells will provide unique opportunities for emerging classes of tissue engineering and cell therapy technologies.

Elucidating the role of transcription in shaping the 3D structure of the bacterial genome

NASA Astrophysics Data System (ADS)

Brandao, Hugo B.; Wang, Xindan; Rudner, David Z.; Mirny, Leonid

Active transcription has been linked to several genome conformation changes in bacteria, including the recruitment of chromosomal DNA to the cell membrane and formation of nucleoid clusters. Using genomic and imaging data as input into mathematical models and polymer simulations, we sought to explore the extent to which bacterial 3D genome structure could be explained by 1D transcription tracks. Using B. subtilis as a model organism, we investigated via polymer simulations the role of loop extrusion and DNA super-coiling on the formation of interaction domains and other fine-scale features that are visible in chromosome conformation capture (Hi-C) data. We then explored the role of the condensin structural maintenance of chromosome complex on the alignment of chromosomal arms. A parameter-free transcription traffic model demonstrated that mean chromosomal arm alignment can be quantitatively explained, and the effects on arm alignment in genomically rearranged strains of B. subtilis were accurately predicted. H.B. acknowledges support from the Natural Sciences and Engineering Research Council of Canada for a PGS-D fellowship.

Connecting Interface Structure to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

Understanding structure-function relationships at aqueous semiconductor interfaces presents fundamental challenges, including the discovery of the key interface structure motifs themselves. Important examples include the alignment of electrochemical redox levels with the semiconductor band edges and the identification of catalytic active sites. We have developed a multistep approach, initially demonstrated for GaN, ZnO and their alloys, motivated by measured high efficiency for photocatalytic water oxidation. The interface structure is simulated using ab initio molecular dynamics (AIMD). The calculated, average interface dipole is combined with the GW approach from many-body perturbation theory to calculate the energy level alignment between the semiconductor band edges and the centroid of the occupied 1b1 energy level of water and thus, the electrochemical levels. Cluster models are used to study reaction pathways. The emergent interface motif is the full (GaN) or partial (ZnO) dissociated interface water layer. Here I will focus on the aqueous interfaces to the stable TiO2 anatase (101) and rutile (110) facets. The AIMD calculations reveal interface water dissociation and reassociation processes through distinct pathways: one direct at the interface and the other via a spectator water molecule from the hydration layer. Comparisons between the two interfaces shows that the energy landscape for these pathways depends on the local hydrogen bonding patterns and the interplay with the interface template. Combined results from different initial conditions and AIMD temperatures demonstrate a partially dissociated interface water layer in both cases. Specifically for rutile, structure and the GW-based analysis of the interface energy level alignment agree with experiment. Finally, hole localization at different interface structure motifs will be discussed. Work performed in collaboration with J. Lyons, N. Kharche, M. Ertem and J. Muckerman, done in part at the CFN, which is a U.S. DOE Office of Science Facility, at BNL under Contract No. DE-SC0012704 and with resources from NERSC under Contract No. DE-AC02-05CH11231.

Dark halos formed via dissipationless collapse. I - Shapes and alignment of angular momentum

NASA Astrophysics Data System (ADS)

Warren, Michael S.; Quinn, Peter J.; Salmon, John K.; Zurek, Wojciech H.

1992-11-01

We use N-body simulations on highly parallel supercomputers to study the structure of Galactic dark matter halos. The systems form by gravitational collapse from scale-free and more general Gaussian initial density perturbations in an expanding 400 Mpc-cubed spherical slice of an Einstein-deSitter universe. We analyze the structure and kinematics of about 100 of the largest relaxed halos in each of 10 separate simulations. A typical halo is a triaxial spheroid which tends to be more often prolate than oblate. These shapes are maintained by anisotropic velocity dispersion rather than by angular momentum. Nevertheless, there is a significant tendency for the total angular momentum vector to be aligned with the minor axis of the density distribution.

Water promotes the sealing of nanoscale packing defects in folding proteins.

PubMed

Fernández, Ariel

2014-05-21

A net dipole moment is shown to arise from a non-Debye component of water polarization created by nanoscale packing defects on the protein surface. Accordingly, the protein electrostatic field exerts a torque on the induced dipole, locally impeding the nucleation of ice at the protein-water interface. We evaluate the solvent orientation steering (SOS) as the reversible work needed to align the induced dipoles with the Debye electrostatic field and computed the SOS for the variable interface of a folding protein. The minimization of the SOS is shown to drive protein folding as evidenced by the entrainment of the total free energy by the SOS energy along trajectories that approach a Debye limit state where no torque arises. This result suggests that the minimization of anomalous water polarization at the interface promotes the sealing of packing defects, thereby maintaining structural integrity and committing the protein chain to fold.

Ferromagnetic Switching of Knotted Vector Fields in Liquid Crystal Colloids.

PubMed

Zhang, Qiaoxuan; Ackerman, Paul J; Liu, Qingkun; Smalyukh, Ivan I

2015-08-28

We experimentally realize polydomain and monodomain chiral ferromagnetic liquid crystal colloids that exhibit solitonic and knotted vector field configurations. Formed by dispersions of ferromagnetic nanoplatelets in chiral nematic liquid crystals, these colloidal ferromagnets exhibit spontaneous long-range alignment of magnetic dipole moments of individual platelets, giving rise to a continuum of the magnetization field M(r). Competing effects of surface confinement and chirality prompt spontaneous formation and enable the optical generation of localized twisted solitonic structures with double-twist tubes and torus knots of M(r), which exhibit a strong sensitivity to the direction of weak magnetic fields ∼1  mT. Numerical modeling, implemented through free energy minimization to arrive at a field-dependent three-dimensional M(r), shows a good agreement with experiments and provides insights into the torus knot topology of observed field configurations and the corresponding physical underpinnings.

Controllable conversion of quasi-freestanding polymer chains to graphene nanoribbons

NASA Astrophysics Data System (ADS)

Ma, Chuanxu; Xiao, Zhongcan; Zhang, Honghai; Liang, Liangbo; Huang, Jingsong; Lu, Wenchang; Sumpter, Bobby G.; Hong, Kunlun; Bernholc, J.; Li, An-Ping

2017-03-01

In the bottom-up synthesis of graphene nanoribbons (GNRs) from self-assembled linear polymer intermediates, surface-assisted cyclodehydrogenations usually take place on catalytic metal surfaces. Here we demonstrate the formation of GNRs from quasi-freestanding polymers assisted by hole injections from a scanning tunnelling microscope (STM) tip. While catalytic cyclodehydrogenations typically occur in a domino-like conversion process during the thermal annealing, the hole-injection-assisted reactions happen at selective molecular sites controlled by the STM tip. The charge injections lower the cyclodehydrogenation barrier in the catalyst-free formation of graphitic lattices, and the orbital symmetry conservation rules favour hole rather than electron injections for the GNR formation. The created polymer-GNR intraribbon heterostructures have a type-I energy level alignment and strongly localized interfacial states. This finding points to a new route towards controllable synthesis of freestanding graphitic layers, facilitating the design of on-surface reactions for GNR-based structures.

GenomeVista

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poliakov, Alexander; Couronne, Olivier

2002-11-04

Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program tomore » find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

DOE PAGES

Wang, Xu; Le, Anh -Thu; Yu, Chao; ...

2016-03-30

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. Lastly, amore » simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.« less

Deformation behavior and mechanical analysis of vertically aligned carbon nanotube (VACNT) bundles

NASA Astrophysics Data System (ADS)

Hutchens, Shelby B.

Vertically aligned carbon nanotubes (VACNTs) serve as integral components in a variety of applications including MEMS devices, energy absorbing materials, dry adhesives, light absorbing coatings, and electron emitters, all of which require structural robustness. It is only through an understanding of VACNT's structural mechanical response and local constitutive stress-strain relationship that future advancements through rational design may take place. Even for applications in which the structural response is not central to device performance, VACNTs must be sufficiently robust and therefore knowledge of their microstructure-property relationship is essential. This thesis first describes the results of in situ uniaxial compression experiments of 50 micron diameter cylindrical bundles of these complex, hierarchical materials as they undergo unusual deformation behavior. Most notably they deform via a series of localized folding events, originating near the bundle base, which propagate laterally and collapse sequentially from bottom to top. This deformation mechanism accompanies an overall foam-like stress-strain response having elastic, plateau, and densification regimes with the addition of undulations in the stress throughout the plateau regime that correspond to the sequential folding events. Microstructural observations indicate the presence of a strength gradient, due to a gradient in both tube density and alignment along the bundle height, which is found to play a key role in both the sequential deformation process and the overall stress-strain response. Using the complicated structural response as both motivation and confirmation, a finite element model based on a viscoplastic solid is proposed. This model is characterized by a flow stress relation that contains an initial peak followed by strong softening and successive hardening. Analysis of this constitutive relation results in capture of the sequential buckling phenomenon and a strength gradient effect. This combination of experimental and modeling approaches motivates discussion of the particular microstructural mechanisms and local material behavior that govern the non-trivial energy absorption via sequential, localized buckle formation in the VACNT bundles.

Comparison of landmark-based and automatic methods for cortical surface registration

PubMed Central

Pantazis, Dimitrios; Joshi, Anand; Jiang, Jintao; Shattuck, David; Bernstein, Lynne E.; Damasio, Hanna; Leahy, Richard M.

2009-01-01

Group analysis of structure or function in cerebral cortex typically involves as a first step the alignment of the cortices. A surface based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages FreeSurfer and BrainVoyager. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for ROIs in the perisylvian region for the landmark based method and FreeSurfer. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and also that automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis. PMID:19796696

Simultaneous fluorescence and quantitative phase microscopy with single-pixel detectors

NASA Astrophysics Data System (ADS)

Liu, Yang; Suo, Jinli; Zhang, Yuanlong; Dai, Qionghai

2018-02-01

Multimodal microscopy offers high flexibilities for biomedical observation and diagnosis. Conventional multimodal approaches either use multiple cameras or a single camera spatially multiplexing different modes. The former needs expertise demanding alignment and the latter suffers from limited spatial resolution. Here, we report an alignment-free full-resolution simultaneous fluorescence and quantitative phase imaging approach using single-pixel detectors. By combining reference-free interferometry with single-pixel detection, we encode the phase and fluorescence of the sample in two detection arms at the same time. Then we employ structured illumination and the correlated measurements between the sample and the illuminations for reconstruction. The recovered fluorescence and phase images are inherently aligned thanks to single-pixel detection. To validate the proposed method, we built a proof-of-concept setup for first imaging the phase of etched glass with the depth of a few hundred nanometers and then imaging the fluorescence and phase of the quantum dot drop. This method holds great potential for multispectral fluorescence microscopy with additional single-pixel detectors or a spectrometer. Besides, this cost-efficient multimodal system might find broad applications in biomedical science and neuroscience.

Spontaneous Magnetic Alignment by Yearling Snapping Turtles: Rapid Association of Radio Frequency Dependent Pattern of Magnetic Input with Novel Surroundings

PubMed Central

Landler, Lukas; Painter, Michael S.; Youmans, Paul W.; Hopkins, William A.; Phillips, John B.

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF (‘RF off → RF off’), but were disoriented when subsequently exposed to RF (‘RF off → RF on’). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF (‘RF on → RF off’), but aligned towards magnetic south when tested with RF (‘RF on → RF on’). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space. PMID:25978736

Spontaneous magnetic alignment by yearling snapping turtles: rapid association of radio frequency dependent pattern of magnetic input with novel surroundings.

PubMed

Landler, Lukas; Painter, Michael S; Youmans, Paul W; Hopkins, William A; Phillips, John B

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF ('RF off → RF off'), but were disoriented when subsequently exposed to RF ('RF off → RF on'). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF ('RF on → RF off'), but aligned towards magnetic south when tested with RF ('RF on → RF on'). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space.

Structure-activity relationships of cannabinoids: A joint CoMFA and pseudoreceptor modelling study

NASA Astrophysics Data System (ADS)

Schmetzer, Silke; Greenidge, Paulette; Kovar, Karl-Artur; Schulze-Alexandru, Meike; Folkers, Gerd

1997-05-01

A cannabinoid pseudoreceptor model for the CB1-receptor has been constructed for 31 cannabinoids using the molecular modelling software YAK. Additionally, two CoMFA studies were performed on these ligands, the first of which was conducted prior to the building of the pseudoreceptor. Its pharmacophore is identical with the initial superposition of ligands used for pseudoreceptor construction. In contrast, the ligand alignment for the second CoMFA study was taken directly from the final cannabinoid pseudoreceptor model. This altered alignment gives markedly improved cross-validated r2 values as compared to those obtained from the original alignment with{{r}}_{{{cross}}}^2 values of 0.79 and 0.63, respectively, for five components. However, the pharmacophore alignment has the better predictive ability. Both the CoMFA and pseudoreceptor methods predict the free energy of binding of test ligands well.

Creating Polymer Hydrogel Microfibres with Internal Alignment via Electrical and Mechanical Stretching

PubMed Central

Zhang, Shuming; Liu, Xi; Barreto-Ortiz, Sebastian F.; Yu, Yixuan; Ginn, Brian; DeSantis, Nicholas; Hutton, Daphne L; Grayson, Warren; Cui, Fu-Zhai; Korgel, Brian A.; Gerecht, Sharon; Mao, Hai-Quan

2014-01-01

Hydrogels have been widely used for 3-dimensional (3D) cell culture and tissue regeneration due to their tunable biochemical and physicochemical properties as well as their high water content, which resembles the aqueous microenvironment of the natural extracellular matrix. While many properties of natural hydrogel matrices are modifiable, their intrinsic isotropic structure limits the control over cellular organization, which is critical to restore tissue function. Here we report a generic approach to incorporate alignment topography inside the hydrogel matrix using a combination of electrical and mechanical stretching. Hydrogel fibres with uniaxial alignment were prepared from aqueous solutions of natural polymers such as alginate, fibrin, gelatin, and hyaluronic acid under ambient conditions. The unique internal alignment feature drastically enhances the mechanical properties of the hydrogel microfibres. Furthermore, the facile, organic solvent-free processing conditions are amenable to the incorporation of live cells within the hydrogel fibre or on the fibre surface; both approaches effectively induce cellular alignment. This work demonstrates a versatile and scalable strategy to create aligned hydrogel microfibres from various natural polymers. PMID:24439410

DOE Office of Scientific and Technical Information (OSTI.GOV)

Finzel, Kati, E-mail: kati.finzel@liu.se

The local conditions for the Pauli potential that are necessary in order to yield self-consistent electron densities from orbital-free calculations are investigated for approximations that are expressed with the help of a local position variable. It is shown that those local conditions also apply when the Pauli potential is given in terms of the electron density. An explicit formula for the Ne atom is given, preserving the local conditions during the iterative procedure. The resulting orbital-free electron density exhibits proper shell structure behavior and is in close agreement with the Kohn-Sham electron density. This study demonstrates that it is possiblemore » to obtain self-consistent orbital-free electron densities with proper atomic shell structure from simple one-point approximations for the Pauli potential at local density level.« less

Quadrupole Alignment and Trajectory Correction for Future Linear Colliders: SLC Tests of a Dispersion-Free Steering Algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Assmann, R

2004-06-08

The feasibility of future linear colliders depends on achieving very tight alignment and steering tolerances. All proposals (NLC, JLC, CLIC, TESLA and S-BAND) currently require a total emittance growth in the main linac of less than 30-100% [1]. This should be compared with a 100% emittance growth in the much smaller SLC linac [2]. Major advances in alignment and beam steering techniques beyond those used in the SLC are necessary for the next generation of linear colliders. In this paper, we present an experimental study of quadrupole alignment with a dispersion-free steering algorithm. A closely related method (wakefield-free steering) takesmore » into account wakefield effects [3]. However, this method can not be studied at the SLC. The requirements for future linear colliders lead to new and unconventional ideas about alignment and beam steering. For example, no dipole correctors are foreseen for the standard trajectory correction in the NLC [4]; beam steering will be done by moving the quadrupole positions with magnet movers. This illustrates the close symbiosis between alignment, beam steering and beam dynamics that will emerge. It is no longer possible to consider the accelerator alignment as static with only a few surveys and realignments per year. The alignment in future linear colliders will be a dynamic process in which the whole linac, with thousands of beam-line elements, is aligned in a few hours or minutes, while the required accuracy of about 5 pm for the NLC quadrupole alignment [4] is a factor of 20 higher than in existing accelerators. The major task in alignment and steering is the accurate determination of the optimum beam-line position. Ideally one would like all elements to be aligned along a straight line. However, this is not practical. Instead a ''smooth curve'' is acceptable as long as its wavelength is much longer than the betatron wavelength of the accelerated beam. Conventional alignment methods are limited in accuracy by errors in the survey and the fiducials. Beam-based alignment methods ideally only depend upon the BPM resolution and generally provide much better precision. Many of those techniques are described in other contributions to this workshop. In this paper we describe our experiences with a dispersion-free steering algorithm for linacs. This algorithm was first suggested by Raubenheimer and Ruth in 1990 [5]. It h as been studied in simulations for NLC [5], TESLA [6], the S-BAND proposal [7] and CLIC [8]. The dispersion-free steering technique can be applied to the whole linac at once and returns the alignment (or trajectory) that minimizes the dispersive emittance growth of the beam. Thus it allows an extremely fast alignment of the beam-line. As we will show dispersion-free steering is only sensitive to quadrupole misalignments. Wakefield-free steering [3] as mentioned before is a closely related technique that minimizes the emittance growth caused by both dispersion and wakefields. Due to hardware limitations (i.e. insufficient relative range of power supplies) we could not study this method experimentally in the SLC. However, its systematics are very similar to those of dispersion-free steering. The studies of dispersion-free steering which are presented made extensive use of the unique potential of the SLC as the only operating linear collider. We used it to study the performance and problems of advanced beam-based optimization tools in a real beam-line environment and on a large scale. We should mention that the SLC has utilized beam-based alignment for years [9], using the difference of electron and positron trajectories. This method, however, cannot be used in future linear colliders. The goal of our work is to demonstrate the performance of advanced beam-based alignment techniques in linear colliders and to anticipate possible reality-related problems. Those can then be solved in the design state for the next generation of linear colliders.« less

Cultivating American- and Japanese-Style Relatedness through Mother-Child Conversation

ERIC Educational Resources Information Center

Crane, Lauren Shapiro; Fernald, Anne

2017-01-01

This study investigated whether European American and Japanese mothers' speech to preschoolers contained exchange- and alignment-oriented structures that reflect and possibly support culture-specific models of self-other relatedness. In each country 12 mothers were observed in free play with their 3-year-olds. Maternal speech was coded for…

On the orientation of the backbone dipoles in native folds

PubMed Central

Ripoll, Daniel R.; Vila, Jorge A.; Scheraga, Harold A.

2005-01-01

The role of electrostatic interactions in determining the native fold of proteins has been investigated by analyzing the alignment of peptide bond dipole moments with the local electrostatic field generated by the rest of the molecule with and without solvent effects. This alignment was calculated for a set of 112 native proteins by using charges from a gas phase potential. Most of the peptide dipoles in this set of proteins are on average aligned with the electrostatic field. The dipole moments associated with α-helical conformations show the best alignment with the electrostatic field, followed by residues in β-strand conformations. The dipole moments associated with other secondary structure elements are on average better aligned than in randomly generated conformations. The alignment of a dipole with the local electrostatic field depends on both the topology of the native fold and the charge distribution assumed for all of the residues. The influences of (i) solvent effects, (ii) different sets of charges, and (iii) the charge distribution assumed for the whole molecule were examined with a subset of 22 proteins each of which contains <30 ionizable groups. The results show that alternative charge distribution models lead to significant differences among the associated electrostatic fields, whereas the electrostatic field is less sensitive to the particular set of the adopted charges themselves (empirical conformational energy program for peptides or parameters for solvation energy). PMID:15894608

A protein block based fold recognition method for the annotation of twilight zone sequences.

PubMed

Suresh, V; Ganesan, K; Parthasarathy, S

2013-03-01

The description of protein backbone was recently improved with a group of structural fragments called Structural Alphabets instead of the regular three states (Helix, Sheet and Coil) secondary structure description. Protein Blocks is one of the Structural Alphabets used to describe each and every region of protein backbone including the coil. According to de Brevern (2000) the Protein Blocks has 16 structural fragments and each one has 5 residues in length. Protein Blocks fragments are highly informative among the available Structural Alphabets and it has been used for many applications. Here, we present a protein fold recognition method based on Protein Blocks for the annotation of twilight zone sequences. In our method, we align the predicted Protein Blocks of a query amino acid sequence with a library of assigned Protein Blocks of 953 known folds using the local pair-wise alignment. The alignment results with z-value ≥ 2.5 and P-value ≤ 0.08 are predicted as possible folds. Our method is able to recognize the possible folds for nearly 35.5% of the twilight zone sequences with their predicted Protein Block sequence obtained by pb_prediction, which is available at Protein Block Export server.

Catalyst-free fabrication of novel ZnO/CuO core-Shell nanowires heterojunction: Controlled growth, structural and optoelectronic properties

NASA Astrophysics Data System (ADS)

Khan, Muhammad Arif; Wahab, Yussof; Muhammad, Rosnita; Tahir, Muhammad; Sakrani, Samsudi

2018-03-01

Development of controlled growth and vertically aligned ZnO/CuO core-shell heterojunction nanowires (NWs) with large area by a catalyst free vapor deposition and oxidation approach has been investigated. Structural characterization reveals successful fabrication of a core ZnO nanowire having single crystalline hexagonal wurtzite structure along [002] direction and CuO nanostructure shell with thickness (8-10 nm) having polycrystalline monoclinic structure. The optical property analysis suggests that the reflectance spectrum of ZnO/CuO heterostructure nanowires is decreased by 18% in the visible range, which correspondingly shows high absorption in this region as compared to pristine ZnO nanowires. The current-voltage (I-V) characteristics of core-shell heterojunction nanowires measured by conductive atomic force microscopy (C-AFM) shows excellent rectifying behavior, which indicates the characteristics of a good p-n junction. The high-resolution transmission electron microscopy (HRTEM) has confirmed the sharp junction interface between the core-shell heterojunction nanowire arrays. The valence band offset and conduction band offset at ZnO/CuO heterointerfaces are measured to be 2.4 ± 0.05 and 0.23 ± 0.005 eV respectively, using X-ray photoelectron spectroscopy (XPS) and a type-II band alignment structure is found. The results of this study contribute to the development of new advanced device heterostructures for solar energy conversion and optoelectronics applications.

Stacking InAs quantum dots over ErAs semimetal nanoparticles on GaAs (0 0 1) using molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Zhang, Yuanchang; Eyink, Kurt G.; Grazulis, Lawrence; Hill, Madelyn; Peoples, Joseph; Mahalingam, Krishnamurthy

2017-11-01

Hybrid nanostructures are known to elicit an enhanced optical response. We study the directed alignment of ErAs metal nanoparticle (NP) and InAs quantum dot (QD) using molecular beam eptaxy (MBE) in a GaAs matrix. Due to high surface free energy caused by the crystal structure difference, overgrowth of an ErAs NP with GaAs forms a depression that condenses subsequent InAs adatoms to form an inverted QD self-aligned to the underlying ErAs NP. The ErAs NP growth, GaAs overgrowth, and InAs QD deposition were carefully controlled and studied with transmission electron microscopy (TEM) and atomic force microscopy (AFM) to investigate their effects on the QD-NP alignment.

Solvent-free fabrication of three dimensionally aligned polycaprolactone microfibers for engineering of anisotropic tissues.

PubMed

An, Jia; Chua, Chee Kai; Leong, Kah Fai; Chen, Chih-Hao; Chen, Jyh-Ping

2012-10-01

Fabrication of aligned microfiber scaffolds is critical in successful engineering of anisotropic tissues such as tendon, ligaments and nerves. Conventionally, aligned microfiber scaffolds are two dimensional and predominantly fabricated by electrospinning which is solvent dependent. In this paper, we report a novel technique, named microfiber melt drawing, to fabricate a bundle of three dimensionally aligned polycaprolactone microfibers without using any organic solvent. This technique is simple yet effective. It has been demonstrated that polycaprolactone microfibers of 10 μm fiber diameter can be directly drawn from a 2 mm orifice. Orifice diameter, temperature and take-up speed significantly influence the final linear density and fiber diameter of the microfibers. Mechanical test suggests that mechanical properties such as stiffness and breaking force of microfiber bundles can be easily adjusted by the number of fibers. In vitro study shows that these microfibers are able to support the proliferation of human dermal fibroblasts over 7 days. In vivo result of Achilles tendon repair in a rabbit model shows that the microfibers were highly infiltrated by tendon tissue as early as in 1 month, besides, the repaired tendon have a well-aligned tissue structure under the guidance of aligned microfibers. However whether these three dimensionally aligned microfibers can induce three dimensionally aligned cells remains inconclusive.

Face Alignment via Regressing Local Binary Features.

PubMed

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.

Silicon microring resonators

NASA Astrophysics Data System (ADS)

Tan, Ying; Dai, Daoxin

2018-05-01

Silicon microring resonators (MRRs) are very popular for many applications because of the advantages of footprint compactness, easy scalability, and functional versatility. Ultra-compact silicon MRRs with box-like spectral responses are realized with a very large free-spectral range (FSR) by introducing bent directional couplers. The measured box-like spectral response has an FSR of >30 nm. The permanent wavelength-alignment techniques for MRRs are also presented, including the laser-induced local-oxidation technique as well as the local-etching technique. With these techniques, one can control finely the permanent wavelength shift, which is also large enough to compensate the random wavelength variation due to the random fabrication errors.

CAFE: aCcelerated Alignment-FrEe sequence analysis

PubMed Central

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A.; Waterman, Michael S.

2017-01-01

Abstract Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^*$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^S$\\end{document} are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. PMID:28472388

Graph wavelet alignment kernels for drug virtual screening.

PubMed

Smalter, Aaron; Huan, Jun; Lushington, Gerald

2009-06-01

In this paper, we introduce a novel statistical modeling technique for target property prediction, with applications to virtual screening and drug design. In our method, we use graphs to model chemical structures and apply a wavelet analysis of graphs to summarize features capturing graph local topology. We design a novel graph kernel function to utilize the topology features to build predictive models for chemicals via Support Vector Machine classifier. We call the new graph kernel a graph wavelet-alignment kernel. We have evaluated the efficacy of the wavelet-alignment kernel using a set of chemical structure-activity prediction benchmarks. Our results indicate that the use of the kernel function yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art chemical classification approaches. In addition, our results also show that the use of wavelet functions significantly decreases the computational costs for graph kernel computation with more than ten fold speedup.

A phantom study of the immobilization and the indications for using virtual isocenter in stereoscopic X‐ray image guidance system referring to position localizer in frameless radiosurgery

PubMed Central

Chang, Hsiao‐Han; Lee, Hsiao‐Fei; Sung, Chien‐Cheng; Liao, Tsung‐I

2013-01-01

A frameless radiosurgery system is using a set of thermoplastic mask for fixation and stereoscopic X‐ray imaging for alignment. The accuracy depends on mask fixation and imaging. Under certain circumstances, the guidance images may contain insufficient bony structures, resulting in lesser accuracy. A virtual isocenter function is designed for such scenarios. In this study, we investigated the immobilization and the indications for using virtual isocenter. Twenty‐four arbitrary imaginary treatment targets (ITTs) in phantom were evaluated. The external Localizer with positioner films was used as reference. The alignments by using actual and virtual isocenter in image guidance were compared. The deviation of the alignment after mask removing and then resetting was also checked. The results illustrated that the mean deviation between the alignment by image guidance using actual isocenter (Isoimg) and the localizer(Isoloc) was 2.26mm±1.16mm (standard deviation, SD), 1.66mm±0.83mm for using virtual isocenter. The deviation of the alignment by the image guidance using actual isocenter to the localizer before and after mask resetting was 7.02mm±5.8mm. The deviations before and after mask resetting were insignificant for the target center from skull edge larger than 80 mm on craniocaudal direction. The deviations between the alignment using actual and virtual isocenter in image guidance were not significant if the minimum distance from target center to skull edge was larger or equal to 30 mm. Due to an unacceptable deviation after mask resetting, the image guidance is necessary to improve the accuracy of frameless immobilization. A treatment isocenter less than 30 mm from the skull bone should be an indication for using virtual isocenter to align in image guidance. The virtual isocenter should be set as caudally as possible, and the sella of skull should be the ideal point. PACS numbers: 87.55.kh, 87.55.ne, 87.55.tm PMID:23835379

Comparative modeling without implicit sequence alignments.

PubMed

Kolinski, Andrzej; Gront, Dominik

2007-10-01

The number of known protein sequences is about thousand times larger than the number of experimentally solved 3D structures. For more than half of the protein sequences a close or distant structural analog could be identified. The key starting point in a classical comparative modeling is to generate the best possible sequence alignment with a template or templates. With decreasing sequence similarity, the number of errors in the alignments increases and these errors are the main causes of the decreasing accuracy of the molecular models generated. Here we propose a new approach to comparative modeling, which does not require the implicit alignment - the model building phase explores geometric, evolutionary and physical properties of a template (or templates). The proposed method requires prior identification of a template, although the initial sequence alignment is ignored. The model is built using a very efficient reduced representation search engine CABS to find the best possible superposition of the query protein onto the template represented as a 3D multi-featured scaffold. The criteria used include: sequence similarity, predicted secondary structure consistency, local geometric features and hydrophobicity profile. For more difficult cases, the new method qualitatively outperforms existing schemes of comparative modeling. The algorithm unifies de novo modeling, 3D threading and sequence-based methods. The main idea is general and could be easily combined with other efficient modeling tools as Rosetta, UNRES and others.

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

PubMed Central

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L.; Yao, Xuebiao

2015-01-01

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression. PMID:26240331

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment.

PubMed

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L; Yao, Xuebiao

2015-08-18

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C-MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.

Non-lethal sampling for the detection of Myxobolus cerebralis in asymptomatic rainbow trout

USGS Publications Warehouse

Schill, Bane; Waldrop, Thomas; Densmore, Christine; Blazer, Vicki

1999-01-01

We have described in previous reports (Schill et al., 1998) the development of a polymerase chain reaction (PCR) amplification of 18S ribosomal RNA for the detection of Myxozoan parasites. Oligonucleotide primers were developed by multiple alignment of Myxozoan sequence information and analysis by a custom-written computer program (PRIM). Candidate pairs of primer sequences were then analyzed for specificity by BLAST (Basic Local Alignment Search Tool). From these, a set of promising primers (MYXFWD and MYXREV) was chosen for further testing. These were chosen because they should direct detection of a number of Myxozoan species (Table 1). PCR using MXYFWD and MYXREV proved to be robust and relatively free of artifact products. Further, we were able to routinely detect Myxobolus cerebralis in fish tissues (Figure 1).

Origin of storm footprints on the sea seen by synthetic aperture radar.

PubMed

Atlas, D

1994-11-25

Spaceborne synthetic aperture radar can detect storm footprints on the sea. Coastal weather radar from Cape Hatteras provides evidence that the echo-free hole at the footprint core is the result of wave damping by rain. The increased radar cross section of the sea surrounding the echo-free hole results from the divergence of the precipitation-forced downdraft impacting the sea. The footprint boundary is the gust front; its oriention is aligned with the direction of the winds aloft, which are transported down with the downdraft, and its length implies downdraft impact 1 hour earlier at a quasi-stationary impact spot. The steady, localized nature of the storm remains a mystery.

A Two-Dimensional Manganese Gallium Nitride Surface Structure Showing Ferromagnetism at Room Temperature.

PubMed

Ma, Yingqiao; Chinchore, Abhijit V; Smith, Arthur R; Barral, María Andrea; Ferrari, Valeria

2018-01-10

Practical applications of semiconductor spintronic devices necessitate ferromagnetic behavior at or above room temperature. In this paper, we demonstrate a two-dimensional manganese gallium nitride surface structure (MnGaN-2D) which is atomically thin and shows ferromagnetic domain structure at room temperature as measured by spin-resolved scanning tunneling microscopy and spectroscopy. Application of small magnetic fields proves that the observed magnetic domains follow a hysteretic behavior. Two initially oppositely oriented MnGaN-2D domains are rotated into alignment with only 120 mT and remain mostly in alignment at remanence. The measurements are further supported by first-principles theoretical calculations which reveal highly spin-polarized and spin-split surface states with spin polarization of up to 95% for manganese local density of states.

Rethinking the polar cap: Eccentric dipole structuring of ULF power at the highest corrected geomagnetic latitudes

NASA Astrophysics Data System (ADS)

Urban, Kevin D.; Gerrard, Andrew J.; Lanzerotti, Louis J.; Weatherwax, Allan T.

2016-09-01

The day-to-day evolution and statistical features of Pc3-Pc7 band ultralow frequency (ULF) power throughout the southern polar cap suggest that the corrected geomagnetic (CGM) coordinates do not adequately organize the observed hydromagnetic spatial structure. It is shown that that the local-time distribution of ULF power at sites along CGM latitudinal parallels exhibit fundamental differences and that the CGM latitude of a site in general is not indicative of the site's projection into the magnetosphere. Thus, ULF characteristics observed at a single site in the polar cap cannot be freely generalized to other sites of similar CGM latitude but separated in magnetic local time, and the inadequacy of CGM coordinates in the polar cap has implications for conjugacy/mapping studies in general. In seeking alternative, observationally motivated systems of "polar cap latitudes," it is found that eccentric dipole (ED) coordinates have several strengths in organizing the hydromagnetic spatial structure in the polar cap region. ED latitudes appear to better classify the local-time ULF power in both magnitude and morphology and better differentiate the "deep polar cap" (where the ULF power is largely UT dependent and nearly free of local-time structure) from the "peripheral polar cap" (where near-magnetic noon pulsations dominate at lower and lower frequencies as one increases in ED latitude). Eccentric local time is shown to better align the local-time profiles in the magnetic east component over several PcX bands but worsen in the magnetic north component. It is suggested that a hybrid ED-CGM coordinate system might capture the strengths of both CGM and ED coordinates. It is shown that the local-time morphology of median ULF power at high-latitude sites is dominantly driven by where they project into the magnetosphere, which is best quantified by their proximity to the low-altitude cusp on the dayside (which is not necessarily quantified by a site's CGM latitude), and that variations in the local-time morphology at sites similar in ED latitude are due to both geographic local-time control (relative amplification or dampening by the diurnal variation in the local ionospheric conductivity) and geomagnetic coastal effects (enhanced power in a coastally mediated direction). Regardless of cause, it is emphasized that the application of CGM latitudes in the polar cap region is not entirely meaningful and likely should be dispensed with in favor of a scheme that is in better accord with the observed hydromagnetic spatial structure.

Local Minima Free Parameterized Appearance Models

PubMed Central

Nguyen, Minh Hoai; De la Torre, Fernando

2010-01-01

Parameterized Appearance Models (PAMs) (e.g. Eigentracking, Active Appearance Models, Morphable Models) are commonly used to model the appearance and shape variation of objects in images. While PAMs have numerous advantages relative to alternate approaches, they have at least two drawbacks. First, they are especially prone to local minima in the fitting process. Second, often few if any of the local minima of the cost function correspond to acceptable solutions. To solve these problems, this paper proposes a method to learn a cost function by explicitly optimizing that the local minima occur at and only at the places corresponding to the correct fitting parameters. To the best of our knowledge, this is the first paper to address the problem of learning a cost function to explicitly model local properties of the error surface to fit PAMs. Synthetic and real examples show improvement in alignment performance in comparison with traditional approaches. PMID:21804750

Theory vs. experiment for molecular clusters: Spectra of OCS trimers and tetramers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evangelisti, Luca; Dipartimento di Chimica “G. Ciamician,” University of Bologna, Via Selmi 2, Bologna 40126; Perez, Cristobal

All singly substituted {sup 13}C, {sup 18}O, and {sup 34}S isotopomers of the previously known OCS trimer are observed in natural abundance in a broad-band spectrum measured with a chirped-pulse Fourier transform microwave spectrometer. The complete substitution structure thus obtained critically tests (and confirms) the common assumption that monomers tend to retain their free structure in a weakly bound cluster. A new OCS trimer isomer is also observed, and its structure is determined to be barrel-shaped but with the monomers all approximately aligned, in contrast to the original trimer which is barrel-shaped with two monomers aligned and one anti-aligned. Anmore » OCS tetramer spectrum is assigned for the first time, and the tetramer structure resembles an original trimer with an OCS monomer added at the end with two sulfur atoms. Infrared spectra observed in the region of the OCS ν{sub 1} fundamental (≈2060 cm{sup −1}) are assigned to the same OCS tetramer, and another infrared band is tentatively assigned to a different tetramer isomer. The experimental results are compared and contrasted with theoretical predictions from the literature and from new cluster calculations which use an accurate OCS pair potential and assume pairwise additivity.« less

Toward optimized light utilization in nanowire arrays using scalable nanosphere lithography and selected area growth.

