Structural Characterization of the Low-Molecular-Weight Heparin Dalteparin by Combining Different Analytical Strategies.

PubMed

Bisio, Antonella; Urso, Elena; Guerrini, Marco; de Wit, Pauline; Torri, Giangiacomo; Naggi, Annamaria

2017-06-24

A number of low molecular weight heparin (LMWH) products are available for clinical use and although all share a similar mechanism of action, they are classified as distinct drugs because of the different depolymerisation processes of the native heparin resulting in substantial pharmacokinetic and pharmacodynamics differences. While enoxaparin has been extensively investigated, little information is available regarding the LMWH dalteparin. The present study is focused on the detailed structural characterization of Fragmin ® by LC-MS and NMR applied both to the whole drug and to its enzymatic products. For a more in-depth approach, size homogeneous octasaccharide and decasaccharide components together with their fractions endowed with high or no affinity toward antithrombin were also isolated and their structural profiles characterized. The combination of different analytical strategies here described represents a useful tool for the assessment of batch-to-batch structural variability and for comparative evaluation of structural features of biosimilar products.

Synthesis and Characterization of Cerium(IV) Metallocenes

DOE PAGES

Sutton, Andrew; Clark, David Lewis; Scott, Brian Lindley; ...

2015-12-11

In this study, by applying a salt metathesis approach between Ce(OtBu 3) 2(NO 3) 2(THF) 2 and the potassium salts of mono- and ditrimethylsilyl substituted cyclopentadienes, we were able to isolate two new Ce(IV) metallocenes, including to the best of our knowledge, the first structurally characterized bis-cyclopentadiene Ce(IV) compound.

A Cross-Cultural Validation of Stage Development: A Rasch Re-Analysis of Longitudinal Socio-Moral Reasoning Data

ERIC Educational Resources Information Center

Boom, Jan; Wouters, Hans; Keller, Monika

2007-01-01

Kohlberg's characterization of moral development as displaying an invariant hierarchical order of structurally consistent stages is losing ground. However, by applying Rasch analysis, Dawson recently gave new interpretation and support to his characterization of stage development. Using Rasch models, we replicated and strengthened her findings in…

Polyvinylidene fluoride membranes probed by electrochemical impedance spectroscopy

NASA Astrophysics Data System (ADS)

Luo, Qi-Zhao; Huang, Qing; Chen, Zhe; Yao, Lei; Fu, Ping; Lin, Zhi-Dong

2018-06-01

Electrochemical impedance spectroscopy (EIS) has been applied to characterize the structure of polyvinylidene fluoride (PVDF) membranes. The characteristic frequency, which directly obtained from the original EIS data, was used to clarify the difference of the membranes’ structures. The experimental data indicated the equivalence between the characteristic frequency and the membrane resistance fitted from the equivalent circuit. The results evidenced that the characteristic frequency obtained directly from original EIS data without any fitting calculation can be used for in situ characterizing a membrane instead of the membrane resistance.

Biaxial deformation in high purity aluminum

DOE PAGES

Livescu, V.; Bingert, J. F.; Liu, C.; ...

2015-09-25

The convergence of multiple characterization tools has been applied to investigate the relationship of microstructure on damage evolution in high purity aluminum. The extremely coarse grain size of the disc-shaped sample provided a quasi-two dimensional structure from which the location of surface-measured features could be inferred. In particular, the role of pre-existing defects on damage growth was accessible due to the presence of casting porosity in the aluminum. Micro tomography, electron backscatter diffraction, and digital image correlation were applied to interrogate the sample in three dimensions. Recently micro-bulge testing apparatus was used to deform the pre-characterized disc of aluminum inmore » biaxial tension, and related analysis techniques were applied to map local strain fields. Subsequent post-mortem characterization of the failed sample was performed to correlate structure to damaged regions. We determined that strain localization and associated damage was most strongly correlated with grain boundary intersections and plastic anisotropy gradients between grains. Pre-existing voids played less of an apparent role than was perhaps initially expected. Finally, these combined techniques provide insight to the mechanism of damage initiation, propagation, and failure, along with a test bed for predictive damage models incorporating anisotropic microstructural effects.« less

Zero torque gear head wrench

NASA Technical Reports Server (NTRS)

Mcdougal, A. R.; Norman, R. M. (Inventor)

1976-01-01

A gear head wrench particularly suited for use in applying torque to bolts without transferring torsional stress to bolt-receiving structures is introduced. The wrench is characterized by a coupling including a socket, for connecting a bolt head with a torque multiplying gear train, provided within a housing having an annulus concentrically related to the socket and adapted to be coupled with a spacer interposed between the bolt head and the juxtaposed surface of the bolt-receiving structure for applying a balancing counter-torque to the spacer as torque is applied to the bolt head whereby the bolt-receiving structure is substantially isolated from torsional stress. As a result of the foregoing, the operator of the wrench is substantially isolated from any forces which may be imposed.