PubMed

Madaria, Anuj R; Yao, Maoqing; Chi, Chunyung; Huang, Ningfeng; Lin, Chenxi; Li, Ruijuan; Povinelli, Michelle L; Dapkus, P Daniel; Zhou, Chongwu

2012-06-13

Vertically aligned, catalyst-free semiconducting nanowires hold great potential for photovoltaic applications, in which achieving scalable synthesis and optimized optical absorption simultaneously is critical. Here, we report combining nanosphere lithography (NSL) and selected area metal-organic chemical vapor deposition (SA-MOCVD) for the first time for scalable synthesis of vertically aligned gallium arsenide nanowire arrays, and surprisingly, we show that such nanowire arrays with patterning defects due to NSL can be as good as highly ordered nanowire arrays in terms of optical absorption and reflection. Wafer-scale patterning for nanowire synthesis was done using a polystyrene nanosphere template as a mask. Nanowires grown from substrates patterned by NSL show similar structural features to those patterned using electron beam lithography (EBL). Reflection of photons from the NSL-patterned nanowire array was used as a measure of the effect of defects present in the structure. Experimentally, we show that GaAs nanowires as short as 130 nm show reflection of <10% over the visible range of the solar spectrum. Our results indicate that a highly ordered nanowire structure is not necessary: despite the "defects" present in NSL-patterned nanowire arrays, their optical performance is similar to "defect-free" structures patterned by more costly, time-consuming EBL methods. Our scalable approach for synthesis of vertical semiconducting nanowires can have application in high-throughput and low-cost optoelectronic devices, including solar cells.

PCV: An Alignment Free Method for Finding Homologous Nucleotide Sequences and its Application in Phylogenetic Study.

PubMed

Kumar, Rajnish; Mishra, Bharat Kumar; Lahiri, Tapobrata; Kumar, Gautam; Kumar, Nilesh; Gupta, Rahul; Pal, Manoj Kumar

2017-06-01

Online retrieval of the homologous nucleotide sequences through existing alignment techniques is a common practice against the given database of sequences. The salient point of these techniques is their dependence on local alignment techniques and scoring matrices the reliability of which is limited by computational complexity and accuracy. Toward this direction, this work offers a novel way for numerical representation of genes which can further help in dividing the data space into smaller partitions helping formation of a search tree. In this context, this paper introduces a 36-dimensional Periodicity Count Value (PCV) which is representative of a particular nucleotide sequence and created through adaptation from the concept of stochastic model of Kolekar et al. (American Institute of Physics 1298:307-312, 2010. doi: 10.1063/1.3516320 ). The PCV construct uses information on physicochemical properties of nucleotides and their positional distribution pattern within a gene. It is observed that PCV representation of gene reduces computational cost in the calculation of distances between a pair of genes while being consistent with the existing methods. The validity of PCV-based method was further tested through their use in molecular phylogeny constructs in comparison with that using existing sequence alignment methods.

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

PubMed Central

Eddy, Sean R.

2008-01-01

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (λ) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty (“Forward” scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores (“Viterbi” scores) are Gumbel-distributed with constant λ = log 2, and the high scoring tail of Forward scores is exponential with the same constant λ. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments. PMID:18516236

Long-wavelength asymptotics of unstable crossflow modes, including the effect of surface curvature

NASA Technical Reports Server (NTRS)

Choudhari, Meelan

1994-01-01

Stationary vortex instabilities with wavelengths significantly larger than the thickness of the underlying three-dimensional boundary layer are studied with asymptotic methods. The long-wavelength Rayleigh modes are locally neutral and are aligned with the direction of the local inviscid streamline. For a spanwise wave number Beta much less than 1, the spatial growth rate of these vortices is O(Beta(exp 3/2)). When Beta becomes O(R(exp -1/7)), the viscous correction associated with a thin sublayer near the surface modifies the inviscid growth rate to the leading order. As Beta is further decreased through this regime, viscous effects assume greater significance and dominate the growth-rate behavior. The spatial growth rate becomes comparable to the real part of the wave number when Beta = O(R(exp -1/4)). At this stage, the disturbance structure becomes fully viscous-inviscid interactive and is described by the triple-deck theory. For even smaller values of Beta, the vortex modes become nearly neutral again and align themselves with the direction of the wall-shear stress. Thus, the study explains the progression of the crossflow-vortex structure from the inflectional upper branch mode to nearly neutral long-wavelength modes that are aligned with the wall-shear direction.

Control superstructure of rigid polyelectrolytes in oppositely charged hydrogels via programmed internal stress

NASA Astrophysics Data System (ADS)

Takahashi, Riku; Wu, Zi Liang; Arifuzzaman, Md; Nonoyama, Takayuki; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

2014-08-01

Biomacromolecules usually form complex superstructures in natural biotissues, such as different alignments of collagen fibres in articular cartilages, for multifunctionalities. Inspired by nature, there are efforts towards developing multiscale ordered structures in hydrogels (recognized as one of the best candidates of soft biotissues). However, creating complex superstructures in gels are hardly realized because of the absence of effective approaches to control the localized molecular orientation. Here we introduce a method to create various superstructures of rigid polyanions in polycationic hydrogels. The control of localized orientation of rigid molecules, which are sensitive to the internal stress field of the gel, is achieved by tuning the swelling mismatch between masked and unmasked regions of the photolithographic patterned gel. Furthermore, we develop a double network structure to toughen the hydrogels with programmed superstructures, which deform reversibly under large strain. This work presents a promising pathway to develop superstructures in hydrogels and should shed light on designing biomimetic materials with intricate molecular alignments.

Cosmic Vorticity and the Origin Halo Spins

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.; Hoffman, Yehuda; Steinmetz, Matthias; Gottlöber, Stefan; Knebe, Alexander; Hess, Steffen

2013-04-01

In the standard model of cosmology, structure emerges out of a non-rotational flow and the angular momentum of collapsing halos is induced by tidal torques. The growth of angular momentum in the linear and quasi-linear phases is associated with a shear, curl-free, flow and it is well described within the linear framework of tidal torque theory (TTT). However, TTT ceases to be applicable as halos approach turnaround when their ambient flow field becomes rotational. Subsequently, halos become embedded in a vortical flow field and the growth of their angular momentum is affected by the vorticity of their ambient velocity field. Using a cosmological simulation, we have examined the importance of the curl of the velocity field in determining halo spin, finding a significant alignment between the two: the vorticity tends to be perpendicular to the axis of the fastest collapse of the velocity shear tensor (e 1). This is independent of halo masses and cosmic web environment. Our results agree with previous findings on the tendency of halo spin to be perpendicular to e 1, and of the spin of (simulated) halos and (observed) galaxies to be aligned with the large-scale structure. It follows that angular momentum growth proceeds in two distinct phases. First, the angular momentum emerges out of a shear, curl-free, potential flow, as described by TTT. In the second phase, in which halos approach virialization, the angular momentum emerges out of a vortical flow and halo spin becomes partially aligned with the vorticity of the ambient flow field.

Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment

DOE PAGES

Zhang, X.; Shen, Z.; Liu, J.; ...

2017-10-10

Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less

Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, X.; Shen, Z.; Liu, J.

Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less

Graded metascreens to enable a new degree of nanoscale light management

PubMed Central

Mohammadi Estakhri, Nasim; Argyropoulos, Christos; Alù, Andrea

2015-01-01

Optical metasurfaces, typically referred to as two-dimensional metamaterials, are arrays of engineered subwavelength inclusions suitably designed to tailor the light properties, including amplitude, phase and polarization state, over deeply subwavelength scales. By exploiting anomalous localized interactions of surface elements with optical waves, metasurfaces can go beyond the functionalities offered by conventional diffractive optical gratings. The innate simplicity of implementation and the distinct underlying physics of their wave–matter interaction distinguish metasurfaces from three-dimensional metamaterials and provide a valuable means of moulding optical waves in the desired manner. Here, we introduce a general approach based on the electromagnetic equivalence principle to develop and synthesize graded, non-periodic metasurfaces to generate arbitrarily prescribed distributions of electromagnetic waves. Graded metasurfaces are realized with a single layer of spatially modulated, electrically polarizable nanoparticles, tailoring the scattering response of the surface with nanoscale resolutions. We discuss promising applications based on the proposed local wave management technique, including the design of ultrathin optical carpet cloaks, alignment-free polarization beam splitters and a novel approach to enable broadband light absorption enhancement in thin-film solar cells. This concept opens up a practical route towards efficient planarized optical structures with potential impact on the integrated nanophotonic technology. PMID:26217059

Measures of three-dimensional anisotropy and intermittency in strong Alfvénic turbulence

NASA Astrophysics Data System (ADS)

Mallet, A.; Schekochihin, A. A.; Chandran, B. D. G.; Chen, C. H. K.; Horbury, T. S.; Wicks, R. T.; Greenan, C. C.

2016-06-01

We measure the local anisotropy of numerically simulated strong Alfvénic turbulence with respect to two local, physically relevant directions: along the local mean magnetic field and along the local direction of one of the fluctuating Elsasser fields. We find significant scaling anisotropy with respect to both these directions: the fluctuations are `ribbon-like' - statistically, they are elongated along both the mean magnetic field and the fluctuating field. The latter form of anisotropy is due to scale-dependent alignment of the fluctuating fields. The intermittent scalings of the nth-order conditional structure functions in the direction perpendicular to both the local mean field and the fluctuations agree well with the theory of Chandran, Schekochihin & Mallet, while the parallel scalings are consistent with those implied by the critical-balance conjecture. We quantify the relationship between the perpendicular scalings and those in the fluctuation and parallel directions, and find that the scaling exponent of the perpendicular anisotropy (I.e. of the aspect ratio of the Alfvénic structures in the plane perpendicular to the mean magnetic field) depends on the amplitude of the fluctuations. This is shown to be equivalent to the anticorrelation of fluctuation amplitude and alignment at each scale. The dependence of the anisotropy on amplitude is shown to be more significant for the anisotropy between the perpendicular and fluctuation-direction scales than it is between the perpendicular and parallel scales.

Scanning wave photopolymerization enables dye-free alignment patterning of liquid crystals

PubMed Central

Hisano, Kyohei; Aizawa, Miho; Ishizu, Masaki; Kurata, Yosuke; Nakano, Wataru; Akamatsu, Norihisa; Barrett, Christopher J.; Shishido, Atsushi

2017-01-01

Hierarchical control of two-dimensional (2D) molecular alignment patterns over large areas is essential for designing high-functional organic materials and devices. However, even by the most powerful current methods, dye molecules that discolor and destabilize the materials need to be doped in, complicating the process. We present a dye-free alignment patterning technique, based on a scanning wave photopolymerization (SWaP) concept, that achieves a spatial light–triggered mass flow to direct molecular order using scanning light to propagate the wavefront. This enables one to generate macroscopic, arbitrary 2D alignment patterns in a wide variety of optically transparent polymer films from various polymerizable mesogens with sufficiently high birefringence (>0.1) merely by single-step photopolymerization, without alignment layers or polarized light sources. A set of 150,000 arrays of a radial alignment pattern with a size of 27.4 μm × 27.4 μm were successfully inscribed by SWaP, in which each individual pattern is smaller by a factor of 104 than that achievable by conventional photoalignment methods. This dye-free inscription of microscopic, complex alignment patterns over large areas provides a new pathway for designing higher-performance optical and mechanical devices. PMID:29152567

Polarization of Magnetic Dipole Emission and Spinning Dust Emission from Magnetic Nanoparticles

NASA Astrophysics Data System (ADS)

Hoang, Thiem; Lazarian, Alex

2016-04-01

Magnetic dipole emission (MDE) from interstellar magnetic nanoparticles is potentially an important Galactic foreground in the microwave frequencies, and its polarization level may pose great challenges for achieving reliable measurements of cosmic microwave background B-mode signal. To obtain realistic predictions for the polarization of MDE, we first compute the degree of alignment of big silicate grains incorporated with magnetic inclusions. We find that thermally rotating big grains with magnetic inclusions are weakly aligned and can achieve alignment saturation when the magnetic alignment rate becomes much faster than the rotational damping rate. We then compute the degree of alignment for free-flying magnetic nanoparticles, taking into account various interaction processes of grains with the ambient gas and radiation field, including neutral collisions, ion collisions, and infrared emission. We find that the rotational damping by infrared emission can significantly decrease the degree of alignment of small particles from the saturation level, whereas the excitation by ion collisions can enhance the alignment of ultrasmall particles. Using the computed degrees of alignment, we predict the polarization level of MDE from free-flying magnetic nanoparticles to be rather low. Such a polarization level is within the upper limits measured for anomalous microwave emission (AME), which indicates that MDE from free-flying iron particles may not be ruled out as a source of AME. We also quantify rotational emission from free-flying iron nanoparticles with permanent magnetic moments and find that its emissivity is about one order of magnitude lower than that from spinning polycyclic aromatic hydrocarbons.

POLARIZATION OF MAGNETIC DIPOLE EMISSION AND SPINNING DUST EMISSION FROM MAGNETIC NANOPARTICLES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoang, Thiem; Lazarian, Alex

2016-04-20

Magnetic dipole emission (MDE) from interstellar magnetic nanoparticles is potentially an important Galactic foreground in the microwave frequencies, and its polarization level may pose great challenges for achieving reliable measurements of cosmic microwave background B-mode signal. To obtain realistic predictions for the polarization of MDE, we first compute the degree of alignment of big silicate grains incorporated with magnetic inclusions. We find that thermally rotating big grains with magnetic inclusions are weakly aligned and can achieve alignment saturation when the magnetic alignment rate becomes much faster than the rotational damping rate. We then compute the degree of alignment for free-flyingmore » magnetic nanoparticles, taking into account various interaction processes of grains with the ambient gas and radiation field, including neutral collisions, ion collisions, and infrared emission. We find that the rotational damping by infrared emission can significantly decrease the degree of alignment of small particles from the saturation level, whereas the excitation by ion collisions can enhance the alignment of ultrasmall particles. Using the computed degrees of alignment, we predict the polarization level of MDE from free-flying magnetic nanoparticles to be rather low. Such a polarization level is within the upper limits measured for anomalous microwave emission (AME), which indicates that MDE from free-flying iron particles may not be ruled out as a source of AME. We also quantify rotational emission from free-flying iron nanoparticles with permanent magnetic moments and find that its emissivity is about one order of magnitude lower than that from spinning polycyclic aromatic hydrocarbons.« less

A theoretical investigation of the aerodynamics of low-aspect-ratio wings with partial leading-edge separation

NASA Technical Reports Server (NTRS)

Mehrotra, S. C.; Lan, C. E.

1978-01-01

A numerical method is developed to predict distributed and total aerodynamic characteristics for low aspect-ratio wings with partial leading-edge separation. The flow is assumed to be steady and inviscid. The wing boundary condition is formulated by the quasi-vortex-lattice method. The leading-edge separated vortices are represented by discrete free vortex elements which are aligned with the local velocity vector at mid-points to satisfy the force free condition. The wake behind the trailing-edge is also force free. The flow tangency boundary condition is satisfied on the wing, including the leading- and trailing-edges. Comparison of the predicted results with complete leading-edge separation has shown reasonably good agreement. For cases with partial leading-edge separation, the lift is found to be highly nonlinear with angle of attack.

A computer program for calculating aerodynamic characteristics of low aspect-ratio wings with partial leading-edge separation

NASA Technical Reports Server (NTRS)

Mehrotra, S. C.; Lan, C. E.

1978-01-01

The necessary information for using a computer program to predict distributed and total aerodynamic characteristics for low aspect ratio wings with partial leading-edge separation is presented. The flow is assumed to be steady and inviscid. The wing boundary condition is formulated by the Quasi-Vortex-Lattice method. The leading edge separated vortices are represented by discrete free vortex elements which are aligned with the local velocity vector at midpoints to satisfy the force free condition. The wake behind the trailing edge is also force free. The flow tangency boundary condition is satisfied on the wing, including the leading and trailing edges. The program is restricted to delta wings with zero thickness and no camber. It is written in FORTRAN language and runs on CDC 6600 computer.

Spontaneous magnetic alignment behaviour in free-living lizards.

PubMed

Diego-Rasilla, Francisco J; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

2017-04-01

Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards (Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

Spontaneous magnetic alignment behaviour in free-living lizards

NASA Astrophysics Data System (ADS)

Diego-Rasilla, Francisco J.; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

2017-04-01

Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards ( Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

Comparison of localized basis and plane-wave basis for density-functional calculations of organic molecules on metals

NASA Astrophysics Data System (ADS)

Lee, Kyuho; Yu, Jaejun; Morikawa, Yoshitada

2007-01-01

Localized pseudoatomic orbitals (PAOs) are mainly optimized and tested for the strong chemical bonds within molecules and solids with their proven accuracy and efficiency, but are prone to significant basis set superposition error (BSSE) for weakly interacting systems. Here we test the accuracy of PAO basis in comparison with the BSSE-free plane-wave basis for the physisorption of pentacene molecule on Au (001) by calculating the binding energy, adsorption height, and energy level alignment. We show that both the large cutoff radius for localized PAOs and the counter-poise correction for BSSE are necessary to obtain well-converged physical properties. Thereby obtained results are as accurate as the plane-wave basis results. The comparison with experiment is given as well.

Adiabatic Field-Free Alignment of Asymmetric Top Molecules with an Optical Centrifuge.

PubMed

Korobenko, A; Milner, V

2016-05-06

We use an optical centrifuge to align asymmetric top SO_{2} molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines the sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment that persists after the molecules are released from the centrifuge. The 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 deg, permanent field-free alignment offers new ways of controlling molecules with laser light.

Structural alignment of protein descriptors - a combinatorial model.

PubMed

Antczak, Maciej; Kasprzak, Marta; Lukasiak, Piotr; Blazewicz, Jacek

2016-09-17

Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D models often exhibit deviations from the native structure. A way to confirm a model is a comparison with other structures. The structural alignment of a pair of proteins can be defined with the use of a concept of protein descriptors. The protein descriptors are local substructures of protein molecules, which allow us to divide the original problem into a set of subproblems and, consequently, to propose a more efficient algorithmic solution. In the literature, one can find many applications of the descriptors concept that prove its usefulness for insight into protein 3D structures, but the proposed approaches are presented rather from the biological perspective than from the computational or algorithmic point of view. Efficient algorithms for identification and structural comparison of descriptors can become crucial components of methods for structural quality assessment as well as tertiary structure prediction. In this paper, we propose a new combinatorial model and new polynomial-time algorithms for the structural alignment of descriptors. The model is based on the maximum-size assignment problem, which we define here and prove that it can be solved in polynomial time. We demonstrate suitability of this approach by comparison with an exact backtracking algorithm. Besides a simplification coming from the combinatorial modeling, both on the conceptual and complexity level, we gain with this approach high quality of obtained results, in terms of 3D alignment accuracy and processing efficiency. All the proposed algorithms were developed and integrated in a computationally efficient tool descs-standalone, which allows the user to identify and structurally compare descriptors of biological molecules, such as proteins and RNAs. Both PDB (Protein Data Bank) and mmCIF (macromolecular Crystallographic Information File) formats are supported. The proposed tool is available as an open source project stored on GitHub ( https://github.com/mantczak/descs-standalone ).

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

PubMed

Fostier, Jan; Proost, Sebastian; Dhoedt, Bart; Saeys, Yvan; Demeester, Piet; Van de Peer, Yves; Vandepoele, Klaas

2011-03-15

Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

Interactions between Skeletal Muscle Myoblasts and their Extracellular Matrix Revealed by a Serum Free Culture System.

PubMed

Chaturvedi, Vishal; Dye, Danielle E; Kinnear, Beverley F; van Kuppevelt, Toin H; Grounds, Miranda D; Coombe, Deirdre R

2015-01-01

Decellularisation of skeletal muscle provides a system to study the interactions of myoblasts with muscle extracellular matrix (ECM). This study describes the efficient decellularisation of quadriceps muscle with the retention of matrix components and the use of this matrix for myoblast proliferation and differentiation under serum free culture conditions. Three decellularisation approaches were examined; the most effective was phospholipase A2 treatment, which removed cellular material while maximizing the retention of ECM components. Decellularised muscle matrices were then solubilized and used as substrates for C2C12 mouse myoblast serum free cultures. The muscle matrix supported myoblast proliferation and differentiation equally as well as collagen and fibronectin. Immunofluorescence analyses revealed that myoblasts seeded on muscle matrix and fibronectin differentiated to form long, well-aligned myotubes, while myoblasts seeded on collagen were less organized. qPCR analyses showed a time dependent increase in genes involved in skeletal muscle differentiation and suggested that muscle-derived matrix may stimulate an increased rate of differentiation compared to collagen and fibronectin. Decellularized whole muscle three-dimensional scaffolds also supported cell adhesion and spreading, with myoblasts aligning along specific tracts of matrix proteins within the scaffolds. Thus, under serum free conditions, intact acellular muscle matrices provided cues to direct myoblast adhesion and migration. In addition, myoblasts were shown to rapidly secrete and organise their own matrix glycoproteins to create a localized ECM microenvironment. This serum free culture system has revealed that the correct muscle ECM facilitates more rapid cell organisation and differentiation than single matrix glycoprotein substrates.

Adaptive Local Realignment of Protein Sequences.

PubMed

DeBlasio, Dan; Kececioglu, John

2018-06-11

While mutation rates can vary markedly over the residues of a protein, multiple sequence alignment tools typically use the same values for their scoring-function parameters across a protein's entire length. We present a new approach, called adaptive local realignment, that in contrast automatically adapts to the diversity of mutation rates along protein sequences. This builds upon a recent technique known as parameter advising, which finds global parameter settings for an aligner, to now adaptively find local settings. Our approach in essence identifies local regions with low estimated accuracy, constructs a set of candidate realignments using a carefully-chosen collection of parameter settings, and replaces the region if a realignment has higher estimated accuracy. This new method of local parameter advising, when combined with prior methods for global advising, boosts alignment accuracy as much as 26% over the best default setting on hard-to-align protein benchmarks, and by 6.4% over global advising alone. Adaptive local realignment has been implemented within the Opal aligner using the Facet accuracy estimator.

Bioinspired engineering study of Plantae vascules for self-healing composite structures.

PubMed

Trask, R S; Bond, I P

2010-06-06

This paper presents the first conceptual study into creating a Plantae-inspired vascular network within a fibre-reinforced polymer composite laminate, which provides an ongoing self-healing functionality without incurring a mass penalty. Through the application of a 'lost-wax' technique, orthogonal hollow vascules, inspired by the 'ray cell' structures found in ring porous hardwoods, were successfully introduced within a carbon fibre-reinforced epoxy polymer composite laminate. The influence on fibre architecture and mechanical behaviour of single vascules (located on the laminate centreline) when aligned parallel and transverse to the local host ply was characterized experimentally using a compression-after-impact test methodology. Ultrasonic C-scanning and high-resolution micro-CT X-ray was undertaken to identify the influence of and interaction between the internal vasculature and impact damage. The results clearly show that damage morphology is influenced by vascule orientation and that a 10 J low-velocity impact damage event is sufficient to breach the vasculature; a prerequisite for any subsequent self-healing function. The residual compressive strength after a 10 J impact was found to be dependent upon vascule orientation. In general, residual compressive strength decreased to 70 per cent of undamaged strength when vasculature was aligned parallel to the local host ply and a value of 63 per cent when aligned transverse. This bioinspired engineering study has illustrated the potential that a vasculature concept has to offer in terms of providing a self-healing function with minimum mass penalty, without initiating premature failure within a composite structure.

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.

PubMed

Cui, Xuefeng; Lu, Zhiwu; Wang, Sheng; Jing-Yan Wang, Jim; Gao, Xin

2016-06-15

Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence-structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM-HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods. Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx : xin.gao@kaust.edu.sa Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

High-Throughput Image Analysis of Fibrillar Materials: A Case Study on Polymer Nanofiber Packing, Alignment, and Defects in Organic Field Effect Transistors.

PubMed

Persson, Nils E; Rafshoon, Joshua; Naghshpour, Kaylie; Fast, Tony; Chu, Ping-Hsun; McBride, Michael; Risteen, Bailey; Grover, Martha; Reichmanis, Elsa

2017-10-18

High-throughput discovery of process-structure-property relationships in materials through an informatics-enabled empirical approach is an increasingly utilized technique in materials research due to the rapidly expanding availability of data. Here, process-structure-property relationships are extracted for the nucleation, growth, and deposition of semiconducting poly(3-hexylthiophene) (P3HT) nanofibers used in organic field effect transistors, via high-throughput image analysis. This study is performed using an automated image analysis pipeline combining existing open-source software and new algorithms, enabling the rapid evaluation of structural metrics for images of fibrillar materials, including local orientational order, fiber length density, and fiber length distributions. We observe that microfluidic processing leads to fibers that pack with unusually high density, while sonication yields fibers that pack sparsely with low alignment. This is attributed to differences in their crystallization mechanisms. P3HT nanofiber packing during thin film deposition exhibits behavior suggesting that fibers are confined to packing in two-dimensional layers. We find that fiber alignment, a feature correlated with charge carrier mobility, is driven by increasing fiber length, and that shorter fibers tend to segregate to the buried dielectric interface during deposition, creating potentially performance-limiting defects in alignment. Another barrier to perfect alignment is the curvature of P3HT fibers; we propose a mechanistic simulation of fiber growth that reconciles both this curvature and the log-normal distribution of fiber lengths inherent to the fiber populations under consideration.

Fabrication and Characterization of Aligned Flexible Lead-Free Piezoelectric Nanofibers for Wearable Device Applications

PubMed Central

Ji, Sang Hyun; Yun, Ji Sun

2018-01-01

Flexible lead-free piezoelectric nanofibers, based on BNT-ST (0.78Bi0.5Na0.5TiO3-0.22SrTiO3) ceramic and poly(vinylidene fluoride-trifluoroethylene) (PVDF-TrFE) copolymers, were fabricated by an electrospinning method and the effects of the degree of alignment in the nanofibers on the piezoelectric characteristics were investigated. The microstructure of the lead-free piezoelectric nanofibers was observed by field emission scanning electron microscope (FE-SEM) and the orientation was analyzed by fast Fourier transform (FFT) images. X-ray diffraction (XRD) analysis confirmed that the phase was not changed by the electrospinning process and maintained a perovskite phase. Polarization-electric field (P-E) loops and piezoresponse force microscopy (PFM) were used to investigate the piezoelectric properties of the piezoelectric nanofibers, according to the degree of alignment—the well aligned piezoelectric nanofibers had higher piezoelectric properties. Furthermore, the output voltage of the aligned lead-free piezoelectric nanofibers was measured according to the vibration frequency and the bending motion and the aligned piezoelectric nanofibers with a collector rotation speed of 1500 rpm performed the best. PMID:29596372

Automated alignment system for optical wireless communication systems using image recognition.

PubMed

Brandl, Paul; Weiss, Alexander; Zimmermann, Horst

2014-07-01

In this Letter, we describe the realization of a tracked line-of-sight optical wireless communication system for indoor data distribution. We built a laser-based transmitter with adaptive focus and ray steering by a microelectromechanical systems mirror. To execute the alignment procedure, we used a CMOS image sensor at the transmitter side and developed an algorithm for image recognition to localize the receiver's position. The receiver is based on a self-developed optoelectronic integrated chip with low requirements on the receiver optics to make the system economically attractive. With this system, we were able to set up the communication link automatically without any back channel and to perform error-free (bit error rate <10⁻⁹) data transmission over a distance of 3.5 m with a data rate of 3 Gbit/s.

Local alignment of two-base encoded DNA sequence

PubMed Central

Homer, Nils; Merriman, Barry; Nelson, Stanley F

2009-01-01

Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. Results We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions. Conclusion The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data. PMID:19508732

Accelerating large-scale protein structure alignments with graphics processing units

PubMed Central

2012-01-01

Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU. PMID:22357132

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

2013-06-01

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

Direct numerical simulation of particle alignment in viscoelastic fluids

NASA Astrophysics Data System (ADS)

Hulsen, Martien; Jaensson, Nick; Anderson, Patrick

2016-11-01

Rigid particles suspended in viscoelastic fluids under shear can align in string-like structures in flow direction. To unravel this phenomenon, we present 3D direct numerical simulations of the alignment of two and three rigid, non-Brownian particles in a shear flow of a viscoelastic fluid. The equations are solved on moving, boundary-fitted meshes, which are locally refined to accurately describe the polymer stresses around and in between the particles. A small minimal gap size between the particles is introduced. The Giesekus model is used and the effect of the Weissenberg number, shear thinning and solvent viscosity is investigated. Alignment of two and three particles is observed. Morphology plots have been created for various combinations of fluid parameters. Alignment is mainly governed by the value of the elasticity parameter S, defined as half of the ratio between the first normal stress difference and shear stress of the suspending fluid. Alignment appears to occur above a critical value of S, which decreases with increasing shear thinning. This result, together with simulations of a shear-thinning Carreau fluid, leads us to the conclusion that normal stress differences are essential for particle alignment to occur, but it is also strongly promoted by shear thinning.

Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

PubMed

Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

2017-08-01

Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Multiple alignment-free sequence comparison

PubMed Central

Ren, Jie; Song, Kai; Sun, Fengzhu; Deng, Minghua; Reinert, Gesine

2013-01-01

Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and , extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequences, and second, , and , averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences. Results: Our investigation uses both simulated data as well as cis-regulatory module data where the task is to identify cis-regulatory modules with similar transcription factor binding sites. We find that although for real data, all of our statistics show a similar performance, on simulated data the Shepp-type statistics are in some instances outperformed by star-type statistics. The multiple alignment-free statistics are more sensitive to contamination in the data than the pairwise average statistics. Availability: Our implementation of the five statistics is available as R package named ‘multiAlignFree’ at be http://www-rcf.usc.edu/∼fsun/Programs/multiAlignFree/multiAlignFreemain.html. Contact: reinert@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23990418

Charleshenge--An Archeo-Astronomy Exercise for the Elementary Astronomy Lab.

ERIC Educational Resources Information Center

Dukes, Robert J. Jr.

1982-01-01

Techniques have been described for using celestial spheres as data-generating devices. Descibes a variation, capitalizing on students' interest in activities related to Stonehenge. Following a movie, students determine whether or not astronomical alignments found at Stonehenge and related structures could arise by chance. Local buildings are used.…

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

PubMed Central

Shih, Arthur Chun-Chieh; Lee, DT; Peng, Chin-Lin; Wu, Yu-Wei

2007-01-01

Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL . PMID:17319966

Efficient alignment-free DNA barcode analytics.

PubMed

Kuksa, Pavel; Pavlovic, Vladimir

2009-11-10

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 species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Interfraction Displacement of Primary Tumor and Involved Lymph Nodes Relative to Anatomic Landmarks in Image Guided Radiation Therapy of Locally Advanced Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jan, Nuzhat; Balik, Salim; Hugo, Geoffrey D.

Purpose: To analyze primary tumor (PT) and lymph node (LN) position changes relative to each other and relative to anatomic landmarks during conventionally fractionated radiation therapy for patients with locally advanced lung cancer. Methods and Materials: In 12 patients with locally advanced non-small cell lung cancer PT, LN, carina, and 1 thoracic vertebra were manually contoured on weekly 4-dimensional fan-beam CT scans. Systematic and random interfraction displacements of all contoured structures were identified in the 3 cardinal directions, and resulting setup margins were calculated. Time trends and the effect of volume changes on displacements were analyzed. Results: Three-dimensional displacement vectorsmore » and systematic/random interfraction displacements were smaller for carina than for vertebra both for PT and LN. For PT, mean (SD) 3-dimensional displacement vectors with carina-based alignment were 7 (4) mm versus 9 (5) mm with bony anatomy (P<.0001). For LN, smaller displacements were found with carina- (5 [3] mm, P<.0001) and vertebra-based (6 [3] mm, P=.002) alignment compared with using PT for setup (8 [5] mm). Primary tumor and LN displacements relative to bone and carina were independent (P>.05). Displacements between PT and bone (P=.04) and between PT and LN (P=.01) were significantly correlated with PT volume regression. Displacements between LN and carina were correlated with LN volume change (P=.03). Conclusions: Carina-based setup results in a more reproducible PT and LN alignment than bony anatomy setup. Considering the independence of PT and LN displacement and the impact of volume regression on displacements over time, repeated CT imaging even with PT-based alignment is recommended in locally advanced disease.« less

Exopolysaccharide microchannels direct bacterial motility and organize multicellular behavior

DOE PAGES

Berleman, James E.; Zemla, Marcin; Remis, Jonathan P.; ...

2016-05-06

The myxobacteria are a family of soil bacteria that form biofilms of complex architecture, aligned multilayered swarms or fruiting body structures that are simple or branched aggregates containing myxospores. Here, we examined the structural role of matrix exopolysaccharide (EPS) in the organization of these surface-dwelling bacterial cells. Using time-lapse light and fluorescence microscopy, as well as transmission electron microscopy and focused ion beam/scanning electron microscopy (FIB/SEM) electron microscopy, we found that Myxococcus xanthus cell organization in biofilms is dependent on the formation of EPS microchannels. Cells are highly organized within the three-dimensional structure of EPS microchannels that are required formore » cell alignment and advancement on surfaces. Mutants lacking EPS showed a lack of cell orientation and poor colony migration. Purified, cell-free EPS retains a channel-like structure, and can complement EPS - mutant motility defects. In addition, EPS provides the cooperative structure for fruiting body formation in both the simple mounds of M. xanthus and the complex, tree-like structures of Chondromyces crocatus. We furthermore investigated the possibility that EPS impacts community structure as a shared resource facilitating cooperative migration among closely related isolates of M. xanthus.« less

Local atomic and magnetic structure of dilute magnetic semiconductor (Ba ,K ) (Zn,Mn ) 2As2

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; Banerjee, Soham; Chen, Bijuan; Jin, Changqing; Feygenson, Mikhail; Uemura, Yasutomo J.; Billinge, Simon J. L.

2016-09-01

We have studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba ,K )(Zn ,Mn )2As2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. We detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5 Å , resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment of Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. We discuss these results in the context of other experiments and theoretical studies on this system.

LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

PubMed

Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

2018-05-07

Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

PubMed

Xu, Qifang; Dunbrack, Roland L

2012-11-01

Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM-HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

PubMed

Bromberg, Raquel; Grishin, Nick V; Otwinowski, Zbyszek

2016-06-01

Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

PubMed Central

Grishin, Nick V.; Otwinowski, Zbyszek

2016-01-01

Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

Reliability of image-free navigation to monitor lower-limb alignment.

PubMed

Pearle, Andrew D; Goleski, Patrick; Musahl, Volker; Kendoff, Daniel

2009-02-01

Proper alignment of the mechanical axis of the lower limb is the principal goal of a high tibial osteotomy. A well-accepted and relevant technical specification is the coronal plane lower-limb alignment. Target values for coronal plane alignment after high tibial osteotomy include 2 degrees of overcorrection, while tolerances for this specification have been established as 2 degrees to 4 degrees. However, the role of axial plane and sagittal plane realignment after high tibial osteotomy is poorly understood; consequently, targets and tolerance for this technical specification remain undefined. This article reviews the literature concerning the reliability and precision of navigation in monitoring the clinically relevant specification of lower-limb alignment in high tibial osteotomy. We conclude that image-free navigation registration may be clinically useful for intraoperative monitoring of the coronal plane only. Only fair and poor results for the axial and sagittal planes can be obtained by image-free navigation systems. In the future, combined image-based data, such as those from radiographs, magnetic resonance imaging, and gait analysis, may be used to help to improve the accuracy and reproducibility of quantitative intraoperative monitoring of lower-limb alignment.

Fine-tuning structural RNA alignments in the twilight zone.

PubMed

Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

2010-04-30

A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

Claustrum of the short-tailed fruit bat, Carollia perspicillata: Alignment of cellular orientation and functional connectivity.

PubMed

Orman, Rena; Kollmar, Richard; Stewart, Mark

2017-04-15

The claustrum is a gray-matter structure that underlies neocortex and reciprocates connections with cortical and subcortical targets. In lower mammals, the claustrum is directly adjacent to neocortex, making the definition of claustral boundaries challenging. Latexin, an endogenous inhibitor of metallocarboxypeptidases, localizes to claustral cells, enabling a clear delineation of claustrum. Given its proportionately large claustrum, we hypothesized that the short-tailed fruit bat, Carollia perspicillata, can be a useful model for claustral structure-function relations. We used latexin immunohistochemistry to identify claustral boundaries and intrinsic structure and multielectrode recordings from brain slices to explore intrinsic excitatory connectivity of the claustrum. Carollia's claustrum contains cells whose intrinsic connectivity and alignment permit the generation of spontaneous, synchronous population events and mirror their pattern of spread in disinhibited brain slices over millimeters. Carollia shows cellular alignment and spontaneous population-activity spread along both horizontal and dorsoventral axes. Carollia claustrum possesses intrinsic excitatory connectivity sufficient to: 1) generate single, spontaneous, synchronized burst discharges, 2) support activity spread along axes where claustral cells are aligned, and 3), because of multiple axes for cell alignment, support activity spread along both rostrocaudal and dorsoventral axes. The smaller event sizes in bat claustrum compared with rat claustrum are consistent with events occurring in population subsets rather than the full claustral cell population. The overall size of claustrum, its pronounced vascularity, and its more complex intrinsic connectivity than rat suggest that the bat is an animal model for claustral structure and function that will permit unique access to claustrum's processing capabilities. J. Comp. Neurol. 525:1459-1474, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.

PubMed

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I; Blackledge, Martin; van Nuland, Nico A J

2009-05-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 muM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (K(d) = 132 +/- 13 muM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein-protein complexes.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex

PubMed Central

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I.; Blackledge, Martin; van Nuland, Nico A. J.

2009-01-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 μM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd = 132 ± 13 μM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes. PMID:19359362

HARMONY: a server for the assessment of protein structures

PubMed Central

Pugalenthi, G.; Shameer, K.; Srinivasan, N.; Sowdhamini, R.

2006-01-01

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at PMID:16844999

Manifold alignment with Schroedinger eigenmaps

NASA Astrophysics Data System (ADS)

Johnson, Juan E.; Bachmann, Charles M.; Cahill, Nathan D.

2016-05-01

The sun-target-sensor angle can change during aerial remote sensing. In an attempt to compensate BRDF effects in multi-angular hyperspectral images, the Semi-Supervised Manifold Alignment (SSMA) algorithm pulls data from similar classes together and pushes data from different classes apart. SSMA uses Laplacian Eigenmaps (LE) to preserve the original geometric structure of each local data set independently. In this paper, we replace LE with Spatial-Spectral Schoedinger Eigenmaps (SSSE) which was designed to be a semisupervised enhancement to the to extend the SSMA methodology and improve classification of multi-angular hyperspectral images captured over Hog Island in the Virginia Coast Reserve.

Microfabric and Structures in Glacial Ice

NASA Astrophysics Data System (ADS)

Monz, M.; Hudleston, P. J.

2017-12-01

Similar to rocks in active orogens, glacial ice develops both structures and fabrics that reflect deformation. Crystallographic preferred orientation (CPO), associated with mechanical anisotropy, develops as ice deforms, and as in rock, directly reflects the conditions and mechanisms of deformation and influences the overall strength. This project aims to better constrain the rheologic properties of natural ice through microstructural analysis and to establish the relationship of microfabric to macroscale structures. The focus is on enigmatic fabric patterns found in coarse grained, "warm" (T > -10oC) ice deep in ice sheets and in valley glaciers. Deformation mechanisms that produce such patterns are poorly understood. Detailed mapping of surface structures, including bedding, foliation, and blue bands (bubble-free veins of ice), was done in the ablation zone of Storglaciären, a polythermal valley glacier in northern Sweden. Microstructural studies on samples from a transect across the ablation zone were carried out in a cold room. Crystal size was too large for use of electron backscattered diffraction to determine CPO, therefore a Rigsby universal stage, designed specifically for ice, was used. In thick and thin sections, recrystallized grains are locally variable in both size (1mm-7cm in one thin section) and shape and clearly reflect recrystallization involving highly mobile grain boundaries. Larger crystals are often branching, and appear multiple times throughout one thin section. There is a clear shape preferred orientation that is generally parallel with foliation defined by bubble alignment and concentration. Locally, there appears to be an inverse correlation between bubble concentration and smoothness of grain boundaries. Fabric in samples that have undergone prolonged shear display roughly symmetrical multimaxima patterns centered around the pole to foliation. The angular distances between maxima suggest a possible twin relationship that may have developed from a preexisting single-maximum fabric.

COSMIC VORTICITY AND THE ORIGIN HALO SPINS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Libeskind, Noam I.; Steinmetz, Matthias; Gottloeber, Stefan

2013-04-01

In the standard model of cosmology, structure emerges out of a non-rotational flow and the angular momentum of collapsing halos is induced by tidal torques. The growth of angular momentum in the linear and quasi-linear phases is associated with a shear, curl-free, flow and it is well described within the linear framework of tidal torque theory (TTT). However, TTT ceases to be applicable as halos approach turnaround when their ambient flow field becomes rotational. Subsequently, halos become embedded in a vortical flow field and the growth of their angular momentum is affected by the vorticity of their ambient velocity field.more » Using a cosmological simulation, we have examined the importance of the curl of the velocity field in determining halo spin, finding a significant alignment between the two: the vorticity tends to be perpendicular to the axis of the fastest collapse of the velocity shear tensor (e{sub 1}). This is independent of halo masses and cosmic web environment. Our results agree with previous findings on the tendency of halo spin to be perpendicular to e{sub 1}, and of the spin of (simulated) halos and (observed) galaxies to be aligned with the large-scale structure. It follows that angular momentum growth proceeds in two distinct phases. First, the angular momentum emerges out of a shear, curl-free, potential flow, as described by TTT. In the second phase, in which halos approach virialization, the angular momentum emerges out of a vortical flow and halo spin becomes partially aligned with the vorticity of the ambient flow field.« less

Fabrication of Free-Standing, Self-Aligned, High-Aspect-Ratio Synthetic Ommatidia.

PubMed

Jun, Brian M; Serra, Francesca; Xia, Yu; Kang, Hong Suk; Yang, Shu

2016-11-16

Free-standing, self-aligned, high-aspect-ratio (length to cross-section, up to 15.5) waveguides that mimic insects' ommatidia are fabricated. Self-aligned waveguides under the lenses are created after exposing photoresist SU-8 film through the negative polydimethylsiloxane (PDMS) lens array. Instead of drying from the developer, the waveguides are coated with poly(vinyl alcohol) and then immersed into a mixture of PDMS precursor and diethyl ether. The slow drying of diethyl ether, followed by curing and peeling off PDMS, allows for the fabrication of free-standing waveguides without collapse. We show that the synthetic ommatidia can confine light and propagate it all the way to the tips.

Interpolation schemes for peptide rearrangements.

PubMed

Bauer, Marianne S; Strodel, Birgit; Fejer, Szilard N; Koslover, Elena F; Wales, David J

2010-02-07

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.

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

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

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.

Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses.

PubMed

Hernandez, Troy; Yang, Jie

2016-10-01

The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate families with the pairwise sequence alignment tool for similar species. The submitter's judgment is then used to determine the most likely species classification. The aim of this article is to show that this process can be automated into a fast, accurate, one-step process using the proposed alignment-free method and properly implemented machine learning techniques. We present a new family of alignment-free vectorizations of the genome, the generalized vector, that maintains the speed of existing alignment-free methods while outperforming all available methods. This new alignment-free vectorization uses the frequency of genomic words (k-mers), as is done in the composition vector, and incorporates descriptive statistics of those k-mers' positional information, as inspired by the natural vector. We analyze five different characterizations of genome similarity using k-nearest neighbor classification and evaluate these on two collections of viruses totaling over 10,000 viruses. We show that our proposed method performs better than, or as well as, other methods at every level of the phylogenetic hierarchy. The data and R code is available upon request.

Effects of interfacial alignments on the stability of graphene on Ru(0001) substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Lei; Liu, Yanmin; Ma, Tianbao, E-mail: mtb@mail.tsinghua.edu.cn

2016-06-27

Structure and electronic properties of two-dimensional materials could be tuned by interfacial misfit or orientation angles. However, graphene grown on Ru(0001) substrate usually shows stable moiré superlattice with a periodicity of 3.0 nm indicating an aligned geometry. The reason for the absence of misaligned structure is still unknown. We have performed first-principles calculation to investigate the microstructure and morphology of graphene on Ru(0001) substrate in both aligned and misaligned geometries with rotation angles of 0°, 7.6°, and 23.4°, respectively. Our results indicate that both the graphene corrugation and moiré superlattice periodicity decrease as the rotation angle increases. Meanwhile the interaction energymore » between graphene and Ru(0001) substrate also becomes weakened with the rotation angle, as the decrease and discretization of intense charge transfer sites at the graphene/Ru interface, which is closely related to the interface stacking structure. Counterintuitively, the strain energy in graphene also increases anomalously with the rotation angle, which is attributed to the highly distorted local deformation of graphene due to the strong but discrete covalent bonding with Ru substrate. The simultaneous increase in both the interaction energy and strain energy in graphene/Ru(0001) heterostructure with rotation angle contributes to the preferred configuration in the aligned state.« less

Cell Guidance on Nanogratings: A Computational Model of the Interplay between PC12 Growth Cones and Nanostructures

PubMed Central

Tonazzini, Ilaria; Cecchini, Marco; Micera, Silvestro

2013-01-01

Background Recently, the effects of nanogratings have been investigated on PC12 with respect to cell polarity, neuronal differentiation, migration, maturation of focal adhesions and alignment of neurites. Methodology/Principal Findings A synergistic procedure was used to study the mechanism of alignment of PC12 neurites with respect to the main direction of nanogratings. Finite Element simulations were used to qualitatively assess the distribution of stresses at the interface between non-spread growth cones and filopodia, and to study their dependence on filopodial length and orientation. After modelling all adhesions under non-spread growth cone and filopodial protrusions, the values of local stress maxima resulted from the length of filopodia. Since the stress was assumed to be the main triggering cause leading to the increase and stabilization of filopodia, the position of the local maxima was directly related to the orientation of neurites. An analytic closed form equation was then written to quantitatively assess the average ridge width needed to achieve a given neuritic alignment (R2 = 0.96), and the alignment course, when the ridge depth varied (R2 = 0.97). A computational framework was implemented within an improved free Java environment (CX3D) and in silico simulations were carried out to reproduce and predict biological experiments. No significant differences were found between biological experiments and in silico simulations (alignment, p = 0.3571; tortuosity, p = 0.2236) with a standard level of confidence (95%). Conclusions/Significance A mechanism involved in filopodial sensing of nanogratings is proposed and modelled through a synergistic use of FE models, theoretical equations and in silico simulations. This approach shows the importance of the neuritic terminal geometry, and the key role of the distribution of the adhesion constraints for the cell/substrate coupling process. Finally, the effects of the geometry of nanogratings were explicitly considered in cell/surface interactions thanks to the analytic framework presented in this work. PMID:23936404

The force-free configuration of flux ropes in geomagnetotail: Cluster observations

NASA Astrophysics Data System (ADS)

Yang, Y. Y.; Shen, C.; Zhang, Y. C.; Rong, Z. J.; Li, X.; Dunlop, M.; Ma, Y. H.; Liu, Z. X.; Carr, C. M.; Rème, H.

2014-08-01

Unambiguous knowledge of magnetic field structure and the electric current distribution is critical for understanding the origin, evolution, and related dynamic properties of magnetic flux ropes (MFRs). In this paper, a survey of 13 MFRs in the Earth's magnetotail are conducted by Cluster multipoint analysis, so that their force-free feature, i.e., the kind of magnetic field structure satisfying J × B = 0, can be probed directly. It is showed that the selected flux ropes with the bipolar signature of the south-north magnetic field component generally lie near the equatorial plane, as expected, and that the magnetic field gradient is rather weak near the axis center, where the curvature radius is large. The current density (up to several tens of nA/m2) reaches their maximum values as the center is approached. It is found that the stronger the current density, the smaller the angles between the magnetic field and current in MFRs. The direct observations show that only quasi force-free structure is observed, and it tends to appear in the low plasma beta regime (in agreement with the theoretic results). The quasi force-free region is generally found to be embedded in the central portion of the MFRs, where the current is approximately field aligned and proportional to the strength of core field. It is shown that ~60% of surveyed MFRs can be globally approximated as force free. The force-free factor α is found to be nonconstantly varied through the quasi force-free MFR, suggesting that the force-free structure is nonlinear.

Fine-tuning structural RNA alignments in the twilight zone

PubMed Central

2010-01-01

Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index. PMID:20433706

Bioinspired engineering study of Plantae vascules for self-healing composite structures

PubMed Central

Trask, R. S.; Bond, I. P.

2010-01-01

This paper presents the first conceptual study into creating a Plantae-inspired vascular network within a fibre-reinforced polymer composite laminate, which provides an ongoing self-healing functionality without incurring a mass penalty. Through the application of a ‘lost-wax’ technique, orthogonal hollow vascules, inspired by the ‘ray cell’ structures found in ring porous hardwoods, were successfully introduced within a carbon fibre-reinforced epoxy polymer composite laminate. The influence on fibre architecture and mechanical behaviour of single vascules (located on the laminate centreline) when aligned parallel and transverse to the local host ply was characterized experimentally using a compression-after-impact test methodology. Ultrasonic C-scanning and high-resolution micro-CT X-ray was undertaken to identify the influence of and interaction between the internal vasculature and impact damage. The results clearly show that damage morphology is influenced by vascule orientation and that a 10 J low-velocity impact damage event is sufficient to breach the vasculature; a prerequisite for any subsequent self-healing function. The residual compressive strength after a 10 J impact was found to be dependent upon vascule orientation. In general, residual compressive strength decreased to 70 per cent of undamaged strength when vasculature was aligned parallel to the local host ply and a value of 63 per cent when aligned transverse. This bioinspired engineering study has illustrated the potential that a vasculature concept has to offer in terms of providing a self-healing function with minimum mass penalty, without initiating premature failure within a composite structure. PMID:19955122

Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.

PubMed

Sheth, Bhavisha P; Thaker, Vrinda S

2015-10-01

Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. A strategy as used here, incorporating the integrated use of DNA barcoding and protein structural analyses could be adopted, as a novel rapid and economic procedure, especially in cases when protein coding loci are considered. Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. A herbal powder was obtained from a herbalist in the local vicinity of Rajkot, Gujarat. An integrated approach using DNA barcoding and structural analyses was carried out to identify the herbal powder. The herbal powder was identified as Cassia javanica L.

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

NASA Astrophysics Data System (ADS)

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.

Micro-structure and motion of two-dimensional dense short spherocylinder liquids

NASA Astrophysics Data System (ADS)

Wang, Wen; Lin, Jyun-Ting; Su, Yen-Shuo; I, Lin

2018-03-01

We numerically investigate the micro-structure and motion of 2D liquids composed of dense short spherocylinders, by reducing the shape aspect ratio from 3. It is found that reducing shape aspect ratio from 3 causes a smooth transition from heterogeneous structures composed of crystalline ordered domains with good tetratic alignment order to those with good hexagonal bond-orientational order at an aspect ratio equaling 1.35. In the intermediate regime, both structural orders are strongly deteriorated, and the translational hopping rate reaches a maximum due to the poor particle interlocking of the disordered structure. Shortening rod length allows easier rotation, induces monotonic increase of rotational hopping rates, and resumes the separation of rotational and translational hopping time scales at the small aspect ratio end, after the crossover of their rates in the intermediate regime. At the large shape aspect ratio end, the poor local tetratic order has the same positive effects on facilitating local rotational and translational hopping. In contrast, at the small shape aspect ratio end, the poor local bond orientational order has the opposite effects on facilitating local rotational and translational hopping.

Efficient alignment-free DNA barcode analytics

PubMed Central

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 species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. Results New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Conclusion Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding. PMID:19900305

Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes.

PubMed Central

Ashbaugh, H S; Garde, S; Hummer, G; Kaler, E W; Paulaitis, M E

1999-01-01

Conformational free energies of butane, pentane, and hexane in water are calculated from molecular simulations with explicit waters and from a simple molecular theory in which the local hydration structure is estimated based on a proximity approximation. This proximity approximation uses only the two nearest carbon atoms on the alkane to predict the local water density at a given point in space. Conformational free energies of hydration are subsequently calculated using a free energy perturbation method. Quantitative agreement is found between the free energies obtained from simulations and theory. Moreover, free energy calculations using this proximity approximation are approximately four orders of magnitude faster than those based on explicit water simulations. Our results demonstrate the accuracy and utility of the proximity approximation for predicting water structure as the basis for a quantitative description of n-alkane conformational equilibria in water. In addition, the proximity approximation provides a molecular foundation for extending predictions of water structure and hydration thermodynamic properties of simple hydrophobic solutes to larger clusters or assemblies of hydrophobic solutes. PMID:10423414

A New Standard Pulsar Magnetosphere

NASA Technical Reports Server (NTRS)

Contopoulos, Ioannis; Kalapotharakos, Constantinos; Kazanas, Demosthenes

2014-01-01

In view of recent efforts to probe the physical conditions in the pulsar current sheet, we revisit the standard solution that describes the main elements of the ideal force-free pulsar magnetosphere. The simple physical requirement that the electric current contained in the current layer consists of the local electric charge moving outward at close to the speed of light yields a new solution for the pulsar magnetosphere everywhere that is ideal force-free except in the current layer. The main elements of the new solution are as follows: (1) the pulsar spindown rate of the aligned rotator is 23% larger than that of the orthogonal vacuum rotator; (2) only 60% of the magnetic flux that crosses the light cylinder opens up to infinity; (3) the electric current closes along the other 40%, which gradually converges to the equator; (4) this transfers 40% of the total pulsar spindown energy flux in the equatorial current sheet, which is then dissipated in the acceleration of particles and in high-energy electromagnetic radiation; and (5) there is no separatrix current layer. Our solution is a minimum free-parameter solution in that the equatorial current layer is electrostatically supported against collapse and thus does not require a thermal particle population. In this respect, it is one more step toward the development of a new standard solution. We discuss the implications for intermittent pulsars and long-duration gamma-ray bursts. We conclude that the physical conditions in the equatorial current layer determine the global structure of the pulsar magnetosphere.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Orientation and Order in Shear-Aligned Thin Films of Cylinder-Forming Block Copolymers

NASA Astrophysics Data System (ADS)

Register, Richard

The regularity and tunability of the nanoscale structure in block copolymers makes their thin films attractive as nanolithographic templates; however, in the absence of a guiding field, self-assembly produces a polygrain structure with no particular orientation and a high density of defects. As demonstrated in the elegant studies of Ed Kramer and coworkers, graphoepitaxy can provide local control over domain orientation, with a dramatic reduction in defect density. Alternatively, cylindrical microdomains lying in the plane of the film can be aligned over macroscopic areas by applying shear stress at the film surface. In non-sheared films of polystyrene-poly(n-hexylmethacrylate) diblocks, PS-PHMA, the PS cylinder axis orientation relative to the surface switches from parallel to perpendicular as a function of film thickness; this oscillation is damped out as the fraction of the PS block increases, away from the sphere-cylinder phase boundary. In aligned films, thicknesses which possess the highest coverage of parallel cylinders prior to shear show the highest quality of alignment post-shear, as measured by the in-plane orientational order parameter. In well-aligned samples of optimal thickness, the quality of alignment is limited by isolated dislocations, whose density is highest at high PS contents, and by undulations in the cylinders' trajectories, whose impact is most severe at low PS contents; consequently, polymers whose compositions lie in the middle of the cylinder-forming region exhibit the highest quality of alignment. The dynamics of the alignment process are also investigated, and fit to a melting-recrystallization model which allows for the determination of two key alignment parameters: the critical stress needed for alignment, and an orientation rate constant. For films containing a monolayer of cylindrical domains, as PS weight fraction or overall molecular weight increases, the critical stress increases moderately, while the rate of alignment drastically decreases. As the number of layers of cylinders in the film increases, the critical stress decreases modestly, while the rate remains unchanged; substrate wetting condition has no measurable influence on alignment response. [Work of Raleigh Davis, in collaboration with Paul Chaikin.

Three-dimensional structure and multistable optical switching of triple-twisted particle-like excitations in anisotropic fluids.

PubMed

Smalyukh, Ivan I; Lansac, Yves; Clark, Noel A; Trivedi, Rahul P

2010-02-01

Control of structures in soft materials with long-range order forms the basis for applications such as displays, liquid-crystal biosensors, tunable lenses, distributed feedback lasers, muscle-like actuators and beam-steering devices. Bistable, tristable and multistable switching of well-defined structures of molecular alignment is of special interest for all of these applications. Here we describe the facile optical creation and multistable switching of localized configurations in the molecular orientation field of a chiral nematic anisotropic fluid. These localized chiro-elastic particle-like excitations--dubbed 'triple-twist torons'--are generated by vortex laser beams and embed the localized three-dimensional (3D) twist into a uniform background. Confocal polarizing microscopy and computer simulations reveal their equilibrium internal structures, manifesting both skyrmion-like and Hopf fibration features. Robust generation of torons at predetermined locations combined with both optical and electrical reversible switching can lead to new ways of multistable structuring of complex photonic architectures in soft materials.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

PubMed

Daily, Jeff

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

The Alignment of the Mean Wind and Stress Vectors in the Unstable Surface Layer

NASA Astrophysics Data System (ADS)

Bernardes, M.; Dias, N. L.

2010-01-01

A significant non-alignment between the mean horizontal wind vector and the stress vector was observed for turbulence measurements both above the water surface of a large lake, and over a land surface (soybean crop). Possible causes for this discrepancy such as flow distortion, averaging times and the procedure used for extracting the turbulent fluctuations (low-pass filtering and filter widths etc.), were dismissed after a detailed analysis. Minimum averaging times always less than 30 min were established by calculating ogives, and error bounds for the turbulent stresses were derived with three different approaches, based on integral time scales (first-crossing and lag-window estimates) and on a bootstrap technique. It was found that the mean absolute value of the angle between the mean wind and stress vectors is highly related to atmospheric stability, with the non-alignment increasing distinctively with increasing instability. Given a coordinate rotation that aligns the mean wind with the x direction, this behaviour can be explained by the growth of the relative error of the u- w component with instability. As a result, under more unstable conditions the u- w and the v- w components become of the same order of magnitude, and the local stress vector gives the impression of being non-aligned with the mean wind vector. The relative error of the v- w component is large enough to make it undistinguishable from zero throughout the range of stabilities. Therefore, the standard assumptions of Monin-Obukhov similarity theory hold: it is fair to assume that the v- w stress component is actually zero, and that the non-alignment is a purely statistical effect. An analysis of the dimensionless budgets of the u- w and the v- w components confirms this interpretation, with both shear and buoyant production of u- w decreasing with increasing instability. In the v- w budget, shear production is zero by definition, while buoyancy displays very low-intensity fluctuations around zero. As local free convection is approached, the turbulence becomes effectively axisymetrical, and a practical limit seems to exist beyond which it is not possible to measure the u- w component accurately.

Legislating tolerance: Spain's national public smoking law.

PubMed

Muggli, Monique E; Lockhart, Nikki J; Ebbert, Jon O; Jiménez-Ruiz, Carlos A; Riesco Miranda, Juan Antonio; Hurt, Richard D

2010-02-01

While Spain's national tobacco control legislation prohibits smoking in many indoor public places, the law provides for an exception to the prohibition of smoking by allowing separate seating sections and ventilation options in certain public places such as bars and restaurants, hotels and airports. Accordingly, Spain's law is not aligned with Article 8 Guidelines of the World Health Organization's Framework Convention on Tobacco Control, which requires parties to ensure universal protection against secondhand smoke exposure in all enclosed public places, workplaces and on all means of public transport. Spain's law is currently being promoted by the tobacco companies in other countries as a model for smoke-free legislation. In order to prevent weakening of smoke-free laws in other countries through industry-supported exceptions, we investigated the tactics used by the tobacco companies before the implementation of the new law and assessed the consequences of these actions in the hospitality sector. Internal tobacco industry documents made public through US litigation settlements dating back to the 1980s were searched in 2008-9. Documents show that tobacco companies sought to protect hospitality venues from smoking restrictions by promoting separate seating for smokers and ineffective ventilation technologies, supporting an unenforceable voluntary agreement between the Madrid local government and the hospitality industry, influencing ventilation standards setting and manipulating Spanish media. The Spanish National Assembly should adopt comprehensive smoke-free legislation that does not accommodate the interests of the tobacco industry. In doing so, Spain's smoke-free public places law would be better aligned with the Framework Convention on Tobacco Control.

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. PMID:19589133

Nick-free formation of reciprocal heteroduplexes: a simple solution to the topological problem.

PubMed Central

Wilson, J H

1979-01-01

Because the individual strands of DNA are intertwined, formation of heteroduplex structures between duplexes--as in presumed recombination intermediates--presents a topological puzzle, known as the winding problem. Previous approaches to this problem have assumed that single-strand breaks are required to permit formation of fully coiled heteroduplexes. This paper describes a simple, nick-free solution to the winding problem that satisfies all topological constraints. Homologous duplexes associated by their minor-groove surfaces can switch strand pairing to form reciprocal heteroduplexes that coil together into a compact, four-stranded helix throughout the region of pairing. Model building shows that this fused heteroduplex structure is plausible, being composed entirely of right-handed primary helices with Watson-Crick base pairing throughout. Its simplicity of formation, structural symmetry, and high degree of specificity are suggestive of a natural mechanism for alignment by base pairing between intact homologous duplexes. Implications for genetic recombination are discussed. Images PMID:291028

QUASAR--scoring and ranking of sequence-structure alignments.

PubMed

Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

2005-12-15

Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

Implementation of a parallel protein structure alignment service on cloud.

PubMed

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.

Implementation of a Parallel Protein Structure Alignment Service on Cloud

PubMed Central

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

Effects of head orientation and lateral body tilt on egocentric coding: cognitive and sensory-motor accuracy.

PubMed

Prieur, J-M; Bourdin, C; Sarès, F; Vercher, J-L

2006-01-01

A major issue in motor control studies is to determine whether and how we use spatial frames of reference to organize our spatially oriented behaviors. In previous experiments we showed that simulated body tilt during off-axis rotation affected the performance in verbal localization and manual pointing tasks. It was hypothesized that the observed alterations were at least partly due to a change in the orientation of the egocentric frame of reference, which was indeed centered on the body but aligned with the gravitational vector. The present experiments were designed to test this hypothesis in a situation where no inertial constraints (except the usual gravitational one) exist and where the orientation of the body longitudinal z-axis was not aligned with the direction of the gravity. Eleven subjects were exposed to real static body tilt and were required to verbally localize (experiment 1) and to point as accurately as possible towards (experiment 2) memorized visual targets, in two conditions, Head-Free and Head-Fixed conditions. Results show that the performance was only affected by real body tilt in the localization task performed when the subject's head was tilted relative to the body. Thus, dissociation between gravity and body longitudinal z-axis alone is not responsible for localization nor for pointing errors. Therefore, the egocentric frame of reference seems independent from the orientation of the gravity with regard to body z-axis as expected from our previous studies. Moreover, the use of spatial referentials appears to be less mandatory than expected for pointing movements (motor task) than for localization task (cognitive task).

Alignments of the galaxies in and around the Virgo cluster with the local velocity shear

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jounghun; Rey, Soo Chang; Kim, Suk, E-mail: jounghun@astro.snu.ac.kr

2014-08-10

Observational evidence is presented for the alignment between the cosmic sheet and the principal axis of the velocity shear field at the position of the Virgo cluster. The galaxies in and around the Virgo cluster from the Extended Virgo Cluster Catalog that was recently constructed by Kim et al. are used to determine the direction of the local sheet. The peculiar velocity field reconstructed from the Sloan Digital Sky Survey Data Release 7 is analyzed to estimate the local velocity shear tensor at the Virgo center. Showing first that the minor principal axis of the local velocity shear tensor ismore » almost parallel to the direction of the line of sight, we detect a clear signal of alignment between the positions of the Virgo satellites and the intermediate principal axis of the local velocity shear projected onto the plane of the sky. Furthermore, the dwarf satellites are found to appear more strongly aligned than their normal counterparts, which is interpreted as an indication of the following. (1) The normal satellites and the dwarf satellites fall in the Virgo cluster preferentially along the local filament and the local sheet, respectively. (2) The local filament is aligned with the minor principal axis of the local velocity shear while the local sheet is parallel to the plane spanned by the minor and intermediate principal axes. Our result is consistent with the recent numerical claim that the velocity shear is a good tracer of the cosmic web.« less

Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

ERIC Educational Resources Information Center

Vanfretti, L.; Milano, F.

2012-01-01

This paper describes how the use of free and open-source software (FOSS) can facilitate the application of constructive alignment theory in power systems engineering education by enabling the deep learning approach in power system analysis courses. With this aim, this paper describes the authors' approach in using the Power System Analysis Toolbox…

Zooming in: high resolution 3D reconstruction of differently stained histological whole slide images

NASA Astrophysics Data System (ADS)

Lotz, Johannes; Berger, Judith; Müller, Benedikt; Breuhahn, Kai; Grabe, Niels; Heldmann, Stefan; Homeyer, André; Lahrmann, Bernd; Laue, Hendrik; Olesch, Janine; Schwier, Michael; Sedlaczek, Oliver; Warth, Arne

2014-03-01

Much insight into metabolic interactions, tissue growth, and tissue organization can be gained by analyzing differently stained histological serial sections. One opportunity unavailable to classic histology is three-dimensional (3D) examination and computer aided analysis of tissue samples. In this case, registration is needed to reestablish spatial correspondence between adjacent slides that is lost during the sectioning process. Furthermore, the sectioning introduces various distortions like cuts, folding, tearing, and local deformations to the tissue, which need to be corrected in order to exploit the additional information arising from the analysis of neighboring slide images. In this paper we present a novel image registration based method for reconstructing a 3D tissue block implementing a zooming strategy around a user-defined point of interest. We efficiently align consecutive slides at increasingly fine resolution up to cell level. We use a two-step approach, where after a macroscopic, coarse alignment of the slides as preprocessing, a nonlinear, elastic registration is performed to correct local, non-uniform deformations. Being driven by the optimization of the normalized gradient field (NGF) distance measure, our method is suitable for differently stained and thus multi-modal slides. We applied our method to ultra thin serial sections (2 μm) of a human lung tumor. In total 170 slides, stained alternately with four different stains, have been registered. Thorough visual inspection of virtual cuts through the reconstructed block perpendicular to the cutting plane shows accurate alignment of vessels and other tissue structures. This observation is confirmed by a quantitative analysis. Using nonlinear image registration, our method is able to correct locally varying deformations in tissue structures and exceeds the limitations of globally linear transformations.

Ultra-stiff large-area carpets of carbon nanotubes

NASA Astrophysics Data System (ADS)

Meysami, Seyyed Shayan; Dallas, Panagiotis; Britton, Jude; Lozano, Juan G.; Murdock, Adrian T.; Ferraro, Claudio; Gutierrez, Eduardo Saiz; Rijnveld, Niek; Holdway, Philip; Porfyrakis, Kyriakos; Grobert, Nicole

2016-06-01

Herewith, we report the influence of post-synthesis heat treatment (<=2350 °C and plasma temperatures) on the crystal structure, defect density, purity, alignment and dispersibility of free-standing large-area (several cm2) carpets of ultra-long (several mm) vertically aligned multi-wall carbon nanotubes (VA-MWCNTs). VA-MWCNTs were produced in large quantities (20-30 g per batch) using a semi-scaled-up aerosol-assisted chemical vapour deposition (AACVD) setup. Electron and X-ray diffraction showed that the heat treatment at 2350 °C under inert atmosphere purifies, removes residual catalyst particles, and partially aligns adjacent single crystals (crystallites) in polycrystalline MWCNTs. The purification and improvement in the crystallites alignment within the MWCNTs resulted in reduced dispersibility of the VA-MWCNTs in liquid media. High-resolution microscopy revealed that the crystallinity is improved in scales of few tens of nanometres while the point defects remain largely unaffected. The heat treatment also had a marked benefit on the mechanical properties of the carpets. For the first time, we report compression moduli as high as 120 MPa for VA-MWCNT carpets, i.e. an order of magnitude higher than previously reported figures. The application of higher temperatures (arc-discharge plasma, >=4000 °C) resulted in the formation of a novel graphite-matrix composite reinforced with CVD and arc-discharge-like carbon nanotubes.Herewith, we report the influence of post-synthesis heat treatment (<=2350 °C and plasma temperatures) on the crystal structure, defect density, purity, alignment and dispersibility of free-standing large-area (several cm2) carpets of ultra-long (several mm) vertically aligned multi-wall carbon nanotubes (VA-MWCNTs). VA-MWCNTs were produced in large quantities (20-30 g per batch) using a semi-scaled-up aerosol-assisted chemical vapour deposition (AACVD) setup. Electron and X-ray diffraction showed that the heat treatment at 2350 °C under inert atmosphere purifies, removes residual catalyst particles, and partially aligns adjacent single crystals (crystallites) in polycrystalline MWCNTs. The purification and improvement in the crystallites alignment within the MWCNTs resulted in reduced dispersibility of the VA-MWCNTs in liquid media. High-resolution microscopy revealed that the crystallinity is improved in scales of few tens of nanometres while the point defects remain largely unaffected. The heat treatment also had a marked benefit on the mechanical properties of the carpets. For the first time, we report compression moduli as high as 120 MPa for VA-MWCNT carpets, i.e. an order of magnitude higher than previously reported figures. The application of higher temperatures (arc-discharge plasma, >=4000 °C) resulted in the formation of a novel graphite-matrix composite reinforced with CVD and arc-discharge-like carbon nanotubes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01660j

MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

PubMed

Valasatava, Yana; Rosato, Antonio; Cavallaro, Gabriele; Andreini, Claudia

2014-08-01

We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

PubMed Central

Dunbrack, Roland L.

2012-01-01

Motivation: Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. Results: We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM–HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. Availability: The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly. Contact: Roland.Dunbracks@fccc.edu PMID:22942020

Magnetic Field Strengths and Grain Alignment Variations in the Local Bubble Wall

NASA Astrophysics Data System (ADS)

Medan, Ilija; Andersson, B.-G.

2018-01-01

Optical and infrared continuum polarization is known to be due to irregular dust grains aligned with the magnetic field. This provides an important tool to probe the geometry and strength of those fields, particularly if the variations in the grain alignment efficiencies can be understood. Here, we examine polarization variations observed throughout the Local Bubble for b>30○, using a large polarization survey of the North Galactic cap from Berdyugin et al. (2014). These data are supported by archival photometric and spectroscopic data along with the mapping of the Local Bubble by Lallement et al. (2003). We can accurately model the observational data assuming that the grain alignment variations are due to the radiation from the OB associations within 1 kpc of the sun. This strongly supports radiatively driven grain alignment. We also probe the relative strength of the magnetic field in the wall of the Local Bubble using the Davis-Chandrasekhar-Fermi method. We find evidence for a bimodal field strength distribution, where the variations in the field are correlated with the variations in grain alignment efficiency, indicating that the higher strength regions might represent a compression of the wall by the interaction of the outflow in the Local Bubble and the opposing flows by the surrounding OB associations.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

PubMed

Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

2012-09-01

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Hydrodynamic Equations for Flocking Models without Velocity Alignment

NASA Astrophysics Data System (ADS)

Peruani, Fernando

2017-10-01

The spontaneous emergence of collective motion patterns is usually associated with the presence of a velocity alignment mechanism that mediates the interactions among the moving individuals. Despite of this widespread view, it has been shown recently that several flocking behaviors can emerge in the absence of velocity alignment and as a result of short-range, position-based, attractive forces that act inside a vision cone. Here, we derive the corresponding hydrodynamic equations of a microscopic position-based flocking model, reviewing and extending previous reported results. In particular, we show that three distinct macroscopic collective behaviors can be observed: i) the coarsening of aggregates with no orientational order, ii) the emergence of static, elongated nematic bands, and iii) the formation of moving, locally polar structures, which we call worms. The derived hydrodynamic equations indicate that active particles interacting via position-based interactions belong to a distinct class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems.

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

PubMed

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Structural re-alignment in an immunologic surface region of ricin A chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

Multiscale Currents Observed by MMS in the Flow Braking Region

NASA Astrophysics Data System (ADS)

Nakamura, Rumi; Varsani, Ali; Genestreti, Kevin J.; Le Contel, Olivier; Nakamura, Takuma; Baumjohann, Wolfgang; Nagai, Tsugunobu; Artemyev, Anton; Birn, Joachim; Sergeev, Victor A.; Apatenkov, Sergey; Ergun, Robert E.; Fuselier, Stephen A.; Gershman, Daniel J.; Giles, Barbara J.; Khotyaintsev, Yuri V.; Lindqvist, Per-Arne; Magnes, Werner; Mauk, Barry; Petrukovich, Anatoli; Russell, Christopher T.; Stawarz, Julia; Strangeway, Robert J.; Anderson, Brian; Burch, James L.; Bromund, Ken R.; Cohen, Ian; Fischer, David; Jaynes, Allison; Kepko, Laurence; Le, Guan; Plaschke, Ferdinand; Reeves, Geoff; Singer, Howard J.; Slavin, James A.; Torbert, Roy B.; Turner, Drew L.

2018-02-01

We present characteristics of current layers in the off-equatorial near-Earth plasma sheet boundary observed with high time-resolution measurements from the Magnetospheric Multiscale mission during an intense substorm associated with multiple dipolarizations. The four Magnetospheric Multiscale spacecraft, separated by distances of about 50 km, were located in the southern hemisphere in the dusk portion of a substorm current wedge. They observed fast flow disturbances (up to about 500 km/s), most intense in the dawn-dusk direction. Field-aligned currents were observed initially within the expanding plasma sheet, where the flow and field disturbances showed the distinct pattern expected in the braking region of localized flows. Subsequently, intense thin field-aligned current layers were detected at the inner boundary of equatorward moving flux tubes together with Earthward streaming hot ions. Intense Hall current layers were found adjacent to the field-aligned currents. In particular, we found a Hall current structure in the vicinity of the Earthward streaming ion jet that consisted of mixed ion components, that is, hot unmagnetized ions, cold E × B drifting ions, and magnetized electrons. Our observations show that both the near-Earth plasma jet diversion and the thin Hall current layers formed around the reconnection jet boundary are the sites where diversion of the perpendicular currents take place that contribute to the observed field-aligned current pattern as predicted by simulations of reconnection jets. Hence, multiscale structure of flow braking is preserved in the field-aligned currents in the off-equatorial plasma sheet and is also translated to ionosphere to become a part of the substorm field-aligned current system.

Automated tilt series alignment and tomographic reconstruction in IMOD.

PubMed

Mastronarde, David N; Held, Susannah R

2017-02-01

Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20% improvement in alignment error for plastic-embedded samples and 10% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

Simultaneous large band gaps and localization of electromagnetic and elastic waves in defect-free quasicrystals.