Simple method for the characterization of intense Laguerre-Gauss vector vortex beams

NASA Astrophysics Data System (ADS)

Allahyari, E.; JJ Nivas, J.; Cardano, F.; Bruzzese, R.; Fittipaldi, R.; Marrucci, L.; Paparo, D.; Rubano, A.; Vecchione, A.; Amoruso, S.

2018-05-01

We report on a method for the characterization of intense, structured optical fields through the analysis of the size and surface structures formed inside the annular ablation crater created on the target surface. In particular, we apply the technique to laser ablation of crystalline silicon induced by femtosecond vector vortex beams. We show that a rapid direct estimate of the beam waist parameter is obtained through a measure of the crater radii. The variation of the internal and external radii of the annular crater as a function of the laser pulse energy, at fixed number of pulses, provides another way to evaluate the beam spot size through numerical fitting of the obtained experimental data points. A reliable estimate of the spot size is of paramount importance to investigate pulsed laser-induced effects on the target material. Our experimental findings offer a facile way to characterize focused, high intensity complex optical vector beams which are more and more applied in laser-matter interaction experiments.

Performance of ZnO based piezo-generators under controlled compression

NASA Astrophysics Data System (ADS)

Tao, Ran; Parmar, Mitesh; Ardila, Gustavo; Oliveira, Paulo; Marques, Daniel; Montès, Laurent; Mouis, Mireille

2017-06-01

This paper reports on the fabrication and characterization of ZnO based vertically integrated nanogenerator (VING) devices under controlled compression. The basic NG structure is a composite material integrating hydrothermally grown vertical piezoelectric zinc oxide (ZnO) nanowires (NWs) into a dielectric matrix (PMMA). A specific characterization set-up has been developed to control the applied compression and the perpendicularity of the applied force on the devices. The role of different fabrication parameters has been evaluated experimentally and compared with previously reported theoretical models, including the thickness of the top PMMA layer and the density of the NWs array in the matrix. Finally, the performance of the VING structure has been evaluated experimentally for different resistive loads obtaining a power density of 85 μW cm-3 considering only the active layer of the device. This has been compared to the performance of a commercial bulk layer of PZT (25 μW cm-3) under the same applied force of 5 N.

Characterization of a subwavelength-scale 3D void structure using the FDTD-based confocal laser scanning microscopic image mapping technique.

PubMed

Choi, Kyongsik; Chon, James W; Gu, Min; Lee, Byoungho

2007-08-20

In this paper, a simple confocal laser scanning microscopic (CLSM) image mapping technique based on the finite-difference time domain (FDTD) calculation has been proposed and evaluated for characterization of a subwavelength-scale three-dimensional (3D) void structure fabricated inside polymer matrix. The FDTD simulation method adopts a focused Gaussian beam incident wave, Berenger's perfectly matched layer absorbing boundary condition, and the angular spectrum analysis method. Through the well matched simulation and experimental results of the xz-scanned 3D void structure, we first characterize the exact position and the topological shape factor of the subwavelength-scale void structure, which was fabricated by a tightly focused ultrashort pulse laser. The proposed CLSM image mapping technique based on the FDTD can be widely applied from the 3D near-field microscopic imaging, optical trapping, and evanescent wave phenomenon to the state-of-the-art bio- and nanophotonics.

High resolution Talbot self-imaging applied to structural characterization of self-assembled monolayers of microspheres.

PubMed

Garcia-Sucerquia, J; Alvarez-Palacio, D C; Kreuzer, H J

2008-09-10

We report the observation of the Talbot self-imaging effect in high resolution digital in-line holographic microscopy (DIHM) and its application to structural characterization of periodic samples. Holograms of self-assembled monolayers of micron-sized polystyrene spheres are reconstructed at different image planes. The point-source method of DIHM and the consequent high lateral resolution allows the true image (object) plane to be identified. The Talbot effect is then exploited to improve the evaluation of the pitch of the assembly and to examine defects in its periodicity.

Method and system for automated on-chip material and structural certification of MEMS devices

DOEpatents

Sinclair, Michael B.; DeBoer, Maarten P.; Smith, Norman F.; Jensen, Brian D.; Miller, Samuel L.

2003-05-20

A new approach toward MEMS quality control and materials characterization is provided by a combined test structure measurement and mechanical response modeling approach. Simple test structures are cofabricated with the MEMS devices being produced. These test structures are designed to isolate certain types of physical response, so that measurement of their behavior under applied stress can be easily interpreted as quality control and material properties information.