PubMed

Yu, Tianbao; Wang, Zhong; Liu, Wenxing; Wang, Tongbiao; Liu, Nianhua; Liao, Qinghua

2016-04-18

We report numerically large and complete photonic and phononic band gaps that simultaneously exist in eight-fold phoxonic quasicrystals (PhXQCs). PhXQCs can possess simultaneous photonic and phononic band gaps over a wide range of geometric parameters. Abundant localized modes can be achieved in defect-free PhXQCs for all photonic and phononic polarizations. These defect-free localized modes exhibit multiform spatial distributions and can confine simultaneously electromagnetic and elastic waves in a large area, thereby providing rich selectivity and enlarging the interaction space of optical and elastic waves. The simulated results based on finite element method show that quasiperiodic structures formed of both solid rods in air and holes in solid materials can simultaneously confine and tailor electromagnetic and elastic waves; these structures showed advantages over the periodic counterparts.

Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics.

PubMed

Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Mabuchi, Hideo; Herschlag, Daniel

2017-09-12

Decades of study of the architecture and function of structured RNAs have led to the perspective that RNA tertiary structure is modular, made of locally stable domains that retain their structure across RNAs. We formalize a hypothesis inspired by this modularity-that RNA folding thermodynamics and kinetics can be quantitatively predicted from separable energetic contributions of the individual components of a complex RNA. This reconstitution hypothesis considers RNA tertiary folding in terms of ΔG align , the probability of aligning tertiary contact partners, and ΔG tert , the favorable energetic contribution from the formation of tertiary contacts in an aligned state. This hypothesis predicts that changes in the alignment of tertiary contacts from different connecting helices and junctions (ΔG HJH ) or from changes in the electrostatic environment (ΔG +/- ) will not affect the energetic perturbation from a mutation in a tertiary contact (ΔΔG tert ). Consistent with these predictions, single-molecule FRET measurements of folding of model RNAs revealed constant ΔΔG tert values for mutations in a tertiary contact embedded in different structural contexts and under different electrostatic conditions. The kinetic effects of these mutations provide further support for modular behavior of RNA elements and suggest that tertiary mutations may be used to identify rate-limiting steps and dissect folding and assembly pathways for complex RNAs. Overall, our model and results are foundational for a predictive understanding of RNA folding that will allow manipulation of RNA folding thermodynamics and kinetics. Conversely, the approaches herein can identify cases where an independent, additive model cannot be applied and so require additional investigation.

Circumferentially aligned fibers guided functional neoartery regeneration in vivo.

PubMed

Zhu, Meifeng; Wang, Zhihong; Zhang, Jiamin; Wang, Lina; Yang, Xiaohu; Chen, Jingrui; Fan, Guanwei; Ji, Shenglu; Xing, Cheng; Wang, Kai; Zhao, Qiang; Zhu, Yan; Kong, Deling; Wang, Lianyong

2015-08-01

An ideal vascular graft should have the ability to guide the regeneration of neovessels with structure and function similar to those of the native blood vessels. Regeneration of vascular smooth muscle cells (VSMCs) with circumferential orientation within the grafts is crucial for functional vascular reconstruction in vivo. To date, designing and fabricating a vascular graft with well-defined geometric cues to facilitate simultaneously VSMCs infiltration and their circumferential alignment remains a great challenge and scarcely reported in vivo. Thus, we have designed a bi-layered vascular graft, of which the internal layer is composed of circumferentially aligned microfibers prepared by wet-spinning and an external layer composed of random nanofibers prepared by electrospinning. While the internal circumferentially aligned microfibers provide topographic guidance for in vivo regeneration of circumferentially aligned VSMCs, the external random nanofibers can offer enhanced mechanical property and prevent bleeding during and after graft implantation. VSMCs infiltration and alignment within the scaffold was then evaluated in vitro and in vivo. Our results demonstrated that the circumferentially oriented VSMCs and longitudinally aligned ECs were successfully regenerated in vivo after the bi-layered vascular grafts were implanted in rat abdominal aorta. No formation of thrombosis or intimal hyperplasia was observed up to 3 month post implantation. Further, the regenerated neoartery exhibited contraction and relaxation property in response to vasoactive agents. This new strategy may bring cell-free small diameter vascular grafts closer to clinical application. Copyright © 2015 Elsevier Ltd. All rights reserved.

Alignment-free genome tree inference by learning group-specific distance metrics.

PubMed

Patil, Kaustubh R; McHardy, Alice C

2013-01-01

Understanding the evolutionary relationships between organisms is vital for their in-depth study. Gene-based methods are often used to infer such relationships, which are not without drawbacks. One can now attempt to use genome-scale information, because of the ever increasing number of genomes available. This opportunity also presents a challenge in terms of computational efficiency. Two fundamentally different methods are often employed for sequence comparisons, namely alignment-based and alignment-free methods. Alignment-free methods rely on the genome signature concept and provide a computationally efficient way that is also applicable to nonhomologous sequences. The genome signature contains evolutionary signal as it is more similar for closely related organisms than for distantly related ones. We used genome-scale sequence information to infer taxonomic distances between organisms without additional information such as gene annotations. We propose a method to improve genome tree inference by learning specific distance metrics over the genome signature for groups of organisms with similar phylogenetic, genomic, or ecological properties. Specifically, our method learns a Mahalanobis metric for a set of genomes and a reference taxonomy to guide the learning process. By applying this method to more than a thousand prokaryotic genomes, we showed that, indeed, better distance metrics could be learned for most of the 18 groups of organisms tested here. Once a group-specific metric is available, it can be used to estimate the taxonomic distances for other sequenced organisms from the group. This study also presents a large scale comparison between 10 methods--9 alignment-free and 1 alignment-based.

A benchmark testing ground for integrating homology modeling and protein docking.

PubMed

Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J; Bonvin, Alexandre M J J; Weng, Zhiping; Vajda, Sandor; Schueler-Furman, Ora; Kozakov, Dima

2017-01-01

Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at http://cluspro.org/benchmark, and is updated on a weekly basis in synchrony with new PDB releases. Proteins 2016; 85:10-16. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Alignment between Protostellar Outflows and Filamentary Structure

NASA Astrophysics Data System (ADS)

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.; Pokhrel, Riwaj; Sadavoy, Sarah I.; Vorobyov, Eduard I.; Tobin, John J.; Pineda, Jaime E.; Offner, Stella S. R.; Lee, Katherine I.; Kristensen, Lars E.; Jørgensen, Jes K.; Goodman, Alyssa A.; Bourke, Tyler L.; Arce, Héctor G.; Plunkett, Adele L.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2-1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ˜3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.

Cross-tail magnetic flux ropes as observed by the GEOTAIL spacecraft

NASA Technical Reports Server (NTRS)

Lepping, R. P.; Fairfield, D. H.; Jones, J.; Frank, L. A.; Paterson, W. R.; Kokubun, S.; Yamamoto, T.

1995-01-01

Ten transient magnetic structures in Earth's magnetotail, as observed in GEOTAIL measurements, selected for early 1993 (at (-) X(sub GSM) = 90 - 130 Earth radii), are shown to have helical magnetic field configurations similar to those of interplanetary magnetic clouds at 1 AU but smaller in size by a factor of approximately = 700. Such structures are shown to be well approximated by a comprehensive magnetic force-free flux-rope model. For this limited set of 10 events the rope axes are seen to be typically aligned with the Y(sub GSM) axis and the average diameter of these structures is approximately = 15 Earth radii.

Simulation of Turbulent Flow Inside and Above Wind Farms: Model Validation and Layout Effects

NASA Astrophysics Data System (ADS)

Wu, Yu-Ting; Porté-Agel, Fernando

2013-02-01

A recently-developed large-eddy simulation framework is validated and used to investigate turbulent flow within and above wind farms under neutral conditions. Two different layouts are considered, consisting of thirty wind turbines occupying the same total area and arranged in aligned and staggered configurations, respectively. The subgrid-scale (SGS) turbulent stress is parametrized using a tuning-free Lagrangian scale-dependent dynamic SGS model. The turbine-induced forces are modelled using two types of actuator-disk models: (a) the `standard' actuator-disk model (ADM-NR), which calculates only the thrust force based on one-dimensional momentum theory and distributes it uniformly over the rotor area; and (b) the actuator-disk model with rotation (ADM-R), which uses blade-element momentum theory to calculate the lift and drag forces (that produce both thrust and rotation), and distributes them over the rotor disk based on the local blade and flow characteristics. Validation is performed by comparing simulation results with turbulence measurements collected with hot-wire anemometry inside and above an aligned model wind farm placed in a boundary-layer wind tunnel. In general, the ADM-R model yields improved predictions compared with the ADM-NR in the wakes of all the wind turbines, where including turbine-induced flow rotation and accounting for the non-uniformity of the turbine-induced forces in the ADM-R appear to be important. Another advantage of the ADM-R model is that, unlike the ADM-NR, it does not require a priori specification of the thrust coefficient (which varies within a wind farm). Finally, comparison of simulations of flow through both aligned and staggered wind farms shows important effects of farm layout on the flow structure and wind-turbine performance. For the limited-size wind farms considered in this study, the lateral interaction between cumulated wakes is stronger in the staggered case, which results in a farm wake that is more homogeneous in the spanwise direction, thus resembling more an internal boundary layer. Inside the staggered farm, the relatively longer separation between consecutive downwind turbines allows the wakes to recover more, exposing the turbines to higher local wind speeds (leading to higher turbine efficiency) and lower turbulence intensity levels (leading to lower fatigue loads), compared with the aligned farm. Above the wind farms, the area-averaged velocity profile is found to be logarithmic, with an effective wind-farm aerodynamic roughness that is larger for the staggered case.

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

PubMed Central

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Local atomic and magnetic structure of dilute magnetic semiconductor ( Ba , K ) ( Zn , Mn ) 2 As 2

DOE PAGES

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; ...

2016-09-06

We studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba,K)(Zn,Mn) 2As 2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. Furthermore, we detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5Å, resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment ofmore » Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. Finally, we discuss these results in the context of other experiments and theoretical studies on this system.« less

Model-based correction for local stress-induced overlay errors

NASA Astrophysics Data System (ADS)

Stobert, Ian; Krishnamurthy, Subramanian; Shi, Hongbo; Stiffler, Scott

2018-03-01

Manufacturing embedded DRAM deep trench capacitors can involve etching very deep holes into silicon wafers1. Due to various design constraints, these holes may not be uniformly distributed across the wafer surface. Some wafer processing steps for these trenches results in stress effects which can distort the silicon wafer in a manner that creates localized alignment issues between the trenches and the structures built above them on the wafer. In this paper, we describe a method to model these localized silicon distortions for complex layouts involving billions of deep trench structures. We describe wafer metrology techniques and data which have been used to verify the stress distortion model accuracy. We also provide a description of how this kind of model can be used to manipulate the polygons in the mask tape out flow to compensate for predicted localized misalignments between design shapes from a deep trench mask and subsequent masks.

Near-field control and imaging of free charge carrier variations in GaN nanowires

NASA Astrophysics Data System (ADS)

Berweger, Samuel; Blanchard, Paul T.; Brubaker, Matt D.; Coakley, Kevin J.; Sanford, Norman A.; Wallis, Thomas M.; Bertness, Kris A.; Kabos, Pavel

2016-02-01

Despite their uniform crystallinity, the shape and faceting of semiconducting nanowires (NWs) can give rise to variations in structure and associated electronic properties. Here, we develop a hybrid scanning probe-based methodology to investigate local variations in electronic structure across individual n-doped GaN NWs integrated into a transistor device. We perform scanning microwave microscopy (SMM), which we combine with scanning gate microscopy to determine the free-carrier SMM signal contribution and image local charge carrier density variations. In particular, we find significant variations in free carriers across NWs, with a higher carrier density at the wire facets. By increasing the local carrier density through tip-gating, we find that the tip injects current into the NW with strongly localized current when positioned over the wire vertices. These results suggest that the strong variations in electronic properties observed within NWs have significant implications for device design and may lead to new paths to optimization.

Automatic classification of protein structures relying on similarities between alignments

PubMed Central

2012-01-01

Background Identification of protein structural cores requires isolation of sets of proteins all sharing a same subset of structural motifs. In the context of an ever growing number of available 3D protein structures, standard and automatic clustering algorithms require adaptations so as to allow for efficient identification of such sets of proteins. Results When considering a pair of 3D structures, they are stated as similar or not according to the local similarities of their matching substructures in a structural alignment. This binary relation can be represented in a graph of similarities where a node represents a 3D protein structure and an edge states that two 3D protein structures are similar. Therefore, classifying proteins into structural families can be viewed as a graph clustering task. Unfortunately, because such a graph encodes only pairwise similarity information, clustering algorithms may include in the same cluster a subset of 3D structures that do not share a common substructure. In order to overcome this drawback we first define a ternary similarity on a triple of 3D structures as a constraint to be satisfied by the graph of similarities. Such a ternary constraint takes into account similarities between pairwise alignments, so as to ensure that the three involved protein structures do have some common substructure. We propose hereunder a modification algorithm that eliminates edges from the original graph of similarities and gives a reduced graph in which no ternary constraints are violated. Our approach is then first to build a graph of similarities, then to reduce the graph according to the modification algorithm, and finally to apply to the reduced graph a standard graph clustering algorithm. Such method was used for classifying ASTRAL-40 non-redundant protein domains, identifying significant pairwise similarities with Yakusa, a program devised for rapid 3D structure alignments. Conclusions We show that filtering similarities prior to standard graph based clustering process by applying ternary similarity constraints i) improves the separation of proteins of different classes and consequently ii) improves the classification quality of standard graph based clustering algorithms according to the reference classification SCOP. PMID:22974051

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Jeffrey A.

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

DOE PAGES

Daily, Jeffrey A.

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

A new statistical framework to assess structural alignment quality using information compression

PubMed Central

Collier, James H.; Allison, Lloyd; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2014-01-01

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html PMID:25161241

Localized Oscillatory Energy Conversion in Magnetopause Reconnection

NASA Astrophysics Data System (ADS)

Burch, J. L.; Ergun, R. E.; Cassak, P. A.; Webster, J. M.; Torbert, R. B.; Giles, B. L.; Dorelli, J. C.; Rager, A. C.; Hwang, K.-J.; Phan, T. D.; Genestreti, K. J.; Allen, R. C.; Chen, L.-J.; Wang, S.; Gershman, D.; Le Contel, O.; Russell, C. T.; Strangeway, R. J.; Wilder, F. D.; Graham, D. B.; Hesse, M.; Drake, J. F.; Swisdak, M.; Price, L. M.; Shay, M. A.; Lindqvist, P.-A.; Pollock, C. J.; Denton, R. E.; Newman, D. L.

2018-02-01

Data from the NASA Magnetospheric Multiscale mission are used to investigate asymmetric magnetic reconnection at the dayside boundary between the Earth's magnetosphere and the solar wind. High-resolution measurements of plasmas and fields are used to identify highly localized ( 15 electron Debye lengths) standing wave structures with large electric field amplitudes (up to 100 mV/m). These wave structures are associated with spatially oscillatory energy conversion, which appears as alternatingly positive and negative values of J · E. For small guide magnetic fields the wave structures occur in the electron stagnation region at the magnetosphere edge of the electron diffusion region. For larger guide fields the structures also occur near the reconnection X-line. This difference is explained in terms of channels for the out-of-plane current (agyrotropic electrons at the stagnation point and guide field-aligned electrons at the X-line).

Characterizing structural transitions using localized free energy landscape analysis.

PubMed

Banavali, Nilesh K; Mackerell, Alexander D

2009-01-01

Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes. Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom. The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

Investigation of thermal conduction in symmetric and asymmetric nanoporous structures

NASA Astrophysics Data System (ADS)

Yu, Ziqi; Ferrer-Argemi, Laia; Lee, Jaeho

2017-12-01

Nanoporous structures with a critical dimension comparable to or smaller than the phonon mean free path have demonstrated significant thermal conductivity reductions that are attractive for thermoelectric applications, but the presence of various geometric parameters complicates the understanding of governing mechanisms. Here, we use a ray tracing technique to investigate phonon boundary scattering phenomena in Si nanoporous structures of varying pore shapes, pore alignments, and pore size distributions, and identify mechanisms that are primarily responsible for thermal conductivity reductions. Our simulation results show that the neck size, or the smallest distance between nearest pores, is the key parameter in understanding nanoporous structures of varying pore shapes and the same porosities. When the neck size and the porosity are both identical, asymmetric pore shapes provide a lower thermal conductivity compared with symmetric pore shapes, due to localized heat fluxes. Asymmetric nanoporous structures show possibilities of realizing thermal rectification even with fully diffuse surface boundaries, in which optimal arrangements of triangular pores show a rectification ratio up to 13 when the injection angles are optimally controlled. For symmetric nanoporous structures, hexagonal-lattice pores achieve larger thermal conductivity reductions than square-lattice pores due to the limited line of sight for phonons. We also show that nanoporous structures of alternating pore size distributions from large to small pores yield a lower thermal conductivity compared with those of uniform pore size distributions in the given porosity. These findings advance the understanding of phonon boundary scattering phenomena in complex geometries and enable optimal designs of artificial nanostructures for thermoelectric energy harvesting and solid-state cooling systems.

Eigenvector synchronization, graph rigidity and the molecule problemR

PubMed Central

Cucuringu, Mihai; Singer, Amit; Cowburn, David

2013-01-01

The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend the previous work and propose the 3D-As-Synchronized-As-Possible (3D-ASAP) algorithm, for the graph realization problem in ℝ3, given a sparse and noisy set of distance measurements. 3D-ASAP is a divide and conquer, non-incremental and non-iterative algorithm, which integrates local distance information into a global structure determination. Our approach starts with identifying, for every node, a subgraph of its 1-hop neighborhood graph, which can be accurately embedded in its own coordinate system. In the noise-free case, the computed coordinates of the sensors in each patch must agree with their global positioning up to some unknown rigid motion, that is, up to translation, rotation and possibly reflection. In other words, to every patch, there corresponds an element of the Euclidean group, Euc(3), of rigid transformations in ℝ3, and the goal was to estimate the group elements that will properly align all the patches in a globally consistent way. Furthermore, 3D-ASAP successfully incorporates information specific to the molecule problem in structural biology, in particular information on known substructures and their orientation. In addition, we also propose 3D-spectral-partitioning (SP)-ASAP, a faster version of 3D-ASAP, which uses a spectral partitioning algorithm as a pre-processing step for dividing the initial graph into smaller subgraphs. Our extensive numerical simulations show that 3D-ASAP and 3D-SP-ASAP are very robust to high levels of noise in the measured distances and to sparse connectivity in the measurement graph, and compare favorably with similar state-of-the-art localization algorithms. PMID:24432187

Surface-restrained growth of vertically aligned carbon nanotube arrays with excellent thermal transport performance.

PubMed

Ping, Linquan; Hou, Peng-Xiang; Liu, Chang; Li, Jincheng; Zhao, Yang; Zhang, Feng; Ma, Chaoqun; Tai, Kaiping; Cong, Hongtao; Cheng, Hui-Ming

2017-06-22

A vertically aligned carbon nanotube (VACNT) array is a promising candidate for a high-performance thermal interface material in high-power microprocessors due to its excellent thermal transport property. However, its rough and entangled free tips always cause poor interfacial contact, which results in serious contact resistance dominating the total thermal resistance. Here, we employed a thin carbon cover to restrain the disorderly growth of the free tips of a VACNT array. As a result, all the free tips are seamlessly connected by this thin carbon cover and the top surface of the array is smoothed. This unique structure guarantees the participation of all the carbon nanotubes in the array in the heat transport. Consequently the VACNT array grown on a Cu substrate shows a record low thermal resistance of 0.8 mm 2 K W -1 including the two-sided contact resistances, which is 4 times lower than the best result previously reported. Remarkably, the VACNT array can be easily peeled away from the Cu substrate and act as a thermal pad with excellent flexibility, adhesive ability and heat transport capability. As a result the CNT array with a thin carbon cover shows great potential for use as a high-performance flexible thermal interface material.

Stripe-PZT Sensor-Based Baseline-Free Crack Diagnosis in a Structure with a Welded Stiffener.

PubMed

An, Yun-Kyu; Shen, Zhiqi; Wu, Zhishen

2016-09-16

This paper proposes a stripe-PZT sensor-based baseline-free crack diagnosis technique in the heat affected zone (HAZ) of a structure with a welded stiffener. The proposed technique enables one to identify and localize a crack in the HAZ using only current data measured using a stripe-PZT sensor. The use of the stripe-PZT sensor makes it possible to significantly improve the applicability to real structures and minimize man-made errors associated with the installation process by embedding multiple piezoelectric sensors onto a printed circuit board. Moreover, a new frequency-wavenumber analysis-based baseline-free crack diagnosis algorithm minimizes false alarms caused by environmental variations by avoiding simple comparison with the baseline data accumulated from the pristine condition of a target structure. The proposed technique is numerically as well as experimentally validated using a plate-like structure with a welded stiffener, reveling that it successfully identifies and localizes a crack in HAZ.

Stripe-PZT Sensor-Based Baseline-Free Crack Diagnosis in a Structure with a Welded Stiffener

PubMed Central

An, Yun-Kyu; Shen, Zhiqi; Wu, Zhishen

2016-01-01

This paper proposes a stripe-PZT sensor-based baseline-free crack diagnosis technique in the heat affected zone (HAZ) of a structure with a welded stiffener. The proposed technique enables one to identify and localize a crack in the HAZ using only current data measured using a stripe-PZT sensor. The use of the stripe-PZT sensor makes it possible to significantly improve the applicability to real structures and minimize man-made errors associated with the installation process by embedding multiple piezoelectric sensors onto a printed circuit board. Moreover, a new frequency-wavenumber analysis-based baseline-free crack diagnosis algorithm minimizes false alarms caused by environmental variations by avoiding simple comparison with the baseline data accumulated from the pristine condition of a target structure. The proposed technique is numerically as well as experimentally validated using a plate-like structure with a welded stiffener, reveling that it successfully identifies and localizes a crack in HAZ. PMID:27649200

Crystal nucleation of colloidal hard dumbbells

NASA Astrophysics Data System (ADS)

Ni, Ran; Dijkstra, Marjolein

2011-01-01

Using computer simulations, we investigate the homogeneous crystal nucleation in suspensions of colloidal hard dumbbells. The free energy barriers are determined by Monte Carlo simulations using the umbrella sampling technique. We calculate the nucleation rates for the plastic crystal and the aperiodic crystal phase using the kinetic prefactor as determined from event driven molecular dynamics simulations. We find good agreement with the nucleation rates determined from spontaneous nucleation events observed in event driven molecular dynamics simulations within error bars of one order of magnitude. We study the effect of aspect ratio of the dumbbells on the nucleation of plastic and aperiodic crystal phases, and we also determine the structure of the critical nuclei. Moreover, we find that the nucleation of the aligned close-packed crystal structure is strongly suppressed by a high free energy barrier at low supersaturations and slow dynamics at high supersaturations.

Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.

PubMed

Guzzi, Pietro Hiram; Milenkovic, Tijana

2018-05-01

Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology.

Dinucleotide controlled null models for comparative RNA gene prediction.

PubMed

Gesell, Tanja; Washietl, Stefan

2008-05-27

Comparative prediction of RNA structures can be used to identify functional noncoding RNAs in genomic screens. It was shown recently by Babak et al. [BMC Bioinformatics. 8:33] that RNA gene prediction programs can be biased by the genomic dinucleotide content, in particular those programs using a thermodynamic folding model including stacking energies. As a consequence, there is need for dinucleotide-preserving control strategies to assess the significance of such predictions. While there have been randomization algorithms for single sequences for many years, the problem has remained challenging for multiple alignments and there is currently no algorithm available. We present a program called SISSIz that simulates multiple alignments of a given average dinucleotide content. Meeting additional requirements of an accurate null model, the randomized alignments are on average of the same sequence diversity and preserve local conservation and gap patterns. We make use of a phylogenetic substitution model that includes overlapping dependencies and site-specific rates. Using fast heuristics and a distance based approach, a tree is estimated under this model which is used to guide the simulations. The new algorithm is tested on vertebrate genomic alignments and the effect on RNA structure predictions is studied. In addition, we directly combined the new null model with the RNAalifold consensus folding algorithm giving a new variant of a thermodynamic structure based RNA gene finding program that is not biased by the dinucleotide content. SISSIz implements an efficient algorithm to randomize multiple alignments preserving dinucleotide content. It can be used to get more accurate estimates of false positive rates of existing programs, to produce negative controls for the training of machine learning based programs, or as standalone RNA gene finding program. Other applications in comparative genomics that require randomization of multiple alignments can be considered. SISSIz is available as open source C code that can be compiled for every major platform and downloaded here: http://sourceforge.net/projects/sissiz.

Local thermodynamic mapping for effective liquid density-functional theory

NASA Technical Reports Server (NTRS)

Kyrlidis, Agathagelos; Brown, Robert A.

1992-01-01

The structural-mapping approximation introduced by Lutsko and Baus (1990) in the generalized effective-liquid approximation is extended to include a local thermodynamic mapping based on a spatially dependent effective density for approximating the solid phase in terms of the uniform liquid. This latter approximation, called the local generalized effective-liquid approximation (LGELA) yields excellent predictions for the free energy of hard-sphere solids and for the conditions of coexistence of a hard-sphere fcc solid with a liquid. Moreover, the predicted free energy remains single valued for calculations with more loosely packed crystalline structures, such as the diamond lattice. The spatial dependence of the weighted density makes the LGELA useful in the study of inhomogeneous solids.

Structural-change localization and monitoring through a perturbation-based inverse problem.

PubMed

Roux, Philippe; Guéguen, Philippe; Baillet, Laurent; Hamze, Alaa

2014-11-01

Structural-change detection and characterization, or structural-health monitoring, is generally based on modal analysis, for detection, localization, and quantification of changes in structure. Classical methods combine both variations in frequencies and mode shapes, which require accurate and spatially distributed measurements. In this study, the detection and localization of a local perturbation are assessed by analysis of frequency changes (in the fundamental mode and overtones) that are combined with a perturbation-based linear inverse method and a deconvolution process. This perturbation method is applied first to a bending beam with the change considered as a local perturbation of the Young's modulus, using a one-dimensional finite-element model for modal analysis. Localization is successful, even for extended and multiple changes. In a second step, the method is numerically tested under ambient-noise vibration from the beam support with local changes that are shifted step by step along the beam. The frequency values are revealed using the random decrement technique that is applied to the time-evolving vibrations recorded by one sensor at the free extremity of the beam. Finally, the inversion method is experimentally demonstrated at the laboratory scale with data recorded at the free end of a Plexiglas beam attached to a metallic support.

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align/. njyudj@njust.edu.cn or zhng@umich.edu. Supplementary data are available at Bioinformatics online.

Thermal Electron Contributions to Current-Driven Instabilities: SCIFER Observations in the 1400-km Cleft Ion Fountain and Their Implications to Thermal Ion Energization

NASA Technical Reports Server (NTRS)

Adrian, Mark L.; Pollock, C. J.; Moore, T. E.; Kintner, P. M.; Arnoldy, R. L.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

SCIFER TECHS observations of the variations in the thermal electron distribution in the 1400-km altitude cleft are associated with periods of intense ion heating and field-aligned currents. Energization of the thermal ion plasma in the mid-altitude cleft occurs within density cavities accompanied by enhanced thermal electron temperatures, large field-aligned thermal electron plasma flows and broadband low-frequency electric fields. Variations in the thermal electron contribution to field-aligned current densities indicate small scale (approximately 100's m) filamentary structure embedded within the ion energization periods. TECHS observations of the field-aligned drift velocities and temperatures of the thermal electron distribution are presented to evaluate the critical velocity thresholds necessary for the generation of electrostatic ion cyclotron and ion acoustic instabilities. This analysis suggests that, during periods of thermal ion energization, sufficient drift exists in the thermal electron distribution to excite the electrostatic ion cyclotron instability. In addition, brief periods exist within the same interval where the drift of the thermal electron distribution is sufficient to marginally excite the ion acoustic instability. In addition, the presence an enhancement in Langmuir emission at the plasma frequency at the center of the ion energization region, accompanied by the emission's second-harmonic, and collocated with observations of high-frequency electric field solitary structures suggest the presence of electron beam driven decay of Langmuir waves to ion acoustic modes as an additional free energy source for ion energization.

Transmembrane Polyproline Helix.

PubMed

Kubyshkin, Vladimir; Grage, Stephan L; Bürck, Jochen; Ulrich, Anne S; Budisa, Nediljko

2018-05-03

The third most abundant polypeptide conformation in nature, the polyproline-II helix, is a polar, extended secondary structure with a local organization stabilized by intercarbonyl interactions within the peptide chain. Here we design a hydrophobic polyproline-II helical peptide based on an oligomeric octahydroindole-2-carboxylic acid scaffold and demonstrate its transmembrane alignment in model lipid bilayers by means of solid-state 19 F NMR. As result, we provide a first example of a purely artificial transmembrane peptide with a structural organization that is not based on hydrogen-bonding.

Planar solar concentrator featuring alignment-free total-internal-reflection collectors and an innovative compound tracker.

PubMed

Teng, Tun-Chien; Lai, Wei-Che

2014-12-15

This study proposed a planar solar concentrator featuring alignment-free total-internal-reflection (TIR) collectors and an innovative compound tracker. The compound tracker, combining a mechanical single-axis tracker and scrollable prism sheets, can achieve a performance on a par with dual-axis tracking while reducing the cost of the tracking system and increasing its robustness. The alignment-free TIR collectors are assembled on the waveguide without requiring alignment, so the planar concentrator is relatively easily manufactured and markedly increases the feasibility for use in large concentrators. Further, the identical TIR collector is applicable to various-sized waveguide slab without requiring modification, which facilitates flexibility regarding the size of the waveguide slab. In the simulation model, the thickness of the slab was 2 mm, and its maximal length reached 6 m. With an average angular tolerance of ±0.6°, and after considering both the Fresnel loss and the angular spread of the sun, the simulation indicates that the waveguide concentrator of a 1000-mm length provides the optical efficiencies of 62-77% at the irradiance concentrations of 387-688, and the one of a 2000-mm length provides the optical efficiencies of 52-64.5% at the irradiance concentrations of 645-1148. Alternatively, if a 100-mm horizontally staggered waveguide slab is collocated with the alignment-free TIR collectors, the optical efficiency would be greatly improved up to 91.5% at an irradiance concentration of 1098 (C(geo) = 1200X).

ShouldeRO, an alignment-free two-DOF rehabilitation robot for the shoulder complex.

PubMed

Dehez, Bruno; Sapin, Julien

2011-01-01

This paper presents a robot aimed to assist the shoulder movements of stroke patients during their rehabilitation process. This robot has the general form of an exoskeleton, but is characterized by an action principle on the patient no longer requiring a tedious and accurate alignment of the robot and patient's joints. It is constituted of a poly-articulated structure whose actuation is deported and transmission is ensured by Bowden cables. It manages two of the three rotational degrees of freedom (DOFs) of the shoulder. Quite light and compact, its proximal end can be rigidly fixed to the patient's back on a rucksack structure. As for its distal end, it is connected to the arm through passive joints and a splint guaranteeing the robot action principle, i.e. exert a force perpendicular to the patient's arm, whatever its configuration. This paper also presents a first prototype of this robot and some experimental results such as the arm angular excursions reached with the robot in the three joint planes. © 2011 IEEE

Ink-jet printing technology enables self-aligned mould patterning for electroplating in a single step

NASA Astrophysics Data System (ADS)

Meissner, M. V.; Spengler, N.; Mager, D.; Wang, N.; Kiss, S. Z.; Höfflin, J.; While, P. T.; Korvink, J. G.

2015-06-01

We present a new self-aligned, mask-free micro-fabrication method with which to form thick-layered conductive metal micro-structures inside electroplating moulds. Seed layer patterning for electroplating was performed by ink-jet printing using a silver nano-particle ink deposited on SU-8 or Ordyl SY permanent resist. The silver ink contact angle on SU-8 was adjusted by oxygen plasma followed by a hard bake. Besides functioning as a seed layer, the printed structures further served as a shadow mask during patterning of electroplating moulds into negative photoresist. The printed silver tracks remained in strong adhesion to the substrate when exposed to the acidic chemistry of the electroplating bath. To demonstrate the process, we manufactured rectangular, low-resistivity planar micro-coils for use in magnetic resonance microscopy. MRI images of a spring onion with an in-plane resolution down to 10 µm × 10 µm were acquired using a micro-coil on an 11.7 T MRI scanner.

Two-way regulation between cells and aligned collagen fibrils: local 3D matrix formation and accelerated neural differentiation of human decidua parietalis placental stem cells.

PubMed

Li, Wen; Zhu, Bofan; Strakova, Zuzana; Wang, Rong

2014-08-08

It has been well established that an aligned matrix provides structural and signaling cues to guide cell polarization and cell fate decision. However, the modulation role of cells in matrix remodeling and the feedforward effect on stem cell differentiation have not been studied extensively. In this study, we report on the concerted changes of human decidua parietalis placental stem cells (hdpPSCs) and the highly ordered collagen fibril matrix in response to cell-matrix interaction. With high-resolution imaging, we found the hdpPSCs interacted with the matrix by deforming the cell shape, harvesting the nearby collagen fibrils, and reorganizing the fibrils around the cell body to transform a 2D matrix to a localized 3D matrix. Such a unique 3D matrix prompted high expression of β-1 integrin around the cell body that mediates and facilitates the stem cell differentiation toward neural cells. The study offers insights into the coordinated, dynamic changes at the cell-matrix interface and elucidates cell modulation of its matrix to establish structural and biochemical cues for effective cell growth and differentiation. Copyright © 2014 Elsevier Inc. All rights reserved.

Optical and electrical stability of viral-templated copper sulfide (Cu1.8S) films

NASA Astrophysics Data System (ADS)

Shahriar Zaman, Mohammed; Bernard Grajeda, Gabriel; Haberer, Elaine D.

2014-04-01

The optical and electrical stabilities of viral-templated non-stoichiometric copper sulfide, digenite (Cu1.8S) films were investigated. The films were composed of large agglomerates of randomly aligned Cu1.8S-coated M13 filamentous phage. Free carrier optical absorption associated with localized surface plasmon resonance (LSPR) was observed in the near infrared spectral region, and the films were electrically active, displaying a linear current-voltage relationship. Under ambient conditions, the magnitude of the LSPR absorption increased, following a power law relationship with time, and the electrical resistance of viral-templated films decreased significantly. In contrast, the resistance of films stored under low oxygen, low humidity conditions experienced a smaller reduction in electrical resistance. Changes in optical and electrical film properties under ambient conditions were associated with an increase in free carrier concentration within the copper chalcogenide material due to oxygen exposure. X-ray photoelectron spectroscopy was used to relate this increase in free carrier concentration to compositional changes on the viral-templated material surface.

Local structure of human hair spatially resolved by sub-micron X-ray beam.

PubMed

Stanić, Vesna; Bettini, Jefferson; Montoro, Fabiano Emmanuel; Stein, Aaron; Evans-Lutterodt, Kenneth

2015-11-30

Human hair has three main regions, the medulla, the cortex, and the cuticle. An existing model for the cortex suggests that the α-keratin- based intermediate filaments (IFs) align with the hair's axis, but are orientationally disordered in-plane. We found that there is a new region in the cortex near the cuticle's boundary in which the IFs are aligned with the hair's axis, but additionally, they are orientationally ordered in-plane due to the presence of the cuticle/hair boundary. Further into the cortex, the IF arrangement becomes disordered, eventually losing all in-plane orientation. We also find that in the cuticle, a key diffraction feature is absent, indicating the presence of the β-keratin rather than that of the α-keratin phase. This is direct structural evidence that the cuticle contains β-keratin sheets. This work highlights the importance of using a sub-micron x-ray beam to unravel the structures of poorly ordered, multi-phase systems.

AlignNemo: a local network alignment method to integrate homology and topology.

PubMed

Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

2012-01-01

Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

Theory of short-scale field-aligned density striations due to ionospheric heating

NASA Technical Reports Server (NTRS)

Lee, M.-C.; Fejer, J. A.

1978-01-01

The theoretical saturation spectrum of parametrically excited Langmuir waves in a locally uniform ionosphere is shown by the present calculations to produce, by ohmic dissipation, short-scale field-aligned density striations. The spectrum of the calculated striations is not inconsistent with observations of field-aligned scatter of VHF and UHF waves in ionospheric modification experiments if local increases of the pump field due to focusing are invoked.

Multiscale Currents Observed by MMS in the Flow Braking Region.

PubMed

Nakamura, Rumi; Varsani, Ali; Genestreti, Kevin J; Le Contel, Olivier; Nakamura, Takuma; Baumjohann, Wolfgang; Nagai, Tsugunobu; Artemyev, Anton; Birn, Joachim; Sergeev, Victor A; Apatenkov, Sergey; Ergun, Robert E; Fuselier, Stephen A; Gershman, Daniel J; Giles, Barbara J; Khotyaintsev, Yuri V; Lindqvist, Per-Arne; Magnes, Werner; Mauk, Barry; Petrukovich, Anatoli; Russell, Christopher T; Stawarz, Julia; Strangeway, Robert J; Anderson, Brian; Burch, James L; Bromund, Ken R; Cohen, Ian; Fischer, David; Jaynes, Allison; Kepko, Laurence; Le, Guan; Plaschke, Ferdinand; Reeves, Geoff; Singer, Howard J; Slavin, James A; Torbert, Roy B; Turner, Drew L

2018-02-01

We present characteristics of current layers in the off-equatorial near-Earth plasma sheet boundary observed with high time-resolution measurements from the Magnetospheric Multiscale mission during an intense substorm associated with multiple dipolarizations. The four Magnetospheric Multiscale spacecraft, separated by distances of about 50 km, were located in the southern hemisphere in the dusk portion of a substorm current wedge. They observed fast flow disturbances (up to about 500 km/s), most intense in the dawn-dusk direction. Field-aligned currents were observed initially within the expanding plasma sheet, where the flow and field disturbances showed the distinct pattern expected in the braking region of localized flows. Subsequently, intense thin field-aligned current layers were detected at the inner boundary of equatorward moving flux tubes together with Earthward streaming hot ions. Intense Hall current layers were found adjacent to the field-aligned currents. In particular, we found a Hall current structure in the vicinity of the Earthward streaming ion jet that consisted of mixed ion components, that is, hot unmagnetized ions, cold E × B drifting ions, and magnetized electrons. Our observations show that both the near-Earth plasma jet diversion and the thin Hall current layers formed around the reconnection jet boundary are the sites where diversion of the perpendicular currents take place that contribute to the observed field-aligned current pattern as predicted by simulations of reconnection jets. Hence, multiscale structure of flow braking is preserved in the field-aligned currents in the off-equatorial plasma sheet and is also translated to ionosphere to become a part of the substorm field-aligned current system.

Non-linear tides in a homogeneous rotating planet or star: global modes and elliptical instability

NASA Astrophysics Data System (ADS)

Barker, Adrian J.; Braviner, Harry J.; Ogilvie, Gordon I.

2016-06-01

We revisit the global modes and instabilities of homogeneous rotating ellipsoidal fluid masses, which are the simplest global models of rotationally and tidally deformed gaseous planets or stars. The tidal flow in a short-period planet may be unstable to the elliptical instability, a hydrodynamic instability that can drive tidal evolution. We perform a global (and local WKB) analysis to study this instability using the elegant formalism of Lebovitz & Lifschitz. We survey the parameter space of global instabilities with harmonic orders ℓ ≤ 5, for planets with spins that are purely aligned (prograde) or anti-aligned (retrograde) with their orbits. In general, the instability has a much larger growth rate if the planetary spin and orbit are anti-aligned rather than aligned. We have identified a violent instability for anti-aligned spins outside of the usual frequency range for the elliptical instability (when n/Ω ≲ -1, where n and Ω are the orbital and spin angular frequencies, respectively) if the tidal amplitude is sufficiently large. We also explore the instability in a rigid ellipsoidal container, which is found to be quantitatively similar to that with a realistic free surface. Finally, we study the effect of rotation and tidal deformation on mode frequencies. We find that larger rotation rates and larger tidal deformations both decrease the frequencies of the prograde sectoral surface gravity modes. This increases the prospect of their tidal excitation, potentially enhancing the tidal response over expectations from linear theory. In a companion paper, we use our results to interpret global simulations of the elliptical instability.

A new standard pulsar magnetosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Contopoulos, Ioannis; Kalapotharakos, Constantinos; Kazanas, Demosthenes, E-mail: icontop@academyofathens.gr

2014-01-20

In view of recent efforts to probe the physical conditions in the pulsar current sheet, we revisit the standard solution that describes the main elements of the ideal force-free pulsar magnetosphere. The simple physical requirement that the electric current contained in the current layer consists of the local electric charge moving outward at close to the speed of light yields a new solution for the pulsar magnetosphere everywhere that is ideal force-free except in the current layer. The main elements of the new solution are as follows: (1) the pulsar spindown rate of the aligned rotator is 23% larger thanmore » that of the orthogonal vacuum rotator; (2) only 60% of the magnetic flux that crosses the light cylinder opens up to infinity; (3) the electric current closes along the other 40%, which gradually converges to the equator; (4) this transfers 40% of the total pulsar spindown energy flux in the equatorial current sheet, which is then dissipated in the acceleration of particles and in high-energy electromagnetic radiation; and (5) there is no separatrix current layer. Our solution is a minimum free-parameter solution in that the equatorial current layer is electrostatically supported against collapse and thus does not require a thermal particle population. In this respect, it is one more step toward the development of a new standard solution. We discuss the implications for intermittent pulsars and long-duration gamma-ray bursts. We conclude that the physical conditions in the equatorial current layer determine the global structure of the pulsar magnetosphere.« less

Evolutionary trade-offs and the structure of polymorphisms.

PubMed

Sheftel, Hila; Szekely, Pablo; Mayo, Avi; Sella, Guy; Alon, Uri

2018-05-26

Populations of organisms show genetic differences called polymorphisms. Understanding the effects of polymorphisms is important for biology and medicine. Here, we ask which polymorphisms occur at high frequency when organisms evolve under trade-offs between multiple tasks. Multiple tasks present a problem, because it is not possible to be optimal at all tasks simultaneously and hence compromises are necessary. Recent work indicates that trade-offs lead to a simple geometry of phenotypes in the space of traits: phenotypes fall on the Pareto front, which is shaped as a polytope: a line, triangle, tetrahedron etc. The vertices of these polytopes are the optimal phenotypes for a single task. Up to now, work on this Pareto approach has not considered its genetic underpinnings. Here, we address this by asking how the polymorphism structure of a population is affected by evolution under trade-offs. We simulate a multi-task selection scenario, in which the population evolves to the Pareto front: the line segment between two archetypes or the triangle between three archetypes. We find that polymorphisms that become prevalent in the population have pleiotropic phenotypic effects that align with the Pareto front. Similarly, epistatic effects between prevalent polymorphisms are parallel to the front. Alignment with the front occurs also for asexual mating. Alignment is reduced when drift or linkage is strong, and is replaced by a more complex structure in which many perpendicular allele effects cancel out. Aligned polymorphism structure allows mating to produce offspring that stand a good chance of being optimal multi-taskers in at least one of the locales available to the species.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform.

PubMed

Lin, Jie; Wei, Jing; Adjeroh, Donald; Jiang, Bing-Hua; Jiang, Yue

2018-05-02

Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts. A new alignment-free sequence similarity analysis method, called SSAW is proposed. SSAW stands for Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification. Using two different types of applications, namely, clustering and classification, we compared SSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or superior performance in terms of standard indicators, such as accuracy, F-score, precision, and recall. The running time was significantly better in most cases. These make SSAW a suitable method for sequence analysis, especially, given the rapidly increasing volumes of sequence data required by most modern applications.

Planform structure and heat transfer in turbulent free convection over horizontal surfaces

NASA Astrophysics Data System (ADS)

Theerthan, S. Ananda; Arakeri, Jaywant H.

2000-04-01

This paper deals with turbulent free convection in a horizontal fluid layer above a heated surface. Experiments have been carried out on a heated surface to obtain and analyze the planform structure and the heat transfer under different conditions. Water is the working fluid and the range of flux Rayleigh numbers (Ra) covered is 3×107-2×1010. The different conditions correspond to Rayleigh-Bénard convection, convection with either the top water surface open to atmosphere or covered with an insulating plate, and with an imposed external flow on the heated boundary. Without the external flow the planform is one of randomly oriented line plumes. At large Rayleigh number Ra and small aspect ratio (AR), these line plumes seem to align along the diagonal, presumably due to a large scale flow. The side views show inclined dyelines, again indicating a large scale flow. When the external flow is imposed, the line plumes clearly align in the direction of external flow. The nondimensional average plume spacing, Raλ1/3, varies between 40 and 90. The heat transfer rate, for all the experiments conducted, represented as RaδT-1/3, where δT is the conduction layer thickness, varies only between 0.1-0.2, showing that in turbulent convection the heat transfer rates are similar under the different conditions.

Combined antenna and localized plasmon resonance in Raman scattering from random arrays of silver-coated, vertically aligned multiwalled carbon nanotubes.

PubMed

Dawson, P; Duenas, J A; Boyle, M G; Doherty, M D; Bell, S E J; Kern, A M; Martin, O J F; Teh, A-S; Teo, K B K; Milne, W I

2011-02-09

The electric field enhancement associated with detailed structure within novel optical antenna nanostructures is modeled using the surface integral equation technique in the context of surface-enhanced Raman scattering (SERS). The antennae comprise random arrays of vertically aligned, multiwalled carbon nanotubes dressed with highly granular Ag. Different types of "hot-spot" underpinning the SERS are identified, but contrasting characteristics are revealed. Those at the outer edges of the Ag grains are antenna driven with field enhancement amplified in antenna antinodes while intergrain hotspots are largely independent of antenna activity. Hot-spots between the tops of antennae leaning towards each other also appear to benefit from antenna amplification.

Aligned 1-D nanorods of a π-gelator exhibit molecular orientation and excitation energy transport different from entangled fiber networks.

PubMed

Sakakibara, Keita; Chithra, Parayalil; Das, Bidisa; Mori, Taizo; Akada, Misaho; Labuta, Jan; Tsuruoka, Tohru; Maji, Subrata; Furumi, Seiichi; Shrestha, Lok Kumar; Hill, Jonathan P; Acharya, Somobrata; Ariga, Katsuhiko; Ajayaghosh, Ayyappanpillai

2014-06-18

Linear π-gelators self-assemble into entangled fibers in which the molecules are arranged perpendicular to the fiber long axis. However, orientation of gelator molecules in a direction parallel to the long axes of the one-dimensional (1-D) structures remains challenging. Herein we demonstrate that, at the air-water interface, an oligo(p-phenylenevinylene)-derived π-gelator forms aligned nanorods of 340 ± 120 nm length and 34 ± 5 nm width, in which the gelator molecules are reoriented parallel to the long axis of the rods. The orientation change of the molecules results in distinct excited-state properties upon local photoexcitation, as evidenced by near-field scanning optical microscopy. A detailed understanding of the mechanism by which excitation energy migrates through these 1-D molecular assemblies might help in the design of supramolecular structures with improved charge-transport properties.

Conserved thioredoxin fold is present in Pisum sativum L. sieve element occlusion-1 protein

PubMed Central

Umate, Pavan; Tuteja, Renu

2010-01-01

Homology-based three-dimensional model for Pisum sativum sieve element occlusion 1 (Ps.SEO1) (forisomes) protein was constructed. A stretch of amino acids (residues 320 to 456) which is well conserved in all known members of forisomes proteins was used to model the 3D structure of Ps.SEO1. The structural prediction was done using Protein Homology/analogY Recognition Engine (PHYRE) web server. Based on studies of local sequence alignment, the thioredoxin-fold containing protein [Structural Classification of Proteins (SCOP) code d1o73a_], a member of the glutathione peroxidase family was selected as a template for modeling the spatial structure of Ps.SEO1. Selection was based on comparison of primary sequence, higher match quality and alignment accuracy. Motif 1 (EVF) is conserved in Ps.SEO1, Vicia faba (Vf.For1) and Medicago truncatula (MT.SEO3); motif 2 (KKED) is well conserved across all forisomes proteins and motif 3 (IGYIGNP) is conserved in Ps.SEO1 and Vf.For1. PMID:20404566

Fe local structure in Pt-free nitrogen-modified carbon based electrocatalysts: XAFS study

NASA Astrophysics Data System (ADS)

Witkowska, Agnieszka; Giuli, Gabriele; Renzi, Marco; Marzorati, Stefania; Yiming, Wubulikasimu; Nobili, Francesco; Longhi, Mariangela

2016-05-01

The paper presents a new results on the bonding environment (coordination number and geometry) and on oxidation states of Fe in nitrogen-modified Fe/C composites used as Pt-free catalysts for oxygen reduction in Direct Hydrogen Fuel Cells. Starting from glucose or fructose, two catalysts displaying different electrochemical performance were prepared and studied in the form of pristine powder and thin catalytic layer of electrode by Fe K-edge XAFS spectroscopy. The results show how the Fe local structure varies as a function of different synthesis conditions and how changes in the structural properties of the catalysts are related to fuel cell electrochemical performance increase during a cell activation period.

Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

DOE PAGES

Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

2015-07-28

Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules

NASA Astrophysics Data System (ADS)

Pitman, Michael C.; Huber, Wolfgang K.; Horn, Hans; Krämer, Andreas; Rice, Julia E.; Swope, William C.

2001-07-01

A three-dimensional field-based similarity search and alignment method for flexible molecules is introduced. The conformational space of a flexible molecule is represented in terms of fragments and torsional angles of allowed conformations. A user-definable property field is used to compute features of fragment pairs. Features are generalizations of CoMMA descriptors (Silverman, B.D. and Platt, D.E., J. Med. Chem., 39 (1996) 2129.) that characterize local regions of the property field by its local moments. The features are invariant under coordinate system transformations. Features taken from a query molecule are used to form alignments with fragment pairs in the database. An assembly algorithm is then used to merge the fragment pairs into full structures, aligned to the query. Key to the method is the use of a context adaptive descriptor scaling procedure as the basis for similarity. This allows the user to tune the weights of the various feature components based on examples relevant to the particular context under investigation. The property fields may range from simple, phenomenological fields, to fields derived from quantum mechanical calculations. We apply the method to the dihydrofolate/methotrexate benchmark system, and show that when one injects relevant contextual information into the descriptor scaling procedure, better results are obtained more efficiently. We also show how the method works and include computer times for a query from a database that represents approximately 23 million conformers of seventeen flexible molecules.

Depth elemental characterization of 1D self-aligned TiO2 nanotubes using calibrated radio frequency glow discharge optical emission spectroscopy (GDOES)

NASA Astrophysics Data System (ADS)

Mohajernia, Shiva; Mazare, Anca; Hwang, Imgon; Gaiaschi, Sofia; Chapon, Patrick; Hildebrand, Helga; Schmuki, Patrik

2018-06-01

In this work we study the depth composition of anodic TiO2 nanotube layers. We use elemental depth profiling with Glow Discharge Optical Emission Spectroscopy and calibrate the results of this technique with X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS). We establish optimized sputtering conditions for nanotubular structures using the pulsed RF mode, which causes minimized structural damage during the depth profiling of the nanotubular structures. This allows to obtain calibrated sputter rates that account for the nanotubular "porous" morphology. Most importantly, sputter-artifact free compositional profiles of these high aspect ratio 3D structures are obtained, as well as, in combination with SEM, elegant depth sectional imaging.

Statistical inference of protein structural alignments using information and compression.

PubMed

Collier, James H; Allison, Lloyd; Lesk, Arthur M; Stuckey, Peter J; Garcia de la Banda, Maria; Konagurthu, Arun S

2017-04-01

Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . arun.konagurthu@monash.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Ferroelectric Domain Structure and Local Piezoelectric Properties of Lead-Free (Ka0.5Na0.5)NbO3 and BiFeO3-Based Piezoelectric Ceramics

PubMed Central

Alikin, Denis; Turygin, Anton; Kholkin, Andrei; Shur, Vladimir

2017-01-01

Recent advances in the development of novel methods for the local characterization of ferroelectric domains open up new opportunities not only to image, but also to control and to create desired domain configurations (domain engineering). The morphotropic and polymorphic phase boundaries that are frequently used to increase the electromechanical and dielectric performance of ferroelectric ceramics have a tremendous effect on the domain structure, which can serve as a signature of complex polarization states and link local and macroscopic piezoelectric and dielectric responses. This is especially important for the study of lead-free ferroelectric ceramics, which is currently replacing traditional lead-containing materials, and great efforts are devoted to increasing their performance to match that of lead zirconate titanate (PZT). In this work, we provide a short overview of the recent progress in the imaging of domain structure in two major families of ceramic lead-free systems based on BiFeO3 (BFO) and (Ka0.5Na0.5)NbO3 (KNN). This can be used as a guideline for the understanding of domain processes in lead-free piezoelectric ceramics and provide further insight into the mechanisms of structure–property relationship in these technologically important material families. PMID:28772408

Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M

2017-07-24

Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

PubMed Central

Knudsen, Vegeir; Caetano-Anollés, Gustavo

2008-01-01

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

Strongly aligned gas-phase molecules at free-electron lasers

DOE PAGES

Kierspel, Thomas; Wiese, Joss; Mullins, Terry; ...

2015-09-16

Here, we demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the linac coherent light source. Chirped laser pulses, i.e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2, 5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment ofmore » $$\\langle {\\mathrm{cos}}^{2}{\\theta }_{2{\\rm{D}}}\\rangle =0.85$$ was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses.« less

Observation time scale, free-energy landscapes, and molecular symmetry

PubMed Central

Wales, David J.; Salamon, Peter

2014-01-01

When structures that interconvert on a given time scale are lumped together, the corresponding free-energy surface becomes a function of the observation time. This view is equivalent to grouping structures that are connected by free-energy barriers below a certain threshold. We illustrate this time dependence for some benchmark systems, namely atomic clusters and alanine dipeptide, highlighting the connections to broken ergodicity, local equilibrium, and “feasible” symmetry operations of the molecular Hamiltonian. PMID:24374625

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

PubMed Central

2010-01-01

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size. PMID:20565983

A flexible statistical model for alignment of label-free proteomics data – incorporating ion mobility and product ion information

PubMed Central

2013-01-01

Background The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these information-rich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing - the matching of peptide measurements across samples. Results We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Conclusions Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods. PMID:24341404

A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.

PubMed

Benjamin, Ashlee M; Thompson, J Will; Soderblom, Erik J; Geromanos, Scott J; Henao, Ricardo; Kraus, Virginia B; Moseley, M Arthur; Lucas, Joseph E

2013-12-16

The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these information-rich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing--the matching of peptide measurements across samples. We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods.

Efficient and robust model-to-image alignment using 3D scale-invariant features.

PubMed

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

Efficient and Robust Model-to-Image Alignment using 3D Scale-Invariant Features

PubMed Central

Toews, Matthew; Wells, William M.

2013-01-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. PMID:23265799

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

PubMed Central

Sievers, Aaron; Bosiek, Katharina; Bisch, Marc; Dreessen, Chris; Riedel, Jascha; Froß, Patrick; Hausmann, Michael; Hildenbrand, Georg

2017-01-01

In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard k-mer analysis. PMID:28422050

An additional reference axis improves femoral rotation alignment in image-free computer navigation assisted total knee arthroplasty.

PubMed

Inui, Hiroshi; Taketomi, Shuji; Nakamura, Kensuke; Sanada, Takaki; Tanaka, Sakae; Nakagawa, Takumi

2013-05-01

Few studies have demonstrated improvement in accuracy of rotational alignment using image-free navigation systems mainly due to the inconsistent registration of anatomical landmarks. We have used an image-free navigation for total knee arthroplasty, which adopts the average algorithm between two reference axes (transepicondylar axis and axis perpendicular to the Whiteside axis) for femoral component rotation control. We hypothesized that addition of another axis (condylar twisting axis measured on a preoperative radiograph) would improve the accuracy. One group using the average algorithm (double-axis group) was compared with the other group using another axis to confirm the accuracy of the average algorithm (triple-axis group). Femoral components were more accurately implanted for rotational alignment in the triple-axis group (ideal: triple-axis group 100%, double-axis group 82%, P<0.05). Copyright © 2013 Elsevier Inc. All rights reserved.

Alignment between Protostellar Outflows and Filamentary Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mixmore » of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.« less

Higher-order mode-based cavity misalignment measurements at the free-electron laser FLASH

NASA Astrophysics Data System (ADS)

Hellert, Thorsten; Baboi, Nicoleta; Shi, Liangliang

2017-12-01

At the Free-Electron Laser in Hamburg (FLASH) and the European X-Ray Free-Electron Laser, superconducting TeV-energy superconducting linear accelerator (TESLA)-type cavities are used for the acceleration of electron bunches, generating intense free-electron laser (FEL) beams. A long rf pulse structure allows one to accelerate long bunch trains, which considerably increases the efficiency of the machine. However, intrabunch-train variations of rf parameters and misalignments of rf structures induce significant trajectory variations that may decrease the FEL performance. The accelerating cavities are housed inside cryomodules, which restricts the ability for direct alignment measurements. In order to determine the transverse cavity position, we use a method based on beam-excited dipole modes in the cavities. We have developed an efficient measurement and signal processing routine and present its application to multiple accelerating modules at FLASH. The measured rms cavity offset agrees with the specification of the TESLA modules. For the first time, the tilt of a TESLA cavity inside a cryomodule is measured. The preliminary result agrees well with the ratio between the offset and angle dependence of the dipole mode which we calculated with eigenmode simulations.

The relationship between free-stream coherent structures and near-wall streaks at high Reynolds numbers

PubMed Central

Deguchi, K.; Hall, P.

2017-01-01

The present work is based on our recent discovery of a new class of exact coherent structures generated near the edge of quite general boundary layer flows. The structures are referred to as free-stream coherent structures and were found using a large Reynolds number asymptotic approach to describe equilibrium solutions of the Navier–Stokes equations. In this paper, first we present results for a new family of free-stream coherent structures existing at relatively large wavenumbers. The new results are consistent with our earlier theoretical result that such structures can generate larger amplitude wall streaks if and only if the local spanwise wavenumber is sufficiently small. In a Blasius boundary layer, the local wavenumber increases in the streamwise direction so the wall streaks can typically exist only over a finite interval. However, here it is shown that they can interact with wall curvature to produce exponentially growing Görtler vortices through the receptivity process by a novel nonparallel mechanism. The theoretical predictions found are confirmed by a hybrid numerical approach. In contrast with previous receptivity investigations, it is shown that the amplitude of the induced vortex is larger than the structures in the free-stream which generate it. This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’. PMID:28167574

The relationship between free-stream coherent structures and near-wall streaks at high Reynolds numbers.

PubMed

Deguchi, K; Hall, P

2017-03-13

The present work is based on our recent discovery of a new class of exact coherent structures generated near the edge of quite general boundary layer flows. The structures are referred to as free-stream coherent structures and were found using a large Reynolds number asymptotic approach to describe equilibrium solutions of the Navier-Stokes equations. In this paper, first we present results for a new family of free-stream coherent structures existing at relatively large wavenumbers. The new results are consistent with our earlier theoretical result that such structures can generate larger amplitude wall streaks if and only if the local spanwise wavenumber is sufficiently small. In a Blasius boundary layer, the local wavenumber increases in the streamwise direction so the wall streaks can typically exist only over a finite interval. However, here it is shown that they can interact with wall curvature to produce exponentially growing Görtler vortices through the receptivity process by a novel nonparallel mechanism. The theoretical predictions found are confirmed by a hybrid numerical approach. In contrast with previous receptivity investigations, it is shown that the amplitude of the induced vortex is larger than the structures in the free-stream which generate it.This article is part of the themed issue 'Toward the development of high-fidelity models of wall turbulence at large Reynolds number'. © 2017 The Author(s).

Dilatancy of Shear Transformations in a Colloidal Glass

NASA Astrophysics Data System (ADS)

Lu, Y. Z.; Jiang, M. Q.; Lu, X.; Qin, Z. X.; Huang, Y. J.; Shen, J.

2018-01-01

Shear transformations, as fundamental rearrangement events operating in local regions, hold the key of plastic flow of amorphous solids. Despite their importance, the dynamic features of shear transformations are far from clear, which is the focus of the present study. Here, we use a colloidal glass under shear as the prototype to directly observe the shear-transformation events in real space. By tracing the colloidal-particle rearrangements, we quantitatively determine two basic properties of shear transformations: local shear strain and dilatation (or free volume). It is revealed that the local free volume undergoes a significantly temporary increase prior to shear transformations, eventually leading to a jump of local shear strain. We clearly demonstrate that shear transformations have no memory of the initial free volume of local regions. Instead, their emergence strongly depends on the dilatancy ability of these local regions, i.e., the dynamic creation of free volume. More specifically, the particles processing the high dilatancy ability directly participate in subsequent shear transformations. These results experimentally enrich Argon's statement about the dilatancy nature of shear transformations and also shed insight into the structural origin of amorphous plasticity.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Mercury free microscopy: an opportunity for core facility directors.

PubMed

Baird, T Regan; Kaufman, Daniel; Brown, Claire M

2014-07-01

Mercury Free Microscopy (MFM) is a new movement that encourages microscope owners to choose modern mercury free light sources to replace more traditional mercury based arc lamps. Microscope performance is enhanced with new solid state technologies because they offer a more stable light intensity output and have a more uniform light output across the visible spectrum. Solid state sources not only eliminate mercury but also eliminate the cost of consumable bulbs (lifetime ∼200 hours), use less energy, reduce the instrument down time when bulbs fail and reduce the staff time required to replace and align bulbs. With lifetimes on the order of tens of thousands of hours, solid state replacements can pay for themselves over their lifetime with the omission of consumable, staff (no need to replace and align bulbs) and energy costs. Solid state sources are also sustainable and comply with institutional and government body mandates to reduce energy consumption, carbon footprints and hazardous waste. MFM can be used as a mechanism to access institutional financial resources for sustainable technology through a variety of stakeholders to defray the cost to microscope owners for the initial purchase of solid state sources or the replacement cost of mercury based sources. Core facility managers can take a lead in this area as "green" ambassadors for their institution by championing a local MFM program that will save their institution money and energy and eliminate mercury from the waste stream. Managers can leverage MFM to increase the visibility of their facility, their impact within the institution, and as a vital educational resource for scientific and administrative consultation.

The shapes and alignments of the satellites of the Milky Way and Andromeda

NASA Astrophysics Data System (ADS)

Sanders, Jason L.; Evans, N. Wyn

2017-12-01

We measure the intrinsic shapes and alignments of the dwarf spheroidal (dSph) galaxies of the Local Group. We find the dSphs of the Milky Way are intrinsically flatter (mean intrinsic ellipticity μE ∼ 0.6) than those of M31 (μE ∼ 0.5) and that the classical Milky Way dSphs (MV < -8.5 mag) are rounder (μE ∼ 0.5) than the ultrafaints (μE ∼ 0.65) whilst in Andromeda (M31) the shapes of the classical and ultrafaint dSphs are very similar. The M31 dSphs are preferentially radially aligned with a dispersion of {˜ }45°. This signal is driven by the ultrafaint population whilst the classical M31 dSphs are consistent with a random orientation. We compare our results to the Aquarius mock stellar catalogues of Lowing et al. and find the subhalo radial alignment distribution matches the Local Group dSphs results, whilst the Aquarius intrinsic ellipticities are significantly smaller than the data (Δ〈E〉 ≈ 0.4). We provide evidence that the major axes of the Milky Way satellites lie within a preferential plane with normal vector pointing towards (ℓ,b)=(127,5)°. We associate this preferred direction with the Vast Polar Orbital structure although their respective great circles are offset by {˜ }30°. No signal in the alignments of the major axes is found in M31, suggesting that the great plane of satellites is formed from recent accretion or chance alignment. Finally, we provide predictions for the discrepancy between the velocity dispersion versus scale radius distributions for the Milky Way and M31 populations and demonstrate that the projection effect from viewing similar populations from two different locations does not account for the discrepancy which is probably caused by increased tidal disruption in M31.

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

PubMed

Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

2016-01-01

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

Communication: Nanoscale electrostatic theory of epistructural fields at the protein-water interface

NASA Astrophysics Data System (ADS)

Fernández, Ariel

2012-12-01

Nanoscale solvent confinement at the protein-water interface promotes dipole orientations that are not aligned with the internal electrostatic field of a protein, yielding what we term epistructural polarization. To quantify this effect, an equation is derived from first principles relating epistructural polarization with the magnitude of local distortions in water coordination causative of interfacial tension. The equation defines a nanoscale electrostatic model of water and enables an estimation of protein denaturation free energies and the inference of hot spots for protein associations. The theoretical results are validated vis-à-vis calorimetric data, revealing the destabilizing effect of epistructural polarization and its molecular origin.

Communication: Nanoscale electrostatic theory of epistructural fields at the protein-water interface.

PubMed

Fernández, Ariel

2012-12-21

Nanoscale solvent confinement at the protein-water interface promotes dipole orientations that are not aligned with the internal electrostatic field of a protein, yielding what we term epistructural polarization. To quantify this effect, an equation is derived from first principles relating epistructural polarization with the magnitude of local distortions in water coordination causative of interfacial tension. The equation defines a nanoscale electrostatic model of water and enables an estimation of protein denaturation free energies and the inference of hot spots for protein associations. The theoretical results are validated vis-à-vis calorimetric data, revealing the destabilizing effect of epistructural polarization and its molecular origin.

Fast-SG: an alignment-free algorithm for hybrid assembly.

PubMed

Di Genova, Alex; Ruz, Gonzalo A; Sagot, Marie-France; Maass, Alejandro

2018-05-01

Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short- and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffoldinggraph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost.

Alfvenic Generation of Field-Aligned Currents and Displacement Currents in the M-I Coupling System and the Formation of Discrete Auroral Arcs

NASA Astrophysics Data System (ADS)

Song, Y.; Lysak, R. L.

2016-12-01

In previous theories (e.g., Hasegawa and Sato, 1979; Sato and Iijima, 1979; Vasyliunas, 1984), field-aligned current (FAC) generation is derived from current continuity assumption plus the force balance between the Lorentz force and other forces in the MHD momentum equation. These theories suggest that the FAC is generated by other forces, such as the inertia and/or pressure gradients. In fact, the FAC cannot be generated by these forces. From Maxwell's equations, FAC generation is associated with enhanced sheared magnetic fields and free magnetic energy where a dynamo action and Alfven waves are needed to generate and transport free magnetic energy. It is obvious that the mechanism of FAC generation cannot be given by analyzing a local force balance. We propose that FACs are generated by Alfvenic interactions in the M-I coupling driven system. From a full set of the dynamical equations, we have found that the generation of the total FAC (J||total ) is associated with spatial gradients of the parallel vorticity, where J||total=J||+J||D, and J||D=(1/4∏)(∂E||/∂t) is the displacement current, which describes E|| generation (Song and Lysak, 2006). The J||total generation is a dynamo process associated with the increase of the azimuthal magnetic flux caused by the axial torque acting on FAC flux tubes. Although the magnitude of the J||D is often very small relative to J||, neglecting this term, we cannot find the mechanism of the E|| generation. When the plasma density is low J||D becomes important relative to the current. We will demonstrate how the generation of E|| and the formation of auroral arcs can redistribute perpendicular mechanical and magnetic stresses which can cause a sudden and violent tail energy release and enhance the total FAC leading to the substorm auroral poleward expansion. We will also show how the nonlinear interaction of incident and reflected Alfven wave packets in the auroral acceleration region can produce quasi-stationary non-propagating electromagnetic plasma structures, such as Alfvenic double layers. These structures will sustain the J||D and can constitute powerful high energy particle accelerators, where electromagnetic energy can be efficiently converted to the particle energy.

CHANGE OF MAGNETIC FIELD-GAS ALIGNMENT AT THE GRAVITY-DRIVEN ALFVÉNIC TRANSITION IN MOLECULAR CLOUDS: IMPLICATIONS FOR DUST POLARIZATION OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 perpendicularmore » 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.« less

A rib-specific multimodal registration algorithm for fused unfolded rib visualization using PET/CT

NASA Astrophysics Data System (ADS)

Kaftan, Jens N.; Kopaczka, Marcin; Wimmer, Andreas; Platsch, Günther; Declerck, Jérôme

2014-03-01

Respiratory motion affects the alignment of PET and CT volumes from PET/CT examinations in a non-rigid manner. This becomes particularly apparent if reviewing fine anatomical structures such as ribs when assessing bone metastases, which frequently occur in many advanced cancers. To make this routine diagnostic task more efficient, a fused unfolded rib visualization for 18F-NaF PET/CT is presented. It allows to review the whole rib cage in a single image. This advanced visualization is enabled by a novel rib-specific registration algorithm that rigidly optimizes the local alignment of each individual rib in both modalities based on a matched filter response function. More specifically, rib centerlines are automatically extracted from CT and subsequently individually aligned to the corresponding bone-specific PET rib uptake pattern. The proposed method has been validated on 20 PET/CT scans acquired at different clinical sites. It has been demonstrated that the presented rib- specific registration method significantly improves the rib alignment without having to run complex deformable registration algorithms. At the same time, it guarantees that rib lesions are not further deformed, which may otherwise affect quantitative measurements such as SUVs. Considering clinically relevant distance thresholds, the centerline portion with good alignment compared to the ground truth improved from 60:6% to 86:7% after registration while approximately 98% can be still considered as acceptably aligned.

The Effect of Professional Learning Activities on Implementation of California's Quality Professional Learning Standards in Alignment with the Local Control Funding Formula Priority 2

ERIC Educational Resources Information Center

Pinotti, Sadie

2017-01-01

The purpose of this Delphi study was to identify the professional learning activities that experts perceive are necessary for local education agencies (LEAs) to effectively implement California's Quality Professional Learning Standards (QPLS) in alignment with the Local Control Funding Formula (LCFF) Priority 2. The study also examined the degree…

Engineering of oriented carbon nanotubes in composite materials

PubMed Central

Beigmoradi, Razieh; Mohebbi-Kalhori, Davod

2018-01-01

The orientation and arrangement engineering of carbon nanotubes (CNTs) in composite structures is considered a challenging issue. In this regard, two groups of in situ and ex situ techniques have been developed. In the first, the arrangement is achieved during CNT growth, while in the latter, the CNTs are initially grown in random orientation and the arrangement is then achieved during the device integration process. As the ex situ techniques are free from growth restrictions and more flexible in terms of controlling the alignment and sorting of the CNTs, they are considered by some as the preferred technique for engineering of oriented CNTs. This review focuses on recent progress in the improvement of the orientation and alignment of CNTs in composite materials. Moreover, the advantages and disadvantages of the processes are discussed as well as their future outlook. PMID:29515955

Collinear masking effect in visual search is independent of perceptual salience.

PubMed

Jingling, Li; Lu, Yi-Hui; Cheng, Miao; Tseng, Chia-Huei

2017-07-01

Searching for a target in a salient region should be easier than looking for one in a nonsalient region. However, we previously discovered a contradictory phenomenon in which a local target in a salient structure was more difficult to find than one in the background. The salient structure was constructed of orientation singletons aligned to each other to form a collinear structure. In the present study, we undertake to determine whether such a masking effect was a result of salience competition between a global structure and the local target. In the first 3 experiments, we increased the salience value of the local target with the hope of adding to its competitive advantage and eventually eliminating the masking effect; nevertheless, the masking effect persisted. In an additional 2 experiments, we reduced salience of the global collinear structure by altering the orientation of the background bars and the masking effect still emerged. Our salience manipulations were validated by a controlled condition in which the global structure was grouped noncollinearly. In this case, local target salience increase (e.g., onset) or global distractor salience reduction (e.g., randomized flanking orientations) effectively removed the facilitation effect of the noncollinear structure. Our data suggest that salience competition is unlikely to explain the collinear masking effect, and other mechanisms such as contour integration, border formation, or the crowding effect may be prospective candidates for further investigation.

StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.

PubMed

Popov, Ya V; Galitsyna, A A; Alexeevski, A V; Karyagina, A S; Spirin, S A

2015-11-01

Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA-protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.

Mass preserving registration for lung CT

NASA Astrophysics Data System (ADS)

Gorbunova, Vladlena; Lo, Pechin; Loeve, Martine; Tiddens, Harm A.; Sporring, Jon; Nielsen, Mads; de Bruijne, Marleen

2009-02-01

In this paper, we evaluate a novel image registration method on a set of expiratory-inspiratory pairs of computed tomography (CT) lung scans. A free-form multi resolution image registration technique is used to match two scans of the same subject. To account for the differences in the lung intensities due to differences in inspiration level, we propose to adjust the intensity of lung tissue according to the local expansion or compression. An image registration method without intensity adjustment is compared to the proposed method. Both approaches are evaluated on a set of 10 pairs of expiration and inspiration CT scans of children with cystic fibrosis lung disease. The proposed method with mass preserving adjustment results in significantly better alignment of the vessel trees. Analysis of local volume change for regions with trapped air compared to normally ventilated regions revealed larger differences between these regions in the case of mass preserving image registration, indicating that mass preserving registration is better at capturing localized differences in lung deformation.

Fast and accurate reference-free alignment of subtomograms.

PubMed

Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

2013-06-01

In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

Thermostructural applications of heat pipes

NASA Technical Reports Server (NTRS)

Peeples, M. E.; Reeder, J. C.; Sontag, K. E.

1979-01-01

The feasibility of integrating heat pipes in high temperature structure to reduce local hot spot temperature was evaluated for a variety of hypersonic aerospace vehicles. From an initial list of twenty-two potential applications, the single stage to orbit wing leading edge showed the greatest promise and was selected for preliminary design of an integrated heat pipe thermostructural system. The design consisted of a Hastelloy X assembly with sodium heat pipe passages aligned normal to the wing leading edge. A d-shaped heat pipe cross section was determined to be optimum from the standpoint of structural weight.