Pinpointing chiral structures with front-back polarized neutron reflectometry.

PubMed

O'Donovan, K V; Borchers, J A; Majkrzak, C F; Hellwig, O; Fullerton, E E

2002-02-11

A new development in spin-polarized neutron reflectometry enables us to more fully characterize the nucleation and growth of buried domain walls in layered magnetic materials. We applied this technique to a thin-film exchange-spring magnet. After first measuring the reflectivity with the neutrons striking the front, we measure with the neutrons striking the back. Simultaneous fits are sensitive to the presence of spiral spin structures. The technique reveals previously unresolved features of field-dependent domain walls in exchange-spring systems and has sufficient generality to apply to a variety of magnetic systems.

High-Temperature Strain Sensing for Aerospace Applications

NASA Technical Reports Server (NTRS)

Piazza, Anthony; Richards, Lance W.; Hudson, Larry D.

2008-01-01

Thermal protection systems (TPS) and hot structures are utilizing advanced materials that operate at temperatures that exceed abilities to measure structural performance. Robust strain sensors that operate accurately and reliably beyond 1800 F are needed but do not exist. These shortcomings hinder the ability to validate analysis and modeling techniques and hinders the ability to optimize structural designs. This presentation examines high-temperature strain sensing for aerospace applications and, more specifically, seeks to provide strain data for validating finite element models and thermal-structural analyses. Efforts have been made to develop sensor attachment techniques for relevant structural materials at the small test specimen level and to perform laboratory tests to characterize sensor and generate corrections to apply to indicated strains. Areas highlighted in this presentation include sensors, sensor attachment techniques, laboratory evaluation/characterization of strain measurement, and sensor use in large-scale structures.

Characterizing the Atomic Structure in Low Concentrations of Weakly Ordered, Weakly Scattering Materials Using the Pair Distribution Function

NASA Astrophysics Data System (ADS)

Terban, Maxwell W.

Nanoscale structural characterization is critical to understanding the physical underpinnings of properties and behavior in materials with technological applications. The work herein shows how the pair distribution function technique can be applied to x-ray total scattering data for material systems which weakly scatter x-rays, a typically difficult task due to the poor signal-to-noise obtained from the structures of interest. Characterization and structural modeling are demonstrated for a variety of molecular and porous systems, along with the detection and characterization of disordered, minority phases and components. In particular, reliable detection and quantitative analysis are demonstrated for nanocrystals of an active pharmaceutical ingredient suspended in dilute solution down to a concentration of 0.25 wt. %, giving a practical limit of detection for ordered nanoscale phases within a disordered matrix. Further work shows that minority nanocrystalline phases can be detected, fingerprinted, and modeled for mixed crystalline and amorphous systems of small molecules and polymers. The crystallization of amorphous lactose is followed under accelerated aging conditions. Melt quenching is shown to produce a different local structure than spray drying or freeze drying, along with increased resistance to crystallization. The initial phases which form in the spray dried formulation are identified as a mixture of polymorphs different from the final alpha-lactose monohydrate form. Hard domain formation in thermoplastic polyurethanes is also characterized as a function of methylene diphenyl diisocyanate and butanediol component ratio, showing that distinct and different hard phase structures can form and are solved by indexing with structures derived from molecular dynamics relaxation. In both cases, phase fractions can be quantified in the mixed crystalline and amorphous systems by fitting with both standards or structure models. Later chapters, demonstrate pair distribution characterization of particle incorporation, structure, and synthesis of nanoporous materials. Nanoparticle size distributions are extracted from platinum nanoparticles nucleating within a zeolite matrix through structural modeling, and validated by transmission electron microscope studies. The structure of zirconium phosphonate-phosphate unconventional metal organic framework is determined to consist of turbostratically disordered nanocrystalline layers of Zr-phenylphosphonate, and the local environment of terbium intercalated between the layers is found to resemble the local environment in scheelite-type terbium phosphate. Finally, the early stages of reaction between aqueous zinc dinitrate hexahydrate and methanolic 2-methylimidazole are characterized using in situ total scattering measurements, showing that secondary building units of tetrahedrally coordinated by 2-methylimidazole initially form upon reaction. Overall, the methodologies are developed and applied toward phase detection, identification, solution, and behavior in pharmaceuticals, polymers, and nanoporous materials along with advice for carrying out experiments and analysis on such materials such that they can be extended to other similar systems.

Nondestructive techniques for characterizing mechanical properties of structural materials: An overview

NASA Technical Reports Server (NTRS)

Vary, A.; Klima, S. J.