Temporal and spatial adaptation of transient responses to local features

PubMed Central

O'Carroll, David C.; Barnett, Paul D.; Nordström, Karin

2012-01-01

Interpreting visual motion within the natural environment is a challenging task, particularly considering that natural scenes vary enormously in brightness, contrast and spatial structure. The performance of current models for the detection of self-generated optic flow depends critically on these very parameters, but despite this, animals manage to successfully navigate within a broad range of scenes. Within global scenes local areas with more salient features are common. Recent work has highlighted the influence that local, salient features have on the encoding of optic flow, but it has been difficult to quantify how local transient responses affect responses to subsequent features and thus contribute to the global neural response. To investigate this in more detail we used experimenter-designed stimuli and recorded intracellularly from motion-sensitive neurons. We limited the stimulus to a small vertically elongated strip, to investigate local and global neural responses to pairs of local “doublet” features that were designed to interact with each other in the temporal and spatial domain. We show that the passage of a high-contrast doublet feature produces a complex transient response from local motion detectors consistent with predictions of a simple computational model. In the neuron, the passage of a high-contrast feature induces a local reduction in responses to subsequent low-contrast features. However, this neural contrast gain reduction appears to be recruited only when features stretch vertically (i.e., orthogonal to the direction of motion) across at least several aligned neighboring ommatidia. Horizontal displacement of the components of elongated features abolishes the local adaptation effect. It is thus likely that features in natural scenes with vertically aligned edges, such as tree trunks, recruit the greatest amount of response suppression. This property could emphasize the local responses to such features vs. those in nearby texture within the scene. PMID:23087617

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

PubMed Central

Steele, Joe; Bastola, Dhundy

2014-01-01

Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base–base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel–Ziv techniques from data compression. PMID:23904502

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Integration of lead-free ferroelectric on HfO2/Si (100) for high performance non-volatile memory applications

PubMed Central

Kundu, Souvik; Maurya, Deepam; Clavel, Michael; Zhou, Yuan; Halder, Nripendra N.; Hudait, Mantu K.; Banerji, Pallab; Priya, Shashank

2015-01-01

We introduce a novel lead-free ferroelectric thin film (1-x)BaTiO3-xBa(Cu1/3Nb2/3)O3 (x = 0.025) (BT-BCN) integrated on to HfO2 buffered Si for non-volatile memory (NVM) applications. Piezoelectric force microscopy (PFM), x-ray diffraction, and high resolution transmission electron microscopy were employed to establish the ferroelectricity in BT-BCN thin films. PFM study reveals that the domains reversal occurs with 180° phase change by applying external voltage, demonstrating its effectiveness for NVM device applications. X-ray photoelectron microscopy was used to investigate the band alignments between atomic layer deposited HfO2 and pulsed laser deposited BT-BCN films. Programming and erasing operations were explained on the basis of band-alignments. The structure offers large memory window, low leakage current, and high and low capacitance values that were easily distinguishable even after ~106 s, indicating strong charge storage potential. This study explains a new approach towards the realization of ferroelectric based memory devices integrated on Si platform and also opens up a new possibility to embed the system within current complementary metal-oxide-semiconductor processing technology. PMID:25683062

Alignment of galaxies relative to their local environment in SDSS-DR8

NASA Astrophysics Data System (ADS)

Hirv, A.; Pelt, J.; Saar, E.; Tago, E.; Tamm, A.; Tempel, E.; Einasto, M.

2017-03-01

Aims: We study the alignment of galaxies relative to their local environment in SDSS-DR8 and, using these data, we discuss evolution scenarios for different types of galaxies. Methods: We defined a vector field of the direction of anisotropy of the local environment of galaxies. We summed the unit direction vectors of all close neighbours of a given galaxy in a particular way to estimate this field. We found the alignment angles between the spin axes of disc galaxies, or the minor axes of elliptical galaxies, and the direction of anisotropy. The distributions of cosines of these angles are compared to the random distributions to analyse the alignment of galaxies. Results: Sab galaxies show perpendicular alignment relative to the direction of anisotropy in a sparse environment, for single galaxies and galaxies of low luminosity. Most of the parallel alignment of Scd galaxies comes from dense regions, from 2...3 member groups and from galaxies with low luminosity. The perpendicular alignment of S0 galaxies does not depend strongly on environmental density nor luminosity; it is detected for single and 2...3 member group galaxies, and for main galaxies of 4...10 member groups. The perpendicular alignment of elliptical galaxies is clearly detected for single galaxies and for members of ≤10 member groups; the alignment increases with environmental density and luminosity. Conclusions: We confirm the existence of fossil tidally induced alignment of Sab galaxies at low z. The alignment of Scd galaxies can be explained via the infall of matter to filaments. S0 galaxies may have encountered relatively massive mergers along the direction of anisotropy. Major mergers along this direction can explain the alignment of elliptical galaxies. Less massive, but repeated mergers are possibly responsible for the formation of elliptical galaxies in sparser areas and for less luminous elliptical galaxies.

A new algorithm for distorted fingerprints matching based on normalized fuzzy similarity measure.

PubMed

Chen, Xinjian; Tian, Jie; Yang, Xin

2006-03-01

Coping with nonlinear distortions in fingerprint matching is a challenging task. This paper proposes a novel algorithm, normalized fuzzy similarity measure (NFSM), to deal with the nonlinear distortions. The proposed algorithm has two main steps. First, the template and input fingerprints were aligned. In this process, the local topological structure matching was introduced to improve the robustness of global alignment. Second, the method NFSM was introduced to compute the similarity between the template and input fingerprints. The proposed algorithm was evaluated on fingerprints databases of FVC2004. Experimental results confirm that NFSM is a reliable and effective algorithm for fingerprint matching with nonliner distortions. The algorithm gives considerably higher matching scores compared to conventional matching algorithms for the deformed fingerprints.

Measuring the distance between multiple sequence alignments.

PubMed

Blackburne, Benjamin P; Whelan, Simon

2012-02-15

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

Self-reported eating rate aligns with laboratory measured eating rate but not with free-living meals.

PubMed

Petty, Amanda J; Melanson, Kathleen J; Greene, Geoffrey W

2013-04-01

Methodological differences may be responsible for variable results from eating rate (ER) studies. It is unknown whether self-reported, lab-measured, and free-living ER's align. This study was the first to explore relationships among self-reported, laboratory-measured and free-living ER's. We investigated this relationship in 60 randomly selected male and female college students who were stratified by self-reported eating rate (SRER) (Slow, Medium, and Fast) from 1110 on-line survey respondents. Test day; subjects ate a prescribed breakfast (∼400kcal) at home, recording meal duration (MD); 4h later they individually ate an ad libitum laboratory pasta lunch at their own (natural) pace; remainder of the day they recorded free-living intake and MD. As expected the three self-reported ER categories aligned with lab ER (Fast=83.9±5.5, Medium=63.1±5.2, Slow=53.0±5.4kcals/min). In all ER categories at all meals, men ate faster than women (Men=80.6±30.7kcals/min: Women=52.0±21.6kcals/min). A difference in lab measured ER by SRER F=(2, 58)=7.677, post hoc Tukey analysis found fast differed from medium and slow. The three free-living meal ER's did not align with self-report categories. Findings suggest various methods of measuring ER may yield differing results, at least in this population, but results support the use of SRER as a valid measure. Copyright © 2012 Elsevier Ltd. All rights reserved.

Process solutions for reducing PR residue over non-planar wafer

NASA Astrophysics Data System (ADS)

Lin, C. H.; Huang, C. H.; Yang, Elvis; Yang, T. H.; Chen, K. C.; Lu, Chih-Yuan

2011-03-01

SAS (Self-Aligned Source) process has been widely adopted on manufacturing NOR Flash devices. To form the SAS structure, the compromise between small space patterning and sufficiently removing photo resist residue in topographical substrate has been a critical challenge as the device scaling down. In this study, photo simulation, layout optimization, resist processing and tri-layer materials were evaluated to form defect-free and highly extendible SAS structure for NOR Flash devices. Photo simulation suggested more coherent light source allowed the incident light to reach the trench bottom that facilitates the removal of photo resist. Mask bias also benefited the process latitude extension for residue-free SAS printing. In the photo resist processing, both lowering the SB (Soft Bake) and raising PEB (Post-Exposure Bake) temperature of photo resist were helpful to broaden the process window but the final pattern profile was not good enough. Thermal flow for pos-exposure pattern shrinkage achieved small CD (Critical Dimension) patterning with residue-free, however the materials loading effect is another issue to be addressed at memory array boundary. Tri-layer scheme demonstrated good results in terms of free from residue, better substrate reflectivity control, enabling smaller space printing to loosen overlay specification and minimizing the poly gate clipping defect. It was finally proposed to combine with etch effort to from the SAS structure. Besides it is also promising to extend to even smaller technology nodes.

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

PubMed

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

2017-08-25

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

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

PubMed

Adhikari, Badri; Hou, Jie; Cheng, Jianlin

2018-03-01

In this study, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution, and machine learning on contact prediction. The first method (MULTICOM-NOVEL) uses only traditional features (sequence profile, secondary structure, and solvent accessibility) with deep learning to predict contacts and serves as a baseline. The second method (MULTICOM-CONSTRUCT) uses our new alignment algorithm to generate deep multiple sequence alignment to derive coevolution-based features, which are integrated by a neural network method to predict contacts. The third method (MULTICOM-CLUSTER) is a consensus combination of the predictions of the first two methods. We evaluated our methods on 94 CASP12 domains. On a subset of 38 free-modeling domains, our methods achieved an average precision of up to 41.7% for top L/5 long-range contact predictions. The comparison of the three methods shows that the quality and effective depth of multiple sequence alignments, coevolution-based features, and machine learning integration of coevolution-based features and traditional features drive the quality of predicted protein contacts. On the full CASP12 dataset, the coevolution-based features alone can improve the average precision from 28.4% to 41.6%, and the machine learning integration of all the features further raises the precision to 56.3%, when top L/5 predicted long-range contacts are evaluated. And the correlation between the precision of contact prediction and the logarithm of the number of effective sequences in alignments is 0.66. © 2017 Wiley Periodicals, Inc.

General Relativistic Radiative Transfer and General Relativistic MHD Simulations of Accretion and Outflows of Black Holes

NASA Technical Reports Server (NTRS)

Fuerst, Steven V.; Mizuno, Yosuke; Nishikawa, Ken-Ichi; Wu, Kinwah

2007-01-01

We have calculated the emission from relativistic flows in black hole systems using a fully general relativistic radiative transfer, with flow structures obtained by general relativistic magnetohydrodynamic simulations. We consider thermal free-free emission and thermal synchrotron emission. Bright filament-like features are found protruding (visually) from the accretion disk surface, which are enhancements of synchrotron emission when the magnetic field is roughly aligned with the line-of-sight in the co-moving frame. The features move back and forth as the accretion flow evolves, but their visibility and morphology are robust. We propose that variations and location drifts of the features are responsible for certain X-ray quasi-periodic oscillations (QPOs) observed in black-hole X-ray binaries.

General Relativistic Radiative Transfer and GeneralRelativistic MHD Simulations of Accretion and Outflows of Black Holes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fuerst, Steven V.; /KIPAC, Menlo Park; Mizuno, Yosuke

2007-01-05

We calculate the emission from relativistic flows in black hole systems using a fully general relativistic radiative transfer formulation, with flow structures obtained by general relativistic magneto-hydrodynamic simulations. We consider thermal free-free emission and thermal synchrotron emission. Bright filament-like features protrude (visually) from the accretion disk surface, which are enhancements of synchrotron emission where the magnetic field roughly aligns with the line-of-sight in the co-moving frame. The features move back and forth as the accretion flow evolves, but their visibility and morphology are robust. We propose that variations and drifts of the features produce certain X-ray quasi-periodic oscillations (QPOs) observedmore » in black-hole X-ray binaries.« less

Electric property measurement of free-standing SrTiO3 nanoparticles assembled by dielectrophoresis

NASA Astrophysics Data System (ADS)

Budiman, Faisal; Kotooka, Takumi; Horibe, Yoichi; Eguchi, Masanori; Tanaka, Hirofumi

2018-06-01

Free-standing strontium titanate (SrTiO3/STO) nanoparticles (NPs) were synthesized by the sol–gel method. X-ray diffractometry revealed that the required minimum annealing temperature to synthesize pure and highly crystalline STO NPs was 500 °C. Moreover, morphological observation by field emission scanning electron microscopy showed that the STO NPs have a spherical structure and their size depended on annealing condition. Electrical properties were measured using a low-temperature probing system. Here, an electrode was fabricated by electron beam lithography and the synthesized STO NPs were aligned at the electrodes by dielectrophoresis. The conductance of a sample was proportional to temperature. Two conduction mechanisms originating from hopping and tunneling appeared in the Arrhenius plot.

Gas-tungsten arc welding of aluminum alloys

DOEpatents

Frye, Lowell D.

1984-01-01

A gas-tungsten arc welding method for joining together structures formed of aluminum alloy with these structures disposed contiguously to a heat-damagable substrate of a metal dissimilar to the aluminum alloy. The method of the present invention is practiced by diamond machining the fay surfaces of the aluminum alloy structures to provide a mirror finish thereon having a surface roughness in the order of about one microinch. The fay surfaces are aligned and heated sufficiently by the tungsten electrode to fuse the aluminum alloy contiguous to the fay surfaces to effect the weld joint. The heat input used to provide an oxide-free weld is significantly less than that required if the fay surfaces were prepared by using conventional chemical and mechanical practices.

LCS-TA to identify similar fragments in RNA 3D structures.

PubMed

Wiedemann, Jakub; Zok, Tomasz; Milostan, Maciej; Szachniuk, Marta

2017-10-23

In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective. Herein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds' rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ . The presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures.

Computational Aerothermodynamic Simulation Issues on Unstructured Grids

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.; White, Jeffery A.

2004-01-01

The synthesis of physical models for gas chemistry and turbulence from the structured grid codes LAURA and VULCAN into the unstructured grid code FUN3D is described. A directionally Symmetric, Total Variation Diminishing (STVD) algorithm and an entropy fix (eigenvalue limiter) keyed to local cell Reynolds number are introduced to improve solution quality for hypersonic aeroheating applications. A simple grid-adaptation procedure is incorporated within the flow solver. Simulations of flow over an ellipsoid (perfect gas, inviscid), Shuttle Orbiter (viscous, chemical nonequilibrium) and comparisons to the structured grid solvers LAURA (cylinder, Shuttle Orbiter) and VULCAN (flat plate) are presented to show current capabilities. The quality of heating in 3D stagnation regions is very sensitive to algorithm options in general, high aspect ratio tetrahedral elements complicate the simulation of high Reynolds number, viscous flow as compared to locally structured meshes aligned with the flow.

Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

PubMed Central

Sheng, Gang; Gogakos, Tasos; Wang, Jiuyu; Zhao, Hongtu; Serganov, Artem; Juranek, Stefan

2017-01-01

Abstract We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6’U7’ and 6’A7’ on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. PMID:28911094

Microstructural Aspects of Localized Corrosion Behavior of Mg Alloys

NASA Astrophysics Data System (ADS)

Chu, Peng-Wei

Combining high specific strength and unique electrochemical properties, magnesium (Mg) alloys are promising lightweight materials for various applications from automotive, consumer electronics, biomedical body implant, to battery electrodes. Engineering solutions such as coatings have enabled the use of Mg alloys, despite their intrinsic low corrosion resistance. Consequently, the fundamental mechanisms responsible for the unique localized corrosion behavior of bare Mg alloys, the associated abnormal hydrogen evolution response, and the relationships between corrosion behavior and alloy microstructure are still unsolved. This thesis aims to uncover the specificities of Mg corrosion and the roles of alloy chemistry and microstructure. To this end, multiscale site-specific microstructure characterization techniques, including in situ optical microscopy, scanning electron microscopy with focused ion beam milling, and transmission electron microscopy, combined with electrochemical analysis and hydrogen evolution rate monitoring, were performed on pure Mg and selected Mg alloys under free corrosion and anodic polarization, revealing key new information on the propagation mode of localized corrosion and the role of alloy microstructures, thereby confirming or disproving the validity of previously proposed corrosion models. Uniform surface corrosion film on Mg alloys immersed in NaCl solution consisted a bi-layered structure, with a porous Mg(OH)2 outer layer on top of a MgO inner layer. Presence of fine scale precipitates in Mg alloys interacted with the corrosion reaction front, reducing the corrosion rate and surface corrosion film thickness. Protruding hemispherical dome-like corrosion products, accompanied by growing hydrogen bubbles, formed on top of the impurity particles in Mg alloys by deposition of Mg(OH)2 via a microgalvanic effect. Localized corrosion on Mg alloys under both free immersion and anodic polarization was found to be governed by a common mechanism, with the corrosion front propagating laterally a few mum inside the alloy and underneath the surface corrosion film, with finger-like features aligned with (0001) Mg basal planes at the localized corrosion/alloy interface. Rising streams of hydrogen bubbles were found to follow the anodic dissolution of Mg and formation of Mg(OH)2 corrosion products at the propagating localized corrosion fronts. Alloying elements segregation to the grain boundaries showed the ability to stop localized corrosion propagation momentarily. By revealing the microstructure of corrosion features on Mg alloys, a descriptive model was proposed. Relationships between the corrosion behavior and alloy microstructures were also identified. This microscopic information can serve as a guideline for future development of Mg alloys by tailoring the microstructure to achieve proper corrosion responses for applications under different environments.

PASS2: an automated database of protein alignments organised as structural superfamilies.

PubMed

Bhaduri, Anirban; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2004-04-02

The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been improved for simpler browsing of the database. The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. Availability of reliable sequence alignments of distantly related proteins despite poor sequence identity and single-member superfamilies permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. PASS2 is accessible at http://www.ncbs.res.in/~faculty/mini/campass/pass2.html

Tunable Band Alignment with Unperturbed Carrier Mobility of On-Surface Synthesized Organic Semiconducting Wires

PubMed Central

2016-01-01

The tunable properties of molecular materials place them among the favorites for a variety of future generation devices. In addition, to maintain the current trend of miniaturization of those devices, a departure from the present top-down production methods may soon be required and self-assembly appears among the most promising alternatives. On-surface synthesis unites the promises of molecular materials and of self-assembly, with the sturdiness of covalently bonded structures: an ideal scenario for future applications. Following this idea, we report the synthesis of functional extended nanowires by self-assembly. In particular, the products correspond to one-dimensional organic semiconductors. The uniaxial alignment provided by our substrate templates allows us to access with exquisite detail their electronic properties, including the full valence band dispersion, by combining local probes with spatial averaging techniques. We show how, by selectively doping the molecular precursors, the product’s energy level alignment can be tuned without compromising the charge carrier’s mobility. PMID:26841052

Fabrication of Vertically Aligned Carbon Nanotube or Zinc Oxide Nanorod Arrays for Optical Diffraction Gratings.

PubMed

Kim, Jeong; Kim, Sun Il; Cho, Seong-Ho; Hwang, Sungwoo; Lee, Young Hee; Hur, Jaehyun

2015-11-01

We report on new fabrication methods for a transparent, hierarchical, and patterned electrode comprised of either carbon nanotubes or zinc oxide nanorods. Vertically aligned carbon nanotubes or zinc oxide nanorod arrays were fabricated by either chemical vapor deposition or hydrothermal growth, in combination with photolithography. A transparent conductive graphene layer or zinc oxide seed layer was employed as the transparent electrode. On the patterned surface defined using photoresist, the vertically grown carbon nanotubes or zinc oxides could produce a concentrated electric field under applied DC voltage. This periodic electric field was used to align liquid crystal molecules in localized areas within the optical cell, effectively modulating the refractive index. Depending on the material and morphology of these patterned electrodes, the diffraction efficiency presented different behavior. From this study, we established the relationship between the hierarchical structure of the different electrodes and their efficiency for modulating the refractive index. We believe that this study will pave a new path for future optoelectronic applications.

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Overcoming Sequence Misalignments with Weighted Structural Superposition

PubMed Central

Khazanov, Nickolay A.; Damm-Ganamet, Kelly L.; Quang, Daniel X.; Carlson, Heather A.

2012-01-01

An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian-weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD’s robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, SSM, CE, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics-scale analysis. HwRMSD can align homologs with low sequence identity and large conformational differences, cases where both sequence-based and structural-based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence-alignment method, substitution matrix, and gap parameters for each unique pair of homologs. PMID:22733542

Method and apparatus for ion mobility spectrometry with alignment of dipole direction (IMS-ADD)

DOEpatents

Shvartsburg, Alexandre A [Richland, WA; Tang, Keqi [Richland, WA; Smith, Richard D [Richland, WA

2007-01-30

Techniques and instrumentation are described for analyses of substances, including complex samples/mixtures that require separation prior to characterization of individual components. A method is disclosed for separation of ion mixtures and identification of ions, including protein and other macromolecular ions and their different structural isomers. Analyte ions are not free to rotate during the separation, but are substantially oriented with respect to the drift direction. Alignment is achieved by applying, at a particular angle to the drift field, a much stronger alternating electric field that "locks" the ion dipoles with moments exceeding a certain value. That value depends on the buffer gas composition, pressure, and temperature, but may be as low as .about.3 Debye under certain conditions. The presently disclosed method measures the direction-specific cross-sections that provide the structural information complementing that obtained from known methods, and, when coupled to those methods, increases the total peak capacity and specificity of gas-phase separations. Simultaneous 2-D separations by direction-specific cross sections along and orthogonally to the ion dipole direction are also possible.

Extraordinary epitaxial alignment of graphene islands on Au(111)

NASA Astrophysics Data System (ADS)

Wofford, Joseph M.; Starodub, Elena; Walter, Andrew L.; Nie, Shu; Bostwick, Aaron; Bartelt, Norman C.; Thürmer, Konrad; Rotenberg, Eli; McCarty, Kevin F.; Dubon, Oscar D.

2012-05-01

Pristine, single-crystalline graphene displays a unique collection of remarkable electronic properties that arise from its two-dimensional, honeycomb structure. Using in situ low-energy electron microscopy, we show that when deposited on the (111) surface of Au carbon forms such a structure. The resulting monolayer, epitaxial film is formed by the coalescence of dendritic graphene islands that nucleate at a high density. Over 95% of these islands can be identically aligned with respect to each other and to the Au substrate. Remarkably, the dominant island orientation is not the better lattice-matched 30° rotated orientation but instead one in which the graphene [01] and Au [011] in-plane directions are parallel. The epitaxial graphene film is only weakly coupled to the Au surface, which maintains its reconstruction under the slightly p-type doped graphene. The linear electronic dispersion characteristic of free-standing graphene is retained regardless of orientation. That a weakly interacting, non-lattice matched substrate is able to lock graphene into a particular orientation is surprising. This ability, however, makes Au(111) a promising substrate for the growth of single crystalline graphene films.

Magnetically aligned H I fibers and the rolling hough transform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clark, S. E.; Putman, M. E.; Peek, J. E. G.

2014-07-01

We present observations of a new group of structures in the diffuse Galactic interstellar medium (ISM): slender, linear H I features we dub 'fibers' that extend for many degrees at high Galactic latitude. To characterize and measure the extent and strength of these fibers, we present the Rolling Hough Transform, a new machine vision method for parameterizing the coherent linearity of structures in the image plane. With this powerful new tool we show that the fibers are oriented along the interstellar magnetic field as probed by starlight polarization. We find that these low column density (N{sub H} {sub I}≃5×10{sup 18}more » cm{sup –2}) fiber features are most likely a component of the local cavity wall, about 100 pc away. The H I data we use to demonstrate this alignment at high latitude are from the Galactic Arecibo L-Band Feed Array H I (GALFA-H I) Survey and the Parkes Galactic All Sky Survey. We find better alignment in the higher resolution GALFA-H I data, where the fibers are more visually evident. This trend continues in our investigation of magnetically aligned linear features in the Riegel-Crutcher H I cold cloud, detected in the Southern Galactic Plane Survey. We propose an application of the RHT for estimating the field strength in such a cloud, based on the Chandrasekhar-Fermi method. We conclude that data-driven, quantitative studies of ISM morphology can be very powerful predictors of underlying physical quantities.« less

Four-dimensional Printing of Liquid Crystal Elastomers.

PubMed

Ambulo, Cedric P; Burroughs, Julia J; Boothby, Jennifer M; Kim, Hyun; Shankar, M Ravi; Ware, Taylor H

2017-10-25

Three-dimensional structures capable of reversible changes in shape, i.e., four-dimensional-printed structures, may enable new generations of soft robotics, implantable medical devices, and consumer products. Here, thermally responsive liquid crystal elastomers (LCEs) are direct-write printed into 3D structures with a controlled molecular order. Molecular order is locally programmed by controlling the print path used to build the 3D object, and this order controls the stimulus response. Each aligned LCE filament undergoes 40% reversible contraction along the print direction on heating. By printing objects with controlled geometry and stimulus response, magnified shape transformations, for example, volumetric contractions or rapid, repetitive snap-through transitions, are realized.

Sensor Network Localization by Eigenvector Synchronization Over the Euclidean Group

PubMed Central

CUCURINGU, MIHAI; LIPMAN, YARON; SINGER, AMIT

2013-01-01

We present a new approach to localization of sensors from noisy measurements of a subset of their Euclidean distances. Our algorithm starts by finding, embedding, and aligning uniquely realizable subsets of neighboring sensors called patches. In the noise-free case, each patch agrees with its global positioning up to an unknown rigid motion of translation, rotation, and possibly reflection. The reflections and rotations are estimated using the recently developed eigenvector synchronization algorithm, while the translations are estimated by solving an overdetermined linear system. The algorithm is scalable as the number of nodes increases and can be implemented in a distributed fashion. Extensive numerical experiments show that it compares favorably to other existing algorithms in terms of robustness to noise, sparse connectivity, and running time. While our approach is applicable to higher dimensions, in the current article, we focus on the two-dimensional case. PMID:23946700

Metallic Glass Wire Based Localization of Kinesin/Microtubule Bio-molecular Motility System

NASA Astrophysics Data System (ADS)

Kim, K.; Sikora, A.; Yaginuma, S.; Nakayama, K. S.; Nakazawa, H.; Umetsu, M.; Hwang, W.; Teizer, W.

2014-03-01

We report electrophoretic accumulation of microtubules along metallic glass (Pd42.5Cu30Ni7.5P20) wires free-standing in solution. Microtubules are dynamic cytoskeletal filaments. Kinesin is a cytoskeletal motor protein. Functions of these bio-molecules are central to various dynamic cellular processes. Functional artificial organization of bio-molecules is a prerequisite for transferring their native functions into device applications. Fluorescence microscopy at the individual-microtubule level reveals microtubules aligning along the wire axis during the electrophoretic migration. Casein-treated electrodes are effective for releasing trapped microtubules upon removal of the external field. Furthermore, we demonstrate gliding motion of microtubules on kinesin-treated metallic glass wires. The reversible manner in the local adsorption of microtubules, the flexibility of wire electrodes, and the compatibility between the wire electrode and the bio-molecules are beneficial for spatio-temporal manipulation of the motility machinery in 3 dimensions.

Nuclear component horizontal seismic restraint

DOEpatents

Snyder, Glenn J.

1988-01-01

A nuclear component horizontal seismic restraint. Small gaps limit horizontal displacement of components during a seismic occurrence and therefore reduce dynamic loadings on the free lower end. The reactor vessel and reactor guard vessel use thicker section roll-forged rings welded between the vessel straight shell sections and the bottom hemispherical head sections. The inside of the reactor guard vessel ring forging contains local vertical dovetail slots and upper ledge pockets to mount and retain field fitted and installed blocks. As an option, the horizontal displacement of the reactor vessel core support cone can be limited by including shop fitted/installed local blocks in opposing alignment with the reactor vessel forged ring. Beams embedded in the wall of the reactor building protrude into apertures in the thermal insulation shell adjacent the reactor guard vessel ring and have motion limit blocks attached thereto to provide to a predetermined clearance between the blocks and reactor guard vessel ring.

The relative phases of basal ganglia activities dynamically shape effective connectivity in Parkinson's disease.

PubMed

Cagnan, Hayriye; Duff, Eugene Paul; Brown, Peter

2015-06-01

Optimal phase alignment between oscillatory neural circuits is hypothesized to optimize information flow and enhance system performance. This theory is known as communication-through-coherence. The basal ganglia motor circuit exhibits exaggerated oscillatory and coherent activity patterns in Parkinson's disease. Such activity patterns are linked to compromised motor system performance as evinced by bradykinesia, rigidity and tremor, suggesting that network function might actually deteriorate once a certain level of net synchrony is exceeded in the motor circuit. Here, we characterize the processes underscoring excessive synchronization and its termination. To this end, we analysed local field potential recordings from the subthalamic nucleus and globus pallidus of five patients with Parkinson's disease (four male and one female, aged 37-64 years). We observed that certain phase alignments between subthalamic nucleus and globus pallidus amplified local neural synchrony in the beta frequency band while others either suppressed it or did not induce any significant change with respect to surrogates. The increase in local beta synchrony directly correlated with how long the two nuclei locked to beta-amplifying phase alignments. Crucially, administration of the dopamine prodrug, levodopa, reduced the frequency and duration of periods during which subthalamic and pallidal populations were phase-locked to beta-amplifying alignments. Conversely ON dopamine, the total duration over which subthalamic and pallidal populations were aligned to phases that left beta-amplitude unchanged with respect to surrogates increased. Thus dopaminergic input shifted circuit dynamics from persistent periods of locking to amplifying phase alignments, associated with compromised motoric function, to more dynamic phase alignment and improved motoric function. This effect of dopamine on local circuit resonance suggests means by which novel electrical interventions might prevent resonance-related pathological circuit interactions. © The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain.

Optical and electrical stability of viral-templated copper sulfide (Cu{sub 1.8}S) films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shahriar Zaman, Mohammed; Bernard Grajeda, Gabriel; Haberer, Elaine D., E-mail: haberer@ucr.edu

The optical and electrical stabilities of viral-templated non-stoichiometric copper sulfide, digenite (Cu{sub 1.8}S) films were investigated. The films were composed of large agglomerates of randomly aligned Cu{sub 1.8}S-coated M13 filamentous phage. Free carrier optical absorption associated with localized surface plasmon resonance (LSPR) was observed in the near infrared spectral region, and the films were electrically active, displaying a linear current-voltage relationship. Under ambient conditions, the magnitude of the LSPR absorption increased, following a power law relationship with time, and the electrical resistance of viral-templated films decreased significantly. In contrast, the resistance of films stored under low oxygen, low humidity conditionsmore » experienced a smaller reduction in electrical resistance. Changes in optical and electrical film properties under ambient conditions were associated with an increase in free carrier concentration within the copper chalcogenide material due to oxygen exposure. X-ray photoelectron spectroscopy was used to relate this increase in free carrier concentration to compositional changes on the viral-templated material surface.« less

Current progress and technical challenges of flexible liquid crystal displays

NASA Astrophysics Data System (ADS)

Fujikake, Hideo; Sato, Hiroto

2009-02-01

We focused on several technical approaches to flexible liquid crystal (LC) display in this report. We have been developing flexible displays using plastic film substrates based on polymer-dispersed LC technology with molecular alignment control. In our representative devices, molecular-aligned polymer walls keep plastic-substrate gap constant without LC alignment disorder, and aligned polymer networks create monostable switching of fast-response ferroelectric LC (FLC) for grayscale capability. In the fabrication process, a high-viscosity FLC/monomer solution was printed, sandwiched and pressed between plastic substrates. Then the polymer walls and networks were sequentially formed based on photo-polymerization-induced phase separation in the nematic phase by two exposure processes of patterned and uniform ultraviolet light. The two flexible backlight films of direct illumination and light-guide methods using small three-primary-color light-emitting diodes were fabricated to obtain high-visibility display images. The fabricated flexible FLC panels were driven by external transistor arrays, internal organic thin film transistor (TFT) arrays, and poly-Si TFT arrays. We achieved full-color moving-image displays using the flexible FLC panel and the flexible backlight film based on field-sequential-color driving technique. Otherwise, for backlight-free flexible LC displays, flexible reflective devices of twisted guest-host nematic LC and cholesteric LC were discussed with molecular-aligned polymer walls. Singlesubstrate device structure and fabrication method using self-standing polymer-stabilized nematic LC film and polymer ceiling layer were also proposed for obtaining LC devices with excellent flexibility.

Towards a Realistic Pulsar Magnetosphere

NASA Technical Reports Server (NTRS)

Kalapotharakos, Constantinos; Kazanas, Demosthenes; Harding, Alice; Contopoulos, Ioannis

2012-01-01

We present the magnetic and electric field structures as well as the currents ami charge densities of pulsar magnetospberes which do not obey the ideal condition, E(raised dot) B = O. Since the acceleration of particles and the production of radiation requires the presence of an electric field component parallel to the magnetic field, E(sub ll) the structure of non-Ideal pulsar magnetospheres is intimately related to the production of pulsar radiation. Therefore, knowledge of the structure of non-Ideal pulsar maglletospheres is important because their comparison (including models for t he production of radiation) with observations will delineate the physics and the parameters underlying the pulsar radiation problem. We implement a variety of prescriptions that support nonzero values for E(sub ll) and explore their effects on the structure of the resulting magnetospheres. We produce families of solutions that span the entire range between the vacuum and the (ideal) Force-Free Electrodynamic solutions. We also compute the amount of dissipation as a fraction of the Poynting flux for pulsars of different angles between the rotation and magnetic axes and conclude that tltis is at most 20-40% (depending on t he non-ideal prescription) in the aligned rotator and 10% in the perpendicular one. We present also the limiting solutions with the property J = pc and discuss their possible implicatioll on the determination of the "on/ off" states of the intermittent pulsars. Finally, we find that solutions with values of J greater than those needed to null E(sub ll) locally produce oscillations, potentially observable in the data.

DockoMatic 2.0: high throughput inverse virtual screening and homology modeling.

PubMed

Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T; McDougal, Owen M; Andersen, Timothy L

2013-08-26

DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly graphical user interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to (1) conduct high throughput inverse virtual screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELER programs and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education.

Ionospheric electron heating, optical emissions, and striations induced by powerful HF radio waves at high latitudes: Aspect angle dependence

NASA Astrophysics Data System (ADS)

Rietveld, M. T.; Kosch, M. J.; Blagoveshchenskaya, N. F.; Kornienko, V. A.; Leyser, T. B.; Yeoman, T. K.

2003-04-01

In recent years, large electron temperature increases of 300% (3000 K above background) caused by powerful HF-radio wave injection have been observed during nighttime using the EISCAT incoherent scatter radar near Tromsø in northern Norway. In a case study we examine the spatial structure of the modified region. The electron heating is accompanied by ion heating of about 100 degrees and magnetic field-aligned measurements show ion outflows increasing with height up to 300 m s-1 at 582 km. The electron density decreases by up to 20%. When the radar antenna was scanned between three elevations from near field-aligned to vertical, the strongest heating effects were always obtained in the field-aligned position. When the HF-pump beam was scanned between the same three positions, the heating was still almost always strongest in the field-aligned direction. Simultaneous images of the 630 nm O(1D) line in the radio-induced aurora showed that the enhancement caused by the HF radio waves also remained localized near the field-aligned position. Coherent HF radar backscatter also appeared strongest when the pump beam was pointed field-aligned. These results are similar to some Langmuir turbulence phenomena which also show a strong preference for excitation by HF rays launched in the field-aligned direction. The correlation of the position of largest temperature enhancement with the position of the radio-induced aurora suggests that a common mechanism, upper-hybrid wave turbulence, is responsible for both effects. Why the strongest heating effects occur for HF rays directed along the magnetic field is still unclear, but self-focusing on field-aligned striations is a candidate mechanism, and possibly ionospheric tilts may be important.

FEAST: sensitive local alignment with multiple rates of evolution.

PubMed

Hudek, Alexander K; Brown, Daniel G

2011-01-01

We present a pairwise local aligner, FEAST, which uses two new techniques: a sensitive extension algorithm for identifying homologous subsequences, and a descriptive probabilistic alignment model. We also present a new procedure for training alignment parameters and apply it to the human and mouse genomes, producing a better parameter set for these sequences. Our extension algorithm identifies homologous subsequences by considering all evolutionary histories. It has higher maximum sensitivity than Viterbi extensions, and better balances specificity. We model alignments with several submodels, each with unique statistical properties, describing strongly similar and weakly similar regions of homologous DNA. Training parameters using two submodels produces superior alignments, even when we align with only the parameters from the weaker submodel. Our extension algorithm combined with our new parameter set achieves sensitivity 0.59 on synthetic tests. In contrast, LASTZ with default settings achieves sensitivity 0.35 with the same false positive rate. Using the weak submodel as parameters for LASTZ increases its sensitivity to 0.59 with high error. FEAST is available at http://monod.uwaterloo.ca/feast/.

Keratinocytes propagated in serum-free, feeder-free culture conditions fail to form stratified epidermis in a reconstituted skin model.

PubMed

Lamb, Rebecca; Ambler, Carrie A

2013-01-01

Primary human epidermal stem cells isolated from skin tissues and subsequently expanded in tissue culture are used for human therapeutic use to reconstitute skin on patients and to generate artificial skin in culture for academic and commercial research. Classically, epidermal cells, known as keratinocytes, required fibroblast feeder support and serum-containing media for serial propagation. In alignment with global efforts to remove potential animal contaminants, many serum-free, feeder-free culture methods have been developed that support derivation and growth of these cells in 2-dimensional culture. Here we show that keratinocytes grown continually in serum-free and feeder-free conditions were unable to form into a stratified, mature epidermis in a skin equivalent model. This is not due to loss of cell potential as keratinocytes propagated in serum-free, feeder-free conditions retain their ability to form stratified epidermis when re-introduced to classic serum-containing media. Extracellular calcium supplementation failed to improve epidermis development. In contrast, the addition of serum to commercial, growth media developed for serum-free expansion of keratinocytes facilitated 3-dimensional stratification in our skin equivalent model. Moreover, the addition of heat-inactivated serum improved the epidermis structure and thickness, suggesting that serum contains factors that both aid and inhibit stratification.

Keratinocytes Propagated in Serum-Free, Feeder-Free Culture Conditions Fail to Form Stratified Epidermis in a Reconstituted Skin Model

PubMed Central

Lamb, Rebecca; Ambler, Carrie A.

2013-01-01

Primary human epidermal stem cells isolated from skin tissues and subsequently expanded in tissue culture are used for human therapeutic use to reconstitute skin on patients and to generate artificial skin in culture for academic and commercial research. Classically, epidermal cells, known as keratinocytes, required fibroblast feeder support and serum-containing media for serial propagation. In alignment with global efforts to remove potential animal contaminants, many serum-free, feeder-free culture methods have been developed that support derivation and growth of these cells in 2-dimensional culture. Here we show that keratinocytes grown continually in serum-free and feeder-free conditions were unable to form into a stratified, mature epidermis in a skin equivalent model. This is not due to loss of cell potential as keratinocytes propagated in serum-free, feeder-free conditions retain their ability to form stratified epidermis when re-introduced to classic serum-containing media. Extracellular calcium supplementation failed to improve epidermis development. In contrast, the addition of serum to commercial, growth media developed for serum-free expansion of keratinocytes facilitated 3-dimensional stratification in our skin equivalent model. Moreover, the addition of heat-inactivated serum improved the epidermis structure and thickness, suggesting that serum contains factors that both aid and inhibit stratification. PMID:23326335

Magnetic field studies of the solar wind interaction with venus from the galileo flyby.

PubMed

Kivelson, M G; Kennel, C F; McPherron, R L; Russell, C T; Southwood, D J; Walker, R J; Hammond, C M; Khurana, K K; Strangeway, R J; Coleman, P J

1991-09-27

During the 10 February 1990 flyby of Venus, the Galileo spacecraft skimmed the downstream flank of the planetary bow shock. This provided an opportunity to examine both the global and the local structure of the shock in an interval during which conditions in the solar wind plasma were quite steady. The data show that the cross section of the shock in planes transverse to the flow is smaller in directions aligned with the projection of the interplanetary magnetic field than in directions not so aligned. Ultralow-frequency waves were present in the unshocked solar wind, and their amplitude peaked when the spacecraft was downstream of the foreshock. At large distances down the tail, the Mach number of the flow normal to the shock is low, thus providing the opportunity to study repeated crossings of the collisionless shock in an interesting parameter regime. Some of the shock crossings reveal structure that comes close to the theoretically predicted form of intermediate shocks, whose existence in collisionless plasmas has not been confirmed.

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

PubMed

Linderälv, Christopher; Lindman, Anders; Erhart, Paul

2018-01-04

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

Magnetic field studies of the solar wind interaction with Venus from the Galileo flyby

NASA Technical Reports Server (NTRS)

Kivelson, M. G.; Kennel, C. F.; Mcpherron, R. L.; Russell, C. T.; Southwood, D. J.; Walker, R. J.; Hammond, C. M.; Khurana, K. K.; Strangeway, R. J.; Coleman, P. J.

1991-01-01

During the February 10, 1990 flyby of Venus, the Galileo spacecraft skimmed the downnstream flank of the planetary bow shock. This provided an opportunity to examine both the global and the local structure of the shock in an interval during which conditions in the solar wind plasma were quite steady. The data show that the cross section of the shock in planes transverse to the flow is smaller in directions aligned with the projection of the interplanetary magnetic field than in directions not so aligned. Ultralow-frequency waves were present in the unshocked solar wind, and their amplitude peaked when the spacecraft was downstream of the foreshock. At large distances down the tail, the Mach number of the flow normal to the shock is low, thus providing the opportunity to study repeated crossings of the collisionless shock in an interesting parameter regime. Some of the shock crossings reveal structure that comes close to the theoretically predicted form of intermediate shocks, whose existence in collisionless plasmas has not been confirmed.

Transformation and Alignment in Similarity

ERIC Educational Resources Information Center

Hodgetts, Carl J.; Hahn, Ulrike; Chater, Nick

2009-01-01

This paper contrasts two structural accounts of psychological similarity: structural alignment (SA) and Representational Distortion (RD). SA proposes that similarity is determined by how readily the structures of two objects can be brought into alignment; RD measures similarity by the complexity of the transformation that "distorts" one…

Teflon/SiO₂ Bilayer Passivation for Improving the Electrical Reliability of Oxide TFTs Fabricated Using a New Two-Photomask Self-Alignment Process.

PubMed

Fan, Ching-Lin; Shang, Ming-Chi; Li, Bo-Jyun; Lin, Yu-Zuo; Wang, Shea-Jue; Lee, Win-Der; Hung, Bohr-Ran

2015-04-13

This study proposes a two-photomask process for fabricating amorphous indium-gallium-zinc oxide (a-IGZO) thin-film transistors (TFTs) that exhibit a self-aligned structure. The fabricated TFTs, which lack etching-stop (ES) layers, have undamaged a-IGZO active layers that facilitate superior performance. In addition, we demonstrate a bilayer passivation method that uses a polytetrafluoroethylene (Teflon) and SiO₂ combination layer for improving the electrical reliability of the fabricated TFTs. Teflon was deposited as a buffer layer through thermal evaporation. The Teflon layer exhibited favorable compatibility with the underlying IGZO channel layer and effectively protected the a-IGZO TFTs from plasma damage during SiO₂ deposition, resulting in a negligible initial performance drop in the a-IGZO TFTs. Compared with passivation-free a-IGZO TFTs, passivated TFTs exhibited superior stability even after 168 h of aging under ambient air at 95% relative humidity.

Conformal Fe3O4 sheath on aligned carbon nanotube scaffolds as high-performance anodes for lithium ion batteries.

PubMed

Wu, Yang; Wei, Yang; Wang, Jiaping; Jiang, Kaili; Fan, Shoushan

2013-02-13

A uniform Fe(3)O(4) sheath is magnetron sputtered onto aligned carbon nanotube (CNT) scaffolds that are directly drawn from CNT arrays. The Fe(3)O(4)-CNT composite electrode, with the size of Fe(3)O(4) confined to 5-7 nm, exhibits a high reversible capacity over 800 mAh g(-1) based on the total electrode mass, remarkable capacity retention, as well as high rate capability. The excellent performance is attributable to the superior electrical conductivity of CNTs, the uniform loading of Fe(3)O(4) sheath, and the structural retention of the composite anode on cycling. As Fe(3)O(4) is inexpensive and environmentally friendly, and the synthesis of Fe(3)O(4)-CNT is free of chemical wastes, this composite anode material holds considerable promise for high-performance lithium ion batteries.

Mesoporous Li4Ti5O12 nanoclusters anchored on super-aligned carbon nanotubes as high performance electrodes for lithium ion batteries.

PubMed

Sun, Li; Kong, Weibang; Wu, Hengcai; Wu, Yang; Wang, Datao; Zhao, Fei; Jiang, Kaili; Li, Qunqing; Wang, Jiaping; Fan, Shoushan

2016-01-07

Mesoporous lithium titanate (LTO) nanoclusters are in situ synthesized in a network of super aligned carbon nanotubes (SACNTs) via a solution-based method followed by heat treatment in air. In the LTO-CNT composite, SACNTs not only serve as the skeleton to support a binder-free electrode, but also render the composite with high conductivity, flexibility, and mechanical strength. The homogeneously dispersed LTO nanoclusters among the SACNTs allow each LTO grain to effectively access the electrolyte and the conductive network, benefiting both ion and electron transport. By the incorporation of LTO into the CNT network, mechanical reinforcement is also achieved. When serving as a negative electrode for lithium ion batteries, such a robust composite-network architecture provides the electrodes with effective charge transport and structural integrity, leading to high-performance flexible electrodes with high capacity, high rate capability, and excellent cycling stability.

A Self-Aligned InGaAs Quantum-Well Metal-Oxide-Semiconductor Field-Effect Transistor Fabricated through a Lift-Off-Free Front-End Process

NASA Astrophysics Data System (ADS)

Lin, Jianqiang; Kim, Tae-Woo; Antoniadis, Dimitri A.; del Alamo, Jesús A.

2012-06-01

We present a novel n-type InGaAs quantum-well metal-oxide-semiconductor field-effect transistor (QW-MOSFET) fabricated by a self-aligned gate-last process and investigate relevant Si-like manufacturing issues in future III-V MOSFETs. The device structure features a composite InP/Al2O3 gate barrier with a capacitance equivalent thickness (CET) of 3 nm and non alloyed Mo ohmic contacts. We have found that RIE introduces significant damage to the intrinsic device resulting in poor current drive and subthreshold swing. The effect is largely removed through a thermal annealing step. Thermally annealed QW-MOSFETs exhibit a subthreshold swing of 95 mV/dec, indicative of excellent interfacial characteristics. The peak mobility of the MOSFET is 2780 cm2 V-1 s-1.

Probing topology and dynamics of the second transmembrane domain (M2δ) of the acetyl choline receptor using magnetically aligned lipid bilayers (bicelles) and EPR spectroscopy.

PubMed

Sahu, Indra D; Mayo, Daniel J; Subbaraman, Nidhi; Inbaraj, Johnson J; McCarrick, Robert M; Lorigan, Gary A

2017-08-01

Characterizing membrane protein structure and dynamics in the lipid bilayer membrane is very important but experimentally challenging. EPR spectroscopy offers a unique set of techniques to investigate a membrane protein structure, dynamics, topology, and distance constraints in lipid bilayers. Previously our lab demonstrated the use of magnetically aligned phospholipid bilayers (bicelles) for probing topology and dynamics of the membrane peptide M2δ of the acetyl choline receptor (AchR) as a proof of concept. In this study, magnetically aligned phospholipid bilayers and rigid spin labels were further utilized to provide improved dynamic information and topology of M2δ peptide. Seven TOAC-labeled AchR M2δ peptides were synthesized to demonstrate the utility of a multi-labeling amino acid substitution alignment strategy. Our data revealed the helical tilts to be 11°, 17°, 9°, 17°, 16°, 11°, 9°±4° for residues I7TOAC, Q13TOAC, A14TOAC, V15TOAC, C16TOAC, L17TOAC, and L18TOAC, respectively. The average helical tilt of the M2δ peptide was determined to be ∼13°. This study also revealed that the TOAC labels were attached to the M2δ peptide with different dynamics suggesting that the sites towards the C-terminal end are more rigid when compared to the sites towards the N-terminus. The dynamics of the TOAC labeled sites were more resolved in the aligned samples when compared to the randomly disordered samples. This study highlights the use of magnetically aligned lipid bilayer EPR technique to determine a more accurate helical tilt and more resolved local dynamics of AchR M2δ peptide. Copyright © 2017 Elsevier B.V. All rights reserved.

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

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/. PMID:24116042

Vertically aligned nanostructure scanning probe microscope tips

DOEpatents

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.

Tunable band alignment in two-phase-coexistence Nb3O7F nanocrystals with enhanced light harvesting and photocatalytic performance

NASA Astrophysics Data System (ADS)

Li, Zhen; Huang, Fei; Feng, Xin; Yan, Aihua; Dong, Haiming; Hu, Miao; Li, Qi

2018-06-01

A two-phase-coexistence technique offers intriguing variables to maneuver novel and enhanced functionality in a single-component material. Most importantly, new band alignment and perfect interfaces between two phases can strongly affect local photoelectronic properties. However, previous efforts to achieve two-phase coexistence were mainly restricted to specific systems and methods. Here we demonstrate a phase-transition route to acquire two-phase-coexistence niobium oxyfluoride (Nb3O7F) nanocrystals for the first time. Based on key distinguishing features of the experimental results and theoretical analysis, the phase transition of Nb3O7F involves an organic/inorganic hybrid, heat treating, Al-doping, lattice deformation and structural rearrangement. The band gap can be effectively tuned from 3.03 eV to 2.84 eV, and the VBM can be tuned from 1.49 eV to 1.69 eV according to the phase proportion. Benefiting from uniform nanocrystal size, tunable band alignment and an optimized interfacial structure, the two-phase coexistence markedly enhances visible-light harvesting and the photocatalytic performance of Nb3O7F nanocrystals. The results not only demonstrate an opportunity to explore two-phase coexistence of novel nanocrystals, but also illustrate the role of two-phase coexistence in achieving enhanced photoelectronic properties.

Tunable band alignment in two-phase-coexistence Nb3O7F nanocrystals with enhanced light harvesting and photocatalytic performance.

PubMed

Li, Zhen; Huang, Fei; Feng, Xin; Yan, Aihua; Dong, Haiming; Hu, Miao; Li, Qi

2018-06-01

A two-phase-coexistence technique offers intriguing variables to maneuver novel and enhanced functionality in a single-component material. Most importantly, new band alignment and perfect interfaces between two phases can strongly affect local photoelectronic properties. However, previous efforts to achieve two-phase coexistence were mainly restricted to specific systems and methods. Here we demonstrate a phase-transition route to acquire two-phase-coexistence niobium oxyfluoride (Nb 3 O 7 F) nanocrystals for the first time. Based on key distinguishing features of the experimental results and theoretical analysis, the phase transition of Nb 3 O 7 F involves an organic/inorganic hybrid, heat treating, Al-doping, lattice deformation and structural rearrangement. The band gap can be effectively tuned from 3.03 eV to 2.84 eV, and the VBM can be tuned from 1.49 eV to 1.69 eV according to the phase proportion. Benefiting from uniform nanocrystal size, tunable band alignment and an optimized interfacial structure, the two-phase coexistence markedly enhances visible-light harvesting and the photocatalytic performance of Nb 3 O 7 F nanocrystals. The results not only demonstrate an opportunity to explore two-phase coexistence of novel nanocrystals, but also illustrate the role of two-phase coexistence in achieving enhanced photoelectronic properties.

The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks.

PubMed

Landau, Itamar D; Egger, Robert; Dercksen, Vincent J; Oberlaender, Marcel; Sompolinsky, Haim

2016-12-07

Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

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

PubMed

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

2013-09-01

Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P < 0.01). This algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P < 0.05), whereas it shows results not significantly different to 3D-COFFEE (P > 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

Electronic structure of a laterally graded ZrO2-TiO2 film on Si(100) prepared by metal-organic chemical vapor deposition in ultrahigh vacuum

NASA Astrophysics Data System (ADS)

Richter, J. H.; Karlsson, P. G.; Sandell, A.

2008-05-01

A TiO2-ZrO2 film with laterally graded stoichiometry has been prepared by metal-organic chemical vapor deposition in ultrahigh vacuum. The film was characterized in situ using synchrotron radiation photoelectron spectroscopy (PES) and x-ray absorption spectroscopy. PES depth profiling clearly shows that Ti ions segregate toward the surface region when mixed with ZrO2. The binding energy of the ZrO2 electronic levels is constant with respect to the local vacuum level. The binding energy of the TiO2 electronic levels is aligned to the Fermi level down to a Ti /Zr ratio of about 0.5. At a Ti /Zr ratio between 0.1 and 0.5, the TiO2 related electronic levels become aligned to the local vacuum level. The addition of small amounts of TiO2 to ZrO2 results in a ZrO2 band alignment relative to the Fermi level that is less asymmetric than for pure ZrO2. The band edge positions shift by -0.6eV for a Ti /Zr ratio of 0.03. This is explained in terms of an increase in the work function when adding TiO2, an effect that becomes emphasized by Ti surface segregation.

Extension of lattice cluster theory to strongly interacting, self-assembling polymeric systems.

PubMed

Freed, Karl F

2009-02-14

A new extension of the lattice cluster theory is developed to describe the influence of monomer structure and local correlations on the free energy of strongly interacting and self-assembling polymer systems. This extension combines a systematic high dimension (1/d) and high temperature expansion (that is appropriate for weakly interacting systems) with a direct treatment of strong interactions. The general theory is illustrated for a binary polymer blend whose two components contain "sticky" donor and acceptor groups, respectively. The free energy is determined as an explicit function of the donor-acceptor contact probabilities that depend, in turn, on the local structure and both the strong and weak interactions.

Detailed Study of Moderately Swept Impinging Oblique Shock/Boundary-Layer Interaction in Mach 2.3 Flow

NASA Astrophysics Data System (ADS)

Threadgill, James; Doerhmann, Adam; Little, Jesse

2017-11-01

A detailed experimental investigation of an impinging oblique Shock/Boundary Layer Interaction (SBLI) with 30° sweep in Mach 2.3 flow has been conducted. Despite its non-dimensional form, this canonical SBLI configuration has attracted little attention and remains poorly understood. Using a 12 .5° shock generator mounted in the freestream over a turbulent boundary layer, the interaction has been characterized with oil flow visualization, fast-response pressure transducers, and particle image velocimetry. Velocity vectors are used to extract the 3D interaction structure. These data are compared to wall pressure measurements and surface skin-friction streamlines. A local collapse of data normal to separation indicates a swept equivalence to Free Interaction Theory, albeit at a lower angle of sweep than imposed by the shock generator. Conditions at reattachment align with the imposed shock. Low-frequency shock motion near separation is observed, analogous to unswept SBLIs, with significant correlations that indicate spanwise traveling ripples in the shock foot. However, the magnitude of wall-pressure unsteadiness in this location is lower and shifted to higher frequencies than observed in equivalent unswept SBLI counterparts. Supported by the Air Force Office of Scientific Research (FA9550-15-1-0430).

What Produce Energetic Flares with X-Shaped Ribbons on the Outskirts of Solar Active Region?

NASA Astrophysics Data System (ADS)

Liu, Rui; Chen, Jun; Wang, Yuming; Kailiu

2016-10-01

Typical solar flares display two quasi-parallel, bright ribbons on the chromosphere. In between is the polarity inversion line separating concentrated magnetic fluxes of opposite polarities in active regions (ARs). Intriguingly a series of flares exhibiting X-shaped ribbons occur at the similar location on the outskirts of NOAA AR 11967, where magnetic fluxes are scattered, yet three of them are alarmingly energetic. The X shape is similar in UV/EUV with hard X-ray emission projected in the center, which cannot be accommodated in the standard flare model. Mapping out magnetic connectivities in potential fields, we found that the X morphology is dictated by the intersection of two quasi-separatrix layers, i.e., a hyperbolic flux tube (HFT), within which a separator connecting a double null is embedded. This topology is not purely local but regulated by fluxes and flows over the whole AR. The nonlinear force-free field model suggests the formation of a current layer at the HFT, where the current dissipation can be mapped to the X-shaped ribbons via field-aligned heat conduction. These results highlight the critical role of structural skeletons in 3D magnetic reconnection.

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

PubMed

Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

2016-08-25

The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

Multiview Locally Linear Embedding for Effective Medical Image Retrieval

PubMed Central

Shen, Hualei; Tao, Dacheng; Ma, Dianfu

2013-01-01

Content-based medical image retrieval continues to gain attention for its potential to assist radiological image interpretation and decision making. Many approaches have been proposed to improve the performance of medical image retrieval system, among which visual features such as SIFT, LBP, and intensity histogram play a critical role. Typically, these features are concatenated into a long vector to represent medical images, and thus traditional dimension reduction techniques such as locally linear embedding (LLE), principal component analysis (PCA), or laplacian eigenmaps (LE) can be employed to reduce the “curse of dimensionality”. Though these approaches show promising performance for medical image retrieval, the feature-concatenating method ignores the fact that different features have distinct physical meanings. In this paper, we propose a new method called multiview locally linear embedding (MLLE) for medical image retrieval. Following the patch alignment framework, MLLE preserves the geometric structure of the local patch in each feature space according to the LLE criterion. To explore complementary properties among a range of features, MLLE assigns different weights to local patches from different feature spaces. Finally, MLLE employs global coordinate alignment and alternating optimization techniques to learn a smooth low-dimensional embedding from different features. To justify the effectiveness of MLLE for medical image retrieval, we compare it with conventional spectral embedding methods. We conduct experiments on a subset of the IRMA medical image data set. Evaluation results show that MLLE outperforms state-of-the-art dimension reduction methods. PMID:24349277

Text Extraction from Scene Images by Character Appearance and Structure Modeling

PubMed Central

Yi, Chucai; Tian, Yingli

2012-01-01

In this paper, we propose a novel algorithm to detect text information from natural scene images. Scene text classification and detection are still open research topics. Our proposed algorithm is able to model both character appearance and structure to generate representative and discriminative text descriptors. The contributions of this paper include three aspects: 1) a new character appearance model by a structure correlation algorithm which extracts discriminative appearance features from detected interest points of character samples; 2) a new text descriptor based on structons and correlatons, which model character structure by structure differences among character samples and structure component co-occurrence; and 3) a new text region localization method by combining color decomposition, character contour refinement, and string line alignment to localize character candidates and refine detected text regions. We perform three groups of experiments to evaluate the effectiveness of our proposed algorithm, including text classification, text detection, and character identification. The evaluation results on benchmark datasets demonstrate that our algorithm achieves the state-of-the-art performance on scene text classification and detection, and significantly outperforms the existing algorithms for character identification. PMID:23316111

Direct observation of impact propagation and absorption in dense colloidal monolayers

NASA Astrophysics Data System (ADS)

Buttinoni, Ivo; Cha, Jinwoong; Lin, Wei-Hsun; Job, Stéphane; Daraio, Chiara; Isa, Lucio

2017-11-01

Dense colloidal suspensions can propagate and absorb large mechanical stresses, including impacts and shocks. The wave transport stems from the delicate interplay between the spatial arrangement of the structural units and solvent-mediated effects. For dynamic microscopic systems, elastic deformations of the colloids are usually disregarded due to the damping imposed by the surrounding fluid. Here, we study the propagation of localized mechanical pulses in aqueous monolayers of micron-sized particles of controlled microstructure. We generate extreme localized deformation rates by exciting a target particle via pulsed-laser ablation. In crystalline monolayers, stress propagation fronts take place, where fast-moving particles (V approximately a few meters per second) are aligned along the symmetry axes of the lattice. Conversely, more viscous solvents and disordered structures lead to faster and isotropic energy absorption. Our results demonstrate the accessibility of a regime where elastic collisions also become relevant for suspensions of microscopic particles, behaving as “billiard balls” in a liquid, in analogy with regular packings of macroscopic spheres. We furthermore quantify the scattering of an impact as a function of the local structural disorder.

Direct observation of impact propagation and absorption in dense colloidal monolayers

PubMed Central

Cha, Jinwoong; Lin, Wei-Hsun; Job, Stéphane; Daraio, Chiara

2017-01-01

Dense colloidal suspensions can propagate and absorb large mechanical stresses, including impacts and shocks. The wave transport stems from the delicate interplay between the spatial arrangement of the structural units and solvent-mediated effects. For dynamic microscopic systems, elastic deformations of the colloids are usually disregarded due to the damping imposed by the surrounding fluid. Here, we study the propagation of localized mechanical pulses in aqueous monolayers of micron-sized particles of controlled microstructure. We generate extreme localized deformation rates by exciting a target particle via pulsed-laser ablation. In crystalline monolayers, stress propagation fronts take place, where fast-moving particles (V approximately a few meters per second) are aligned along the symmetry axes of the lattice. Conversely, more viscous solvents and disordered structures lead to faster and isotropic energy absorption. Our results demonstrate the accessibility of a regime where elastic collisions also become relevant for suspensions of microscopic particles, behaving as “billiard balls” in a liquid, in analogy with regular packings of macroscopic spheres. We furthermore quantify the scattering of an impact as a function of the local structural disorder. PMID:29087329

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.

PubMed

Chen, Xiang; He, Si-Min; Bu, Dongbo; Zhang, Fa; Wang, Zhiyong; Chen, Runsheng; Gao, Wen

2008-09-15

RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has local instead of global minimum free energy. This implies that we may improve the performance of RNA secondary structure prediction by taking kinetics into account and minimize free energy in a local area. we propose a novel algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Still based on MFE criterion, FlexStem adopts comprehensive energy models that allow complex pseudoknots. Unlike classical thermodynamic methods, our approach aims to simulate the RNA folding process by successive addition of maximal stems, reducing the search space while maintaining or even improving the prediction accuracy. This reduced space is constructed by our maximal stem strategy and stem-adding rule induced from elaborate statistical experiments on real RNA secondary structures. The strategy and the rule also reflect the folding characteristic of RNA from a new angle and help compensate for the deficiency of merely relying on MFE in RNA structure prediction. We validate FlexStem by applying it to tRNAs, 5SrRNAs and a large number of pseudoknotted structures and compare it with the well-known algorithms such as RNAfold, PKNOTS, PknotsRG, HotKnots and ILM according to their overall sensitivities and specificities, as well as positive and negative controls on pseudoknots. The results show that FlexStem significantly increases the prediction accuracy through its local search strategy. Software is available at http://pfind.ict.ac.cn/FlexStem/. Supplementary data are available at Bioinformatics online.

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.

PubMed

Bonham-Carter, Oliver; Steele, Joe; Bastola, Dhundy

2014-11-01

Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Impact of the Nanoscale Gap Morphology on the Plasmon Coupling in Asymmetric Nanoparticle Dimer Antennas.

PubMed

Popp, Paul S; Herrmann, Janning F; Fritz, Eva-Corinna; Ravoo, Bart Jan; Höppener, Christiane

2016-03-23

Coupling of plasmon resonances in metallic gap antennas is of interest for a wide range of applications due to the highly localized strong electric fields supported by these structures, and their high sensitivity to alterations of their structure, geometry, and environment. Morphological alterations of asymmetric nanoparticle dimer antennas with (sub)-nanometer size gaps are assigned to changes of their optical response in correlative dark-field spectroscopy and high-resolution transmission electron microscopy (HR-TEM) investigations. This multimodal approach to investigate individual dimer structures clearly demonstrates that the coupling of the plasmon modes, in addition to well-known parameters such as the particle geometry and the gap size, is also affected by the relative alignment of both nanoparticles. The investigations corroborate that the alignment of the gap forming facets, and with that the gap area, is crucial for their scattering properties. The impact of a flat versus a rounded gap structure on the optical properties of equivalent dimers becomes stronger with decreasing gap size. These results hint at a higher confinement of the electric field in the gap and possibly a different onset of quantum transport effects for flat and rounded gap antennas in corresponding structures for very narrow gaps. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

PubMed

Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

2015-01-01

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

DNA motif alignment by evolving a population of Markov chains.

PubMed

Bi, Chengpeng

2009-01-30

Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

Possible Mechanism for Damping of Electrostatic Instability Related to Inhomogeneous Distribution of Energy Density in the Auroral Ionosphere

NASA Astrophysics Data System (ADS)

Golovchanskaya, I. V.; Kozelov, B. V.; Chernyshov, A. A.; Ilyasov, A. A.; Mogilevsky, M. M.

2018-03-01

Satellite observations show that the electrostatic instability, which is expected to occur in most cases due to an inhomogeneous energy density caused by a strongly inhomogeneous transverse electric field (shear of plasma convection velocity), occasionally does not develop inside nonlinear plasma structures in the auroral ionosphere, even though the velocity shear is sufficient for its excitation. In this paper, it is shown that the instability damping can be caused by out-of-phase variations of the electric field and field-aligned current acting in these structures. Therefore, the mismatch of sources of free energy required for the wave generation nearly nullifies their common effect.

ST5 Observations of the Imbalance of Region 1 and 2 Field-Aligned Currents and its Implication to Ionospheric Closure Currents

NASA Technical Reports Server (NTRS)

Le, G.

2008-01-01

A major unsolved question in the physics of ionosphere-magnetosphere coupling is how field-aligned currents (FACs) close. In order to maintain the divergence free condition, overall downward FACs (carried mainly by upward electrons) must eventually balance the overall upward FACs associated with the precipitating electrons through ionospheric Pedersen currents. Although much of the current closure may take place via local Pedersen currents flowing between Region 1 (R1) and Region 2 (R2) FACs, there is a generally an imbalance, i.e., more currents in R1 than in R2, in total currents between them. The net currents may be closed within R1 via cross-polar cap Pedersen currents. In this study, we use the magnetic field observations from Space Technology 5 mission to quantify the imbalance of R1 and R2 currents. We will determine the net R1-R2 currents under various solar wind conditions and discuss the implication of such imbalance to the ionospheric closure currents.

Design of an Fiber-Coupled Laser Heterodyne Interferometer for the FLARE

NASA Astrophysics Data System (ADS)

Frank, Samuel; Yoo, Jongsoo; Ji, Hantao; Jara-Almonte, Jon

2016-10-01

The FLARE (Facility for Laboratory Reconnection Experiments), which is currently under construction at PPPL, requires a complete set of laboratory plasma diagnostics. The Langmuir probes that will be used in the device to gather local density data require a reliable interferometer system to serve as baseline for density measurement calibration. A fully fiber-coupled infrared laser heterodyne interferometer has been designed in order to serve as the primary line-integrated electron density diagnostic. Thanks to advances in the communications industry many fiber optic devices and phase detection methods have advanced significantly becoming increasingly reliable and inexpensive. Fully fiber coupling a plasma interferometer greatly simplifies alignment procedures needed since the only free space laser path needing alignment is through the plasma itself. Fiber-coupling also provides significant resistance to vibrational noise, a common problem in plasma interferometry systems. This device also uses a greatly simplified phase detection scheme in which chips, originally developed for the communications industry, capable of directly detecting the phase shift of a signal with high time resolution. The design and initial performance of the system will be discussed.

Decentralized semi-active damping of free structural vibrations by means of structural nodes with an on/off ability to transmit moments

NASA Astrophysics Data System (ADS)

Poplawski, Blazej; Mikułowski, Grzegorz; Mróz, Arkadiusz; Jankowski, Łukasz

2018-02-01

This paper proposes, tests numerically and verifies experimentally a decentralized control algorithm with local feedback for semi-active mitigation of free vibrations in frame structures. The algorithm aims at transferring the vibration energy of low-order, lightly-damped structural modes into high-frequency modes of vibration, where it is quickly damped by natural mechanisms of material damping. Such an approach to mitigation of vibrations, known as the prestress-accumulation release (PAR) strategy, has been earlier applied only in global control schemes to the fundamental vibration mode of a cantilever beam. In contrast, the decentralization and local feedback allows the approach proposed here to be applied to more complex frame structures and vibration patterns, where the global control ceases to be intuitively obvious. The actuators (truss-frame nodes with controllable ability to transmit moments) are essentially unblockable hinges that become unblocked only for very short time periods in order to trigger local modal transfer of energy. The paper proposes a computationally simple model of the controllable nodes, specifies the control performance measure, yields basic characteristics of the optimum control, proposes the control algorithm and then tests it in numerical and experimental examples.

Stepwise Elastic Behavior in a Model Elastomer

NASA Astrophysics Data System (ADS)

Bhawe, Dhananjay M.; Cohen, Claude; Escobedo, Fernando A.

2004-12-01

MonteCarlo simulations of an entanglement-free cross-linked polymer network of semiflexible chains reveal a peculiar stepwise elastic response. For increasing stress, step jumps in strain are observed that do not correlate with changes in the number of aligned chains. We show that this unusual behavior stems from the ability of the system to form multiple ordered chain domains that exclude the cross-linking species. This novel elastomer shows a toughening behavior similar to that observed in biological structural materials, such as muscle proteins and abalone shell adhesive.

Water-Assisted Highly Efficient Synthesis of Impurity-Free Single-Walled Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Hata, Kenji; Futaba, Don N.; Mizuno, Kohei; Namai, Tatsunori; Yumura, Motoo; Iijima, Sumio

2004-11-01

We demonstrate the efficient chemical vapor deposition synthesis of single-walled carbon nanotubes where the activity and lifetime of the catalysts are enhanced by water. Water-stimulated enhanced catalytic activity results in massive growth of superdense and vertically aligned nanotube forests with heights up to 2.5 millimeters that can be easily separated from the catalysts, providing nanotube material with carbon purity above 99.98%. Moreover, patterned, highly organized intrinsic nanotube structures were successfully fabricated. The water-assisted synthesis method addresses many critical problems that currently plague carbon nanotube synthesis.

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

PubMed

Tan, Yen Hock; Huang, He; Kihara, Daisuke

2006-08-15

Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

Wave models for turbulent free shear flows

NASA Technical Reports Server (NTRS)

Liou, W. W.; Morris, P. J.

1991-01-01

New predictive closure models for turbulent free shear flows are presented. They are based on an instability wave description of the dominant large scale structures in these flows using a quasi-linear theory. Three model were developed to study the structural dynamics of turbulent motions of different scales in free shear flows. The local characteristics of the large scale motions are described using linear theory. Their amplitude is determined from an energy integral analysis. The models were applied to the study of an incompressible free mixing layer. In all cases, predictions are made for the development of the mean flow field. In the last model, predictions of the time dependent motion of the large scale structure of the mixing region are made. The predictions show good agreement with experimental observations.

Improving oncoplastic breast tumor bed localization for radiotherapy planning using image registration algorithms

NASA Astrophysics Data System (ADS)

Wodzinski, Marek; Skalski, Andrzej; Ciepiela, Izabela; Kuszewski, Tomasz; Kedzierawski, Piotr; Gajda, Janusz

2018-02-01

Knowledge about tumor bed localization and its shape analysis is a crucial factor for preventing irradiation of healthy tissues during supportive radiotherapy and as a result, cancer recurrence. The localization process is especially hard for tumors placed nearby soft tissues, which undergo complex, nonrigid deformations. Among them, breast cancer can be considered as the most representative example. A natural approach to improving tumor bed localization is the use of image registration algorithms. However, this involves two unusual aspects which are not common in typical medical image registration: the real deformation field is discontinuous, and there is no direct correspondence between the cancer and its bed in the source and the target 3D images respectively. The tumor no longer exists during radiotherapy planning. Therefore, a traditional evaluation approach based on known, smooth deformations and target registration error are not directly applicable. In this work, we propose alternative artificial deformations which model the tumor bed creation process. We perform a comprehensive evaluation of the most commonly used deformable registration algorithms: B-Splines free form deformations (B-Splines FFD), different variants of the Demons and TV-L1 optical flow. The evaluation procedure includes quantitative assessment of the dedicated artificial deformations, target registration error calculation, 3D contour propagation and medical experts visual judgment. The results demonstrate that the currently, practically applied image registration (rigid registration and B-Splines FFD) are not able to correctly reconstruct discontinuous deformation fields. We show that the symmetric Demons provide the most accurate soft tissues alignment in terms of the ability to reconstruct the deformation field, target registration error and relative tumor volume change, while B-Splines FFD and TV-L1 optical flow are not an appropriate choice for the breast tumor bed localization problem, even though the visual alignment seems to be better than for the Demons algorithm. However, no algorithm could recover the deformation field with sufficient accuracy in terms of vector length and rotation angle differences.

Biclustering as a method for RNA local multiple sequence alignment.

PubMed

Wang, Shu; Gutell, Robin R; Miranker, Daniel P

2007-12-15

Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address. We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences. BlockMSA was tested on the subsets of the BRAliBase 2.1 benchmark suite that display high variability and on an extension to that suite to larger problem sizes. Also, alignments were evaluated of two large datasets of current biological interest, T box sequences and Group IC1 Introns. The results were compared with alignments computed by ClustalW, MAFFT, MUCLE and PROBCONS alignment programs using Sum of Pairs (SPS) and Consensus Count. Results for the benchmark suite are sensitive to problem size. On problems of 15 or greater sequences, BlockMSA is consistently the best. On none of the problems in the test suite are there appreciable differences in scores among BlockMSA, MAFFT and PROBCONS. On the T box sequences, BlockMSA does the most faithful job of reproducing known annotations. MAFFT and PROBCONS do not. On the Intron sequences, BlockMSA, MAFFT and MUSCLE are comparable at identifying conserved regions. BlockMSA is implemented in Java. Source code and supplementary datasets are available at http://aug.csres.utexas.edu/msa/

Coordinate alignment of combined measurement systems using a modified common points method

NASA Astrophysics Data System (ADS)

Zhao, G.; Zhang, P.; Xiao, W.

2018-03-01

The co-ordinate metrology has been extensively researched for its outstanding advantages in measurement range and accuracy. The alignment of different measurement systems is usually achieved by integrating local coordinates via common points before measurement. The alignment errors would accumulate and significantly reduce the global accuracy, thus need to be minimized. In this thesis, a modified common points method (MCPM) is proposed to combine different traceable system errors of the cooperating machines, and optimize the global accuracy by introducing mutual geometric constraints. The geometric constraints, obtained by measuring the common points in individual local coordinate systems, provide the possibility to reduce the local measuring uncertainty whereby enhance the global measuring certainty. A simulation system is developed in Matlab to analyze the feature of MCPM using the Monto-Carlo method. An exemplary setup is constructed to verify the feasibility and efficiency of the proposed method associated with laser tracker and indoor iGPS systems. Experimental results show that MCPM could significantly improve the alignment accuracy.

MultiSETTER: web server for multiple RNA structure comparison.

PubMed

Čech, Petr; Hoksza, David; Svozil, Daniel

2015-08-12

Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Field-aligned currents, convection electric fields, and ULF-ELF waves in the cusp

NASA Technical Reports Server (NTRS)

Saflekos, N. A.; Potemra, T. A.; Kintner, P. M., Jr.; Green, J. L.

1979-01-01

Nearly simultaneous observations from the Triad and Hawkeye satellites over the Southern Hemisphere, at low altitudes near the noon meridian and close to the usual polar cusp latitudes, show that in and near the polar cusp there exist several relationships between field-aligned currents (FACs), convection electric fields, ULF-ELF magnetic noise, broadband electrostatic noise and interplanetary magnetic fields. The most important findings are (1) the FACs directed into the ionosphere in the noon-to-dusk local time sector and directed away from the ionosphere in the noon-to-dawn local time sector and identified as region-1 permanent FACs (Iijima and Potemra, 1976a) and are located equatorward of the regions of antisunward (westward) convection; (2) the observations are consistent with a two-cell convection pattern symmetric in one case (throat positioned at noon) and asymmetric in another (throat located in a sector on the forenoon side in juxtaposition to the region of strong convection on the afternoon side); and (3) fine-structure FACs are responsible for the generation of ULF-ELF noise in the polar cusp.

PSO-based methods for medical image registration and change assessment of pigmented skin

NASA Astrophysics Data System (ADS)

Kacenjar, Steve; Zook, Matthew; Balint, Michael

2011-03-01

There are various scientific and technological areas in which it is imperative to rapidly detect and quantify changes in imagery over time. In fields such as earth remote sensing, aerospace systems, and medical imaging, searching for timedependent, regional changes across deformable topographies is complicated by varying camera acquisition geometries, lighting environments, background clutter conditions, and occlusion. Under these constantly-fluctuating conditions, the use of standard, rigid-body registration approaches often fail to provide sufficient fidelity to overlay image scenes together. This is problematic because incorrect assessments of the underlying changes of high-level topography can result in systematic errors in the quantification and classification of interested areas. For example, in the current naked-eye detection strategies of melanoma, a dermatologist often uses static morphological attributes to identify suspicious skin lesions for biopsy. This approach does not incorporate temporal changes which suggest malignant degeneration. By performing the co-registration of time-separated skin imagery, a dermatologist may more effectively detect and identify early morphological changes in pigmented lesions; enabling the physician to detect cancers at an earlier stage resulting in decreased morbidity and mortality. This paper describes an image processing system which will be used to detect changes in the characteristics of skin lesions over time. The proposed system consists of three main functional elements: 1.) coarse alignment of timesequenced imagery, 2.) refined alignment of local skin topographies, and 3.) assessment of local changes in lesion size. During the coarse alignment process, various approaches can be used to obtain a rough alignment, including: 1.) a manual landmark/intensity-based registration method1, and 2.) several flavors of autonomous optical matched filter methods2. These procedures result in the rough alignment of a patient's back topography. Since the skin is a deformable membrane, this process only provides an initial condition for subsequent refinements in aligning the localized topography of the skin. To achieve a refined enhancement, a Particle Swarm Optimizer (PSO) is used to optimally determine the local camera models associated with a generalized geometric transform. Here the optimization process is driven using the minimization of entropy between the multiple time-separated images. Once the camera models are corrected for local skin deformations, the images are compared using both pixel-based and regional-based methods. Limits on the detectability of change are established by the fidelity to which the algorithm corrects for local skin deformation and background alterations. These limits provide essential information in establishing early-warning thresholds for Melanoma detection. Key to this work is the development of a PSO alignment algorithm to perform the refined alignment in local skin topography between the time sequenced imagery (TSI). Test and validation of this alignment process is achieved using a forward model producing known geometric artifacts in the images and afterwards using a PSO algorithm to demonstrate the ability to identify and correct for these artifacts. Specifically, the forward model introduces local translational, rotational, and magnification changes within the image. These geometric modifiers are expected during TSI acquisition because of logistical issues to precisely align the patient to the image recording geometry and is therefore of paramount importance to any viable image registration system. This paper shows that the PSO alignment algorithm is effective in autonomously determining and mitigating these geometric modifiers. The degree of efficacy is measured by several statistically and morphologically based pre-image filtering operations applied to the TSI imagery before applying the PSO alignment algorithm. These trade studies show that global image threshold binarization provides rapid and superior convergence characteristics relative to that of morphologically based methods.

Sequence analysis by iterated maps, a review.

PubMed

Almeida, Jonas S

2014-05-01

Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results.

Boundary layer polarization and voltage in the 14 MLT region

NASA Astrophysics Data System (ADS)

Lundin, R.; Yamauchi, M.; Woch, J.; Marklund, G.

1995-05-01

Viking midlatitude observations of ions and electrons in the postnoon auroral region show that field-aligned acceleration of electrons and ions with energies up to a few kiloelectron volts takes place. The characteristics of the upgoing ion beams and the local transverse electric field observed by Viking indicate that parallel ion acceleration is primarily due to a quasi-electrostatic field-aligned acceleration process below Viking altitudes, i.e., below 10,000-13,500 km. A good correlation is found between the maximum upgoing ion beam energy and the depth of the local potential well determined by the Viking electric field experiment within dayside 'ion inverted Vs.' The total transverse potential throughout the entire region near the ion inverted Vs. is generally much higher than the field-aligned potential and may reach well above 10 kV. However, the detailed mapping of the transverse potential out to the boundary layer, a fundamental issue which remains controversial, was not attempted here. An important finding in this study is the strong correlation between the maximum up going ion beam energy of dayside ion inverted Vs and the solar wind velocity. This suggests a direct coupling of the solar wind plasma dynamo/voltage generator to the region of field-aligned particle acceleration. The fact that the center of dayside ion inverted Vs coincide with convection reversals/flow stagnation and upward Birkeland currents on what appears to be closed field lines (Woch et al., 1993), suggests that field-aligned potential structures connect to the inner part of an MHD dyanmo in the low-latitude boundary layer. Thus the Viking observations substantiate the idea of a solar wind induced boundary layer polarization where negatively charged perturbations in the postnoon sector persistently develops along the magnetic field lines, establishing accelerating potential drops along the geomagnetic field lines in the 0.5-10 kV range.

Gas-tungsten arc welding of aluminum alloys

DOEpatents

Frye, L.D.

1982-03-25

The present invention is directed to a gas-tungsten arc welding method for joining together structures formed of aluminum alloy with these structures disposed contiguously to a heat-damagable substrate of a metal dissimilar to the aluminum alloy. The method of the present invention is practiced by diamond machining the fay surfaces of the aluminum alloy structures to profice a mirror finish thereon having a surface roughness in the order of about one microinch. The fay surface are aligned and heated sufficiently by the tungsten electrode to fuse the aluminum alloy continguous to the fay surfaces to effect the weld joint. The heat input used to provide an oxide-free weld is significantly less than that required if the fay surfaces were prepared by using conventional chemical and mechanical practices.

Effect of Serum and Insulin Modulation on the Organization and Morphology of Matrix Synthesized by Bovine Corneal Stromal Cells

PubMed Central

Bueno, Ericka M.; Saeidi, Nima; Melotti, Suzanna

2009-01-01

The in vitro production of highly organized collagen fibrils by corneal keratocytes in a three-dimensional scaffold-free culture system presents a unique opportunity for the direct observation of organized matrix formation. The objective of this investigation was to develop such a culture system in a glass substrate (for optical accessibility) and to directly examine the effect of reducing serum and/or increasing insulin on the stratification and secretion of aligned matrix by fourth- to fifth-passage bovine corneal stromal keratocytes. Medium concentrations of 0%, 1%, or 10% fetal bovine serum and 0% or 1% insulin–transferrin–selenium were investigated. High-resolution differential interference contrast microscopy, quick-freeze/deep-etch, and conventional transmission electron microscopy were used to monitor the evolution, morphology, and ultrastructure of the cell–matrix constructs. In a medium containing 1% each of serum and insulin–transferrin–selenium, stromal cells stratified and secreted abundant and locally aligned matrix, generating the thickest cell–matrix constructs (allowing handling with forceps). The results of this study have the potential to significantly advance the field of developmental functional engineering of load-bearing tissues by (i) elucidating cues that modulate in vitro cell secretion of organized matrix and (ii) establishing an optically accessible cell culture system for investigating the mechanism of cell secretion of aligned collagen fibrils. PMID:19480568

Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

PubMed

Cornilescu, Gabriel; Ramos Alvarenga, René F; Wyche, Thomas P; Bugni, Tim S; Gil, Roberto R; Cornilescu, Claudia C; Westler, William M; Markley, John L; Schwieters, Charles D

2017-08-18

Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.

The f ( R ) halo mass function in the cosmic web

DOE Office of Scientific and Technical Information (OSTI.GOV)

Braun-Bates, F. von; Winther, H.A.; Alonso, D.

An important indicator of modified gravity is the effect of the local environment on halo properties. This paper examines the influence of the local tidal structure on the halo mass function, the halo orientation, spin and the concentration-mass relation. We use the excursion set formalism to produce a halo mass function conditional on large-scale structure. Our simple model agrees well with simulations on large scales at which the density field is linear or weakly non-linear. Beyond this, our principal result is that f ( R ) does affect halo abundances, the halo spin parameter and the concentration-mass relationship in anmore » environment-independent way, whereas we find no appreciable deviation from \\text(ΛCDM) for the mass function with fixed environment density, nor the alignment of the orientation and spin vectors of the halo to the eigenvectors of the local cosmic web. There is a general trend for greater deviation from \\text(ΛCDM) in underdense environments and for high-mass haloes, as expected from chameleon screening.« less

Mixing and chemical reaction in sheared and nonsheared homogeneous turbulence

NASA Technical Reports Server (NTRS)

Leonard, Andy D.; Hill, James C.

1992-01-01

Direct numerical simulations were made to examine the local structure of the reaction zone for a moderately fast reaction between unmixed species in decaying, homogeneous turbulence and in a homogeneous turbulent shear flow. Pseudospectral techniques were used in domains of 64 exp 3 and higher wavenumbers. A finite-rate, single step reaction between non-premixed reactants was considered, and in one case temperature-dependent Arrhenius kinetics was assumed. Locally intense reaction rates that tend to persist throughout the simulations occur in locations where the reactant concentration gradients are large and are amplified by the local rate of strain. The reaction zones are more organized in the case of a uniform mean shear than in isotropic turbulence, and regions of intense reaction rate appear to be associated with vortex structures such as horseshoe vortices and fingers seen in mixing layers. Concentration gradients tend to align with the direction of the most compressive principal strain rate, more so in the isotropic case.

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

ERIC Educational Resources Information Center

Asante, Keith K.

2010-01-01

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

Local dynamics of glass-forming polystyrene thin films from atomistic simulation

NASA Astrophysics Data System (ADS)

Zhou, Yuxing; Milner, Scott

Despite a wide technological application ranging from protective coatings to organic solar cells, there still no consensus on the mechanism for the glass transition in polymer thin films a manifestation of the infamous glass problem under confinement. Many experimental and computational studies have observed a large deviation of nanoscale dynamical properties in thin films from the corresponding properties in bulk. In this work, we perform extensive united-atom simulations on atactic polystyrene free-standing thin films near the glass transition temperature and focus on the effect of free surface on the local dynamics. We study the segmental dynamics as a function of distance from the surface for different temperatures, from which relaxation time and thereby local Tg is obtained for each layer. We find the dynamics near free surface is not only enhanced but becomes less strongly temperature dependent as Tg is approached compared to the bulk. We find an increasing length scale associated with mobility propagation from the free surface as temperature decreases, but no correlation between local structure and enhanced relaxation rates near the surface, consistent with studies on bead-spring chains.

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

NASA Astrophysics Data System (ADS)

Sicard, François; Senet, Patrick

2013-06-01

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics.

PubMed

Sicard, François; Senet, Patrick

2013-06-21

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

Effect of aqueous environment in chemical reactivity of monolignols. A New Fukui Function Study.

PubMed

Martínez, Carmen; Sedano, Miriam; Mendoza, Jorge; Herrera, Rafael; Rutiaga, Jose G; Lopez, Pablo

2009-09-01

The free radical reactivity of monolignols can be explained in terms of the Fukui function and the local hard and soft acids and bases (HSAB) principle to determine the potential linkages among them for reactions involving free radicals. Our results in gas-phase and aqueous environment elucidate the most probable free radical resonance structures in monolignols. Their reactivity toward nucleophilic or electrophilic species was described applying the Fukui function after a second analysis of the selected resonance structures. Methodology herein described could differentiate the inherent nature of one radical from another.

PDBFlex: exploring flexibility in protein structures

PubMed Central

Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

2016-01-01

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

SU-E-J-24: Image-Guidance Using Cone-Beam CT for Stereotactic Body Radiotherapy (SBRT) of Lung Cancer Patients: Bony Alignment or Soft Tissue Alignment?

PubMed

Wang, L; Turaka, A; Meyer, J; Spoka, D; Jin, L; Fan, J; Ma, C

2012-06-01

To assess the reliability of soft tissue alignment by comparing pre- and post-treatment cone-beam CT (CBCT) for image guidance in stereotactic body radiotherapy (SBRT) of lung cancers. Our lung SBRT procedures require all patients undergo 4D CT scan in order to obtain patient-specific target motion information through reconstructed 4D data using the maximum-intensity projection (MIP) algorithm. The internal target volume (ITV) was outlined directly from the MIP images and a 3-5 mm margin expansion was then applied to the ITV to create the PTV. Conformal treatment planning was performed on the helical images, to which the MIP images were fused. Prior to each treatment, CBCT was used for image guidance by comparing with the simulation CT and for patient relocalization based on the bony anatomy. Any displacement of the patient bony structure would be considered as setup errors and would be corrected by couch shifts. Theoretically, as the PTV definition included target internal motion, no further shifts other than setup corrections should be made. However, it is our practice to have treating physicians further check target localization within the PTV. Whenever the shifts based on the soft-tissue alignment (that is, target alignment) exceeded a certain value (e.g. 5 mm), a post-treatment CBCT was carried out to ensure that the tissue alignment is reliable by comparing between pre- and post-treatment CBCT. Pre- and post-CBCT has been performed for 7 patients so far who had shifts beyond 5 mm despite bony alignment. For all patients, post CBCT confirmed that the visualized target position was kept in the same position as before treatment after adjusting for soft-tissue alignment. For the patient population studied, it is shown that soft-tissue alignment is necessary and reliable in the lung SBRT for individual cases. © 2012 American Association of Physicists in Medicine.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujii, Mami N., E-mail: f-mami@ms.naist.jp; Ishikawa, Yasuaki; Bermundo, Juan Paolo Soria

In a previous work, we reported the high field effect mobility of ZnO-doped In{sub 2}O{sub 3} (IZO) thin film transistors (TFTs) irradiated by excimer laser annealing (ELA) [M. Fujii et al., Appl. Phys. Lett. 102, 122107 (2013)]. However, a deeper understanding of the effect of ELA on the IZO film characteristics based on crystallinity, carrier concentrations, and optical properties is needed to control localized carrier concentrations for fabricating self-aligned structures in the same oxide film and to adequately explain the physical characteristics. In the case of as-deposited IZO film used as the channel, a high carrier concentration due to amore » high density of oxygen vacancies was observed; such a film does not show the required TFT characteristics but can act as a conductive film. We achieved a decrease in the carrier concentration of IZO films by crystallization using ELA. This means that ELA can form localized conductive or semi-conductive areas on the IZO film. We confirmed that the reason for the carrier concentration decrease was the decrease of oxygen-deficient regions and film crystallization. The annealed IZO films showed nano-crystalline phase, and the temperature at the substrate was substantially less than the temperature limit for flexible films such as plastic, which is 50°C. This paves the way for the formation of self-aligned structures and separately formed conductive and semi-conductive regions in the same oxide film.« less

Cascaded face alignment via intimacy definition feature

NASA Astrophysics Data System (ADS)

Li, Hailiang; Lam, Kin-Man; Chiu, Man-Yau; Wu, Kangheng; Lei, Zhibin

2017-09-01

Recent years have witnessed the emerging popularity of regression-based face aligners, which directly learn mappings between facial appearance and shape-increment manifolds. We propose a random-forest based, cascaded regression model for face alignment by using a locally lightweight feature, namely intimacy definition feature. This feature is more discriminative than the pose-indexed feature, more efficient than the histogram of oriented gradients feature and the scale-invariant feature transform feature, and more compact than the local binary feature (LBF). Experimental validation of our algorithm shows that our approach achieves state-of-the-art performance when testing on some challenging datasets. Compared with the LBF-based algorithm, our method achieves about twice the speed, 20% improvement in terms of alignment accuracy and saves an order of magnitude on memory requirement.

Combined CT-based and image-free navigation systems in TKA reduces postoperative outliers of rotational alignment of the tibial component.

PubMed

Mitsuhashi, Shota; Akamatsu, Yasushi; Kobayashi, Hideo; Kusayama, Yoshihiro; Kumagai, Ken; Saito, Tomoyuki

2018-02-01

Rotational malpositioning of the tibial component can lead to poor functional outcome in TKA. Although various surgical techniques have been proposed, precise rotational placement of the tibial component was difficult to accomplish even with the use of a navigation system. The purpose of this study is to assess whether combined CT-based and image-free navigation systems replicate accurately the rotational alignment of tibial component that was preoperatively planned on CT, compared with the conventional method. We compared the number of outliers for rotational alignment of the tibial component using combined CT-based and image-free navigation systems (navigated group) with those of conventional method (conventional group). Seventy-two TKAs were performed between May 2012 and December 2014. In the navigated group, the anteroposterior axis was prepared using CT-based navigation system and the tibial component was positioned under control of the navigation. In the conventional group, the tibial component was placed with reference to the Akagi line that was determined visually. Fisher's exact probability test was performed to evaluate the results. There was a significant difference between the two groups with regard to the number of outliers: 3 outliers in the navigated group compared with 12 outliers in the conventional group (P < 0.01). We concluded that combined CT-based and image-free navigation systems decreased the number of rotational outliers of tibial component, and was helpful for the replication of the accurate rotational alignment of the tibial component that was preoperatively planned.

Limitations of outsourcing on-the-ground biodiversity conservation.

PubMed

Iacona, Gwenllian D; Bode, Michael; Armsworth, Paul R

2016-12-01

To counteract global species decline, modern biodiversity conservation engages in large projects, spends billions of dollars, and includes many organizations working simultaneously within regions. To add to this complexity, the conservation sector has hierarchical structure, where conservation actions are often outsourced by funders (foundations, government, etc.) to local organizations that work on-the-ground. In contrast, conservation science usually assumes that a single organization makes resource allocation decisions. This discrepancy calls for theory to understand how the expected biodiversity outcomes change when interactions between organizations are accounted for. Here, we used a game theoretic model to explore how biodiversity outcomes are affected by vertical and horizontal interactions between 3 conservation organizations: a funder that outsourced its actions and 2 local conservation organizations that work on-the-ground. Interactions between the organizations changed the spending decisions made by individual organizations, and thereby the magnitude and direction of the conservation benefits. We showed that funders would struggle to incentivize recipient organizations with set priorities to perform desired actions, even when they control substantial amounts of the funding and employ common contracting approaches to enhance outcomes. Instead, biodiversity outcomes depended on priority alignment across the organizations. Conservation outcomes for the funder were improved by strategic interactions when organizational priorities were well aligned, but decreased when priorities were misaligned. Meanwhile, local organizations had improved outcomes regardless of alignment due to additional funding in the system. Given that conservation often involves the aggregate actions of multiple organizations with different objectives, strategic interactions between organizations need to be considered if we are to predict possible outcomes of conservation programs or costs of achieving conservation targets. © 2016 Society for Conservation Biology.

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

PubMed

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

PubMed Central

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA. PMID:29511354

Individual Differences in the Alignment of Structural and Functional Markers of the V5/MT Complex in Primates

PubMed Central

Large, I.; Bridge, H.; Ahmed, B.; Clare, S.; Kolasinski, J.; Lam, W. W.; Miller, K. L.; Dyrby, T. B.; Parker, A. J.; Smith, J. E. T.; Daubney, G.; Sallet, J.; Bell, A. H.; Krug, K.

2016-01-01

Extrastriate visual area V5/MT in primates is defined both structurally by myeloarchitecture and functionally by distinct responses to visual motion. Myelination is directly identifiable from postmortem histology but also indirectly by image contrast with structural magnetic resonance imaging (sMRI). First, we compared the identification of V5/MT using both sMRI and histology in Rhesus macaques. A section-by-section comparison of histological slices with in vivo and postmortem sMRI for the same block of cortical tissue showed precise correspondence in localizing heavy myelination for V5/MT and neighboring MST. Thus, sMRI in macaques accurately locates histologically defined myelin within areas known to be motion selective. Second, we investigated the functionally homologous human motion complex (hMT+) using high-resolution in vivo imaging. Humans showed considerable intersubject variability in hMT+ location, when defined with myelin-weighted sMRI signals to reveal structure. When comparing sMRI markers to functional MRI in response to moving stimuli, a region of high myelin signal was generally located within the hMT+ complex. However, there were considerable differences in the alignment of structural and functional markers between individuals. Our results suggest that variation in area identification for hMT+ based on structural and functional markers reflects individual differences in human regional brain architecture. PMID:27371764

Studies on the in vivo sensitivity of spindle microtubules to calcium ions and evidence for a vesicular calcium-sequestering system

PubMed Central

1981-01-01

I microinjected calcium ions into echinoderm eggs during mitosis to determine the calcium sensitivity of microtubules (Mts) in vivo. Spindle birefringence (BR), a measure of the number of aligned Mts in the spindle, is locally, rapidly, and reversibly abolished by small volumes of microinjected CaCl2 (1 mM). Rapid return of BR is followed by anaphase, and subsequent divisions are normal. Similar doses of MgCl2, BaCl2, KCl, NaCl, pH buffers, distilled water, or vegetable oil have no effect on spindle BR, whereas large doses of such agents sometimes cause slow, uniform loss in BR over the course of a minute or more. Of the ions tested, only Sr++ causes effects comparable to Ca++. Ca-EGTA buffers, containing greater than micromolar free Ca++, abolishes BR in a manner similar to millimolar concentrations of injected CaCl2. Caffeine, a potent uncoupler of the Ca++-pump/ATPase of sarcoplasmic reticulum, causes a local, transient depression in spindle BR in the injected region. Finally, injection of potassium oxalate results in the formation of small, highly BR crystals, presumably CA- oxalate, in Triton-sensitive compartments in the cytoplasm. Taken together, these findings demonstrate that spindle Mts are sensitive to levels of free Ca++ in the physiological range, provide evidence for the existence of a strong cytoplasmic Ca++-sequestering system, and support the notion that Mt assembly and disassembly in local regions of the spindle may be orchestrated by local changes in the cytoplasmic free Ca++ concentration during mitosis. An appendix offers the design of a new chamber for immobilizing echinoderm eggs for injection, a new method for determining the volume of the injected solution, and a description of the microinjection technique, which was designed, but never fully described, by Hiramoto (Y. Hiramoto, Exp. Cell. Res., 1962, 27:416-426.). PMID:7194345

Accountability and Alignment under No Child Left Behind: Multi-Level Perspectives for Educational Leaders

ERIC Educational Resources Information Center

Choi, Daniel

2011-01-01

Educational leaders have faced the challenges of trying to align schoolwide reforms priorities with accountability demands under the No Child Left Behind law. This article examines the barriers that complicate meaningful alignment among federal, state and local levels. This article also offers the following recommendations: Schools and districts…

Sidewall patterning—a new wafer-scale method for accurate patterning of vertical silicon structures

NASA Astrophysics Data System (ADS)

Westerik, P. J.; Vijselaar, W. J. C.; Berenschot, J. W.; Tas, N. R.; Huskens, J.; Gardeniers, J. G. E.

2018-01-01

For the definition of wafer scale micro- and nanostructures, in-plane geometry is usually controlled by optical lithography. However, options for precisely patterning structures in the out-of-plane direction are much more limited. In this paper we present a versatile self-aligned technique that allows for reproducible sub-micrometer resolution local modification along vertical silicon sidewalls. Instead of optical lithography, this method makes smart use of inclined ion beam etching to selectively etch the top parts of structures, and controlled retraction of a conformal layer to define a hard mask in the vertical direction. The top, bottom or middle part of a structure could be selectively exposed, and it was shown that these exposed regions can, for example, be selectively covered with a catalyst, doped, or structured further.

Nanofiber Orientation and Surface Functionalization Modulate Human Mesenchymal Stem Cell Behavior In Vitro

PubMed Central

Kolambkar, Yash M.; Bajin, Mehmet; Wojtowicz, Abigail; Hutmacher, Dietmar W.; García, Andrés J.

2014-01-01

Electrospun nanofiber meshes have emerged as a new generation of scaffold membranes possessing a number of features suitable for tissue regeneration. One of these features is the flexibility to modify their structure and composition to orchestrate specific cellular responses. In this study, we investigated the effects of nanofiber orientation and surface functionalization on human mesenchymal stem cell (hMSC) migration and osteogenic differentiation. We used an in vitro model to examine hMSC migration into a cell-free zone on nanofiber meshes and mitomycin C treatment to assess the contribution of proliferation to the observed migration. Poly (ɛ-caprolactone) meshes with oriented topography were created by electrospinning aligned nanofibers on a rotating mandrel, while randomly oriented controls were collected on a stationary collector. Both aligned and random meshes were coated with a triple-helical, type I collagen-mimetic peptide, containing the glycine-phenylalanine-hydroxyproline-glycine-glutamate-arginine (GFOGER) motif. Our results indicate that nanofiber GFOGER peptide functionalization and orientation modulate cellular behavior, individually, and in combination. GFOGER significantly enhanced the migration, proliferation, and osteogenic differentiation of hMSCs on nanofiber meshes. Aligned nanofiber meshes displayed increased cell migration along the direction of fiber orientation compared to random meshes; however, fiber alignment did not influence osteogenic differentiation. Compared to each other, GFOGER coating resulted in a higher proliferation-driven cell migration, whereas fiber orientation appeared to generate a larger direct migratory effect. This study demonstrates that peptide surface modification and topographical cues associated with fiber alignment can be used to direct cellular behavior on nanofiber mesh scaffolds, which may be exploited for tissue regeneration. PMID:24020454

Aligning Optical Fibers by Means of Actuated MEMS Wedges

NASA Technical Reports Server (NTRS)

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.

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

PubMed

Bauer, Markus; Klau, Gunnar W; Reinert, Knut

2007-07-27

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. 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. 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.

On the relation between photospheric flow fields and the magnetic field distribution on the solar surface

NASA Technical Reports Server (NTRS)

Simon, George W.; Title, A. M.; Topka, K. P.; Tarbell, T. D.; Shine, R. A.

1988-01-01

Using the technique of local correlation tracking on a 28 minute time sequence of white-light images of solar granulation, the horizontal flow field on the solar surface is measured. The time series was obtained by the Solar Optical Universal Polarimeter (SOUP) on Spacelab 2 (Space Shuttle flight 51-F) and is free from atmospheric blurring and distortion. The SOUP flow fields have been compared with carefully aligned magnetograms taken over a nine hour period at the Big Bear Solar Observatory before, during, and after the SOUP images. The flow field and the magnetic field agree in considerable detail: vectors which define the flow of the white-light intensity pattern (granulation) point toward magnetic field regions, magnetic fields surround flow cells, and magnetic features move along the flow arrows. The projected locations of free particles ('corks') in the measured flow field congregate at the same locations where the magnetic field is observed.

Probabilistic visual and electromagnetic data fusion for robust drift-free sequential mosaicking: application to fetoscopy

PubMed Central

Tella-Amo, Marcel; Peter, Loic; Shakir, Dzhoshkun I.; Deprest, Jan; Iglesias, Juan Eugenio; Ourselin, Sebastien

2018-01-01

Abstract. The most effective treatment for twin-to-twin transfusion syndrome is laser photocoagulation of the shared vascular anastomoses in the placenta. Vascular connections are extremely challenging to locate due to their caliber and the reduced field-of-view of the fetoscope. Therefore, mosaicking techniques are beneficial to expand the scene, facilitate navigation, and allow vessel photocoagulation decision-making. Local vision-based mosaicking algorithms inherently drift over time due to the use of pairwise transformations. We propose the use of an electromagnetic tracker (EMT) sensor mounted at the tip of the fetoscope to obtain camera pose measurements, which we incorporate into a probabilistic framework with frame-to-frame visual information to achieve globally consistent sequential mosaics. We parametrize the problem in terms of plane and camera poses constrained by EMT measurements to enforce global consistency while leveraging pairwise image relationships in a sequential fashion through the use of local bundle adjustment. We show that our approach is drift-free and performs similarly to state-of-the-art global alignment techniques like bundle adjustment albeit with much less computational burden. Additionally, we propose a version of bundle adjustment that uses EMT information. We demonstrate the robustness to EMT noise and loss of visual information and evaluate mosaics for synthetic, phantom-based and ex vivo datasets. PMID:29487889

On the Measure and the Structure of the Free Boundary of the Lower Dimensional Obstacle Problem

NASA Astrophysics Data System (ADS)

Focardi, Matteo; Spadaro, Emanuele

2018-04-01

We provide a thorough description of the free boundary for the lower dimensional obstacle problem in R^{n+1} up to sets of null H^{n-1} measure. In particular, we prove (i) local finiteness of the (n-1)-dimensional Hausdorff measure of the free boundary, (ii) H^{n-1}-rectifiability of the free boundary, (iii) classification of the frequencies up to a set of Hausdorff dimension at most (n-2) and classification of the blow-ups at H^{n-1} almost every free boundary point.

The correlation of fractal structures in the photospheric and the coronal magnetic field

NASA Astrophysics Data System (ADS)

Dimitropoulou, M.; Georgoulis, M.; Isliker, H.; Vlahos, L.; Anastasiadis, A.; Strintzi, D.; Moussas, X.

2009-10-01

Context: This work examines the relation between the fractal properties of the photospheric magnetic patterns and those of the coronal magnetic fields in solar active regions. Aims: We investigate whether there is any correlation between the fractal dimensions of the photospheric structures and the magnetic discontinuities formed in the corona. Methods: To investigate the connection between the photospheric and coronal complexity, we used a nonlinear force-free extrapolation method that reconstructs the 3d magnetic fields using 2d observed vector magnetograms as boundary conditions. We then located the magnetic discontinuities, which are considered as spatial proxies of reconnection-related instabilities. These discontinuities form well-defined volumes, called here unstable volumes. We calculated the fractal dimensions of these unstable volumes and compared them to the fractal dimensions of the boundary vector magnetograms. Results: Our results show no correlation between the fractal dimensions of the observed 2d photospheric structures and the extrapolated unstable volumes in the corona, when nonlinear force-free extrapolation is used. This result is independent of efforts to (1) bring the photospheric magnetic fields closer to a nonlinear force-free equilibrium and (2) omit the lower part of the modeled magnetic field volume that is almost completely filled by unstable volumes. A significant correlation between the fractal dimensions of the photospheric and coronal magnetic features is only observed at the zero level (lower limit) of approximation of a current-free (potential) magnetic field extrapolation. Conclusions: We conclude that the complicated transition from photospheric non-force-free fields to coronal force-free ones hampers any direct correlation between the fractal dimensions of the 2d photospheric patterns and their 3d counterparts in the corona at the nonlinear force-free limit, which can be considered as a second level of approximation in this study. Correspondingly, in the zero and first levels of approximation, namely, the potential and linear force-free extrapolation, respectively, we reveal a significant correlation between the fractal dimensions of the photospheric and coronal structures, which can be attributed to the lack of electric currents or to their purely field-aligned orientation.

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information.

PubMed

Song, Jiangning; Burrage, Kevin; Yuan, Zheng; Huber, Thomas

2006-03-09

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Locality-Conscious Lock-Free Linked Lists

NASA Astrophysics Data System (ADS)

Braginsky, Anastasia; Petrank, Erez

We extend state-of-the-art lock-free linked lists by building linked lists with special care for locality of traversals. These linked lists are built of sequences of entries that reside on consecutive chunks of memory. When traversing such lists, subsequent entries typically reside on the same chunk and are thus close to each other, e.g., in same cache line or on the same virtual memory page. Such cache-conscious implementations of linked lists are frequently used in practice, but making them lock-free requires care. The basic component of this construction is a chunk of entries in the list that maintains a minimum and a maximum number of entries. This basic chunk component is an interesting tool on its own and may be used to build other lock-free data structures as well.

The twilight zone of cis element alignments.

PubMed

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.

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

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. PMID:23268451

Field-Aligned Currents in Saturn's Magnetosphere: Observations From the F-Ring Orbits

NASA Astrophysics Data System (ADS)

Hunt, G. J.; Provan, G.; Bunce, E. J.; Cowley, S. W. H.; Dougherty, M. K.; Southwood, D. J.

2018-05-01

We investigate the azimuthal magnetic field signatures associated with high-latitude field-aligned currents observed during Cassini's F-ring orbits (October 2016-April 2017). The overall ionospheric meridional current profiles in the northern and southern hemispheres, that is, the regions poleward and equatorward of the field-aligned currents, differ most from the 2008 observations. We discuss these differences in terms of the seasonal change between data sets and local time (LT) differences, as the 2008 data cover the nightside while the F-ring data cover the post-dawn and dusk sectors in the northern and southern hemispheres, respectively. The F-ring field-aligned currents typically have a similar four current sheet structure to those in 2008. We investigate the properties of the current sheets and show that the field-aligned currents in a hemisphere are modulated by that hemisphere's "planetary period oscillation" (PPO) systems. We separate the PPO-independent and PPO-related currents in both hemispheres using their opposite symmetry. The average PPO-independent currents peak at 1.5 MA/rad just equatorward of the open closed field line boundary, similar to the 2008 observations. However, the PPO-related currents in both hemispheres are reduced by 50% to 0.4 MA/rad. This may be evidence of reduced PPO amplitudes, similar to the previously observed weaker equatorial oscillations at similar dayside LTs. We do not detect the PPO current systems' interhemispheric component, likely a result of the weaker PPO-related currents and their closure within the magnetosphere. We also do not detect previously proposed lower latitude discrete field-aligned currents that act to "turn off" the PPOs.

The Alignment Test System for AXAF-I's High Resolution Mirror Assembly

NASA Technical Reports Server (NTRS)

Waldman, Mark

1995-01-01

The AXAF-1 High Resolution Mirror Assembly (HRMA) consists of four nested mirror pairs of Wolter Type-1 grazing incidence optics. The HRMA assembly and alignment will take place in a vibration-isolated, cleanliness class 100, 18 meter high tower at an Eastman Kodak Company facility in Rochester, NY. Each mirror pair must be aligned such that its image is coma-free, and the four pairs must be aligned such that their images are coincident. In addition, both the HRMA optical axis and focal point must be precisely known with respect to physical references on the HRMA. The alignment of the HRMA mirrors is measured by the HRMA Alignment Test System (HATS), which is an integral part of the tower facility. The HATS is configured as a double-pass, autocollimating Hartmann test where each mirror aperture is scanned to determine the state of alignment. This paper will describe the design and operation of the HATS.

An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids

PubMed Central

Li, Yushuang; Yang, Jiasheng; Zhang, Yi

2016-01-01

In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences. We then apply this method into the ND5 dataset consisting of the ND5 protein sequences of 9 species, and the F10 and G11 datasets representing two of the xylanases containing glycoside hydrolase families, i.e., families 10 and 11. As a result, our method achieves a correlation coefficient of 0.962 with the canonical protein sequence aligner ClustalW in the ND5 dataset, much higher than those of other 5 popular alignment-free methods. In addition, we successfully separate the xylanases sequences in the F10 family and the G11 family and illustrate that the F10 family is more heat stable than the G11 family, consistent with a few previous studies. Moreover, we prove mathematically an identity equation involving the Pseudo-Markov transition probability vector and the amino acids content ratio vector. PMID:27918587

Homology modeling of a Class A GPCR in the inactive conformation: A quantitative analysis of the correlation between model/template sequence identity and model accuracy.

PubMed

Costanzi, Stefano; Skorski, Matthew; Deplano, Alessandro; Habermehl, Brett; Mendoza, Mary; Wang, Keyun; Biederman, Michelle; Dawson, Jessica; Gao, Jia

2016-11-01

With the present work we quantitatively studied the modellability of the inactive state of Class A G protein-coupled receptors (GPCRs). Specifically, we constructed models of one of the Class A GPCRs for which structures solved in the inactive state are available, namely the β 2 AR, using as templates each of the other class members for which structures solved in the inactive state are also available. Our results showed a detectable linear correlation between model accuracy and model/template sequence identity. This suggests that the likely accuracy of the homology models that can be built for a given receptor can be generally forecasted on the basis of the available templates. We also probed whether sequence alignments that allow for the presence of gaps within the transmembrane domains to account for structural irregularities afford better models than the classical alignment procedures that do not allow for the presence of gaps within such domains. As our results indicated, although the overall differences are very subtle, the inclusion of internal gaps within the transmembrane domains has a noticeable a beneficial effect on the local structural accuracy of the domain in question. Copyright © 2016 Elsevier Inc. All rights reserved.

3D-Printing of Meso-structurally Ordered Carbon Fiber/Polymer Composites with Unprecedented Orthotropic Physical Properties

NASA Astrophysics Data System (ADS)

Lewicki, James P.; Rodriguez, Jennifer N.; Zhu, Cheng; Worsley, Marcus A.; Wu, Amanda S.; Kanarska, Yuliya; Horn, John D.; Duoss, Eric B.; Ortega, Jason M.; Elmer, William; Hensleigh, Ryan; Fellini, Ryan A.; King, Michael J.

2017-03-01

Here we report the first example of a class of additively manufactured carbon fiber reinforced composite (AMCFRC) materials which have been achieved through the use of a latent thermal cured aromatic thermoset resin system, through an adaptation of direct ink writing (DIW) 3D-printing technology. We have developed a means of printing high performance thermoset carbon fiber composites, which allow the fiber component of a resin and carbon fiber fluid to be aligned in three dimensions via controlled micro-extrusion and subsequently cured into complex geometries. Characterization of our composite systems clearly show that we achieved a high order of fiber alignment within the composite microstructure, which in turn allows these materials to outperform equivalently filled randomly oriented carbon fiber and polymer composites. Furthermore, our AM carbon fiber composite systems exhibit highly orthotropic mechanical and electrical responses as a direct result of the alignment of carbon fiber bundles in the microscale which we predict will ultimately lead to the design of truly tailorable carbon fiber/polymer hybrid materials having locally programmable complex electrical, thermal and mechanical response.