1985-01-01

An overview of nondestructive evaluation (NDE) is presented to indicate the availability and application potentials of techniques for quantitative characterization of the mechanical properties of structural materials. The purpose is to review NDE techniques that go beyond the usual emphasis on flaw detection and characterization. Discussed are current and emerging NDE techniques that can verify and monitor entrinsic properties (e.g., tensile, shear, and yield strengths; fracture toughness, hardness, ductility; elastic moduli) and underlying microstructural and morphological factors. Most of the techniques described are, at present, neither widely applied nor widely accepted in commerce and industry because they are still emerging from the laboratory. The limitations of the techniques may be overcome by advances in applications research and instrumentation technology and perhaps by accommodations for their use in the design of structural parts.

Nondestructive Evaluation Techniques for Development and Characterization of Carbon Nanotube Based Superstructures

NASA Technical Reports Server (NTRS)

Wincheski, Buzz; Kim, Jae-Woo; Sauti, Godfrey; Wainwright, Elliot; Williams, Phillip; Siochi, Emile J.

2014-01-01

Recently, multiple commercial vendors have developed capability for the production of large-scale quantities of high-quality carbon nanotube sheets and yarns. While the materials have found use in electrical shielding applications, development of structural systems composed of a high volume fraction of carbon nanotubes is still lacking. A recent NASA program seeks to address this by prototyping a structural nanotube composite with strength-toweight ratio exceeding current state-of-the-art carbon fiber composites. Commercially available carbon nanotube sheets, tapes, and yarns are being processed into high volume fraction carbon nanotube-polymer nanocomposites. Nondestructive evaluation techniques have been applied throughout this development effort for material characterization and process control. This paper will report on the progress of these efforts, including magnetic characterization of residual catalyst content, Raman scattering characterization of nanotube diameter, defect ratio, and nanotube strain, and polarized Raman scattering for characterization of nanotube alignment.

From protein structure to function via single crystal optical spectroscopy

PubMed Central

Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

2015-01-01

The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. PMID:25988179

Hierarchical structures of amorphous solids characterized by persistent homology

PubMed Central

Hiraoka, Yasuaki; Nakamura, Takenobu; Hirata, Akihiko; Escolar, Emerson G.; Matsue, Kaname; Nishiura, Yasumasa

2016-01-01

This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods. PMID:27298351

Physical interpretation and development of ultrasonic nondestructive evaluation techniques applied to the quantitative characterization of textile composite materials

NASA Technical Reports Server (NTRS)

Miller, James G.

1994-01-01

In this Progress Report, we describe our continuing research activities concerning the development and implementation of advanced ultrasonic nondestructive evaluation methods applied to the inspection and characterization of complex composite structures. We explore the feasibility of implementing medical linear array imaging technology as a viable ultrasonic-based nondestructive evaluation method to inspect and characterize complex materials. As an initial step toward the application of linear array imaging technology to the interrogation of a wide range of complex composite structures, we present images obtained using an unmodified medical ultrasonic imaging system of two epoxy-bonded aluminum plate specimens, each with intentionally disbonded regions. These images are compared with corresponding conventional ultrasonic contact transducer measurements in order to assess whether these images can detect disbonded regions and provide information regarding the nature of the disbonded region. We present a description of a standoff/delay fixture which has been designed, constructed, and implemented on a Hewlett-Packard SONOS 1500 medical imaging system. This standoff/delay fixture, when attached to a 7.5 MHz linear array probe, greatly enhances our ability to interrogate flat plate specimens. The final section of this Progress Report describes a woven composite plate specimen that has been specially machined to include intentional flaws. This woven composite specimen will allow us to assess the feasibility of applying linear array imaging technology to the inspection and characterization of complex textile composite materials. We anticipate the results of this on-going investigation may provide a step toward the development of a rapid, real-time, and portable method of ultrasonic inspection and characterization based on linear array technology.

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

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

Pidatala, Venkataramana R.; Mahboubi, Amir; Mortimer, Jenny C.

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharidemore » fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.« less

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE.

PubMed

Pidatala, Venkataramana R; Mahboubi, Amir; Mortimer, Jenny C

2017-10-16

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

DOE PAGES

Pidatala, Venkataramana R.; Mahboubi, Amir; Mortimer, Jenny C.

2017-10-16

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharidemore » fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.« less

Can enzyme engineering benefit from the modulation of protein motions? Lessons learned from NMR relaxation dispersion experiments.

PubMed

Doucet, Nicolas

2011-04-01

Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed evolution and computational methods have paved the way to exciting engineering examples and are now offering a new perspective on the structural requirements of enzyme activity. However, these structure-function analyses are usually guided by the time-averaged static models offered by enzyme crystal structures, which often fail to describe the functionally relevant 'invisible states' adopted by proteins in space and time. To alleviate such limitations, NMR relaxation dispersion experiments coupled to mutagenesis studies have recently been applied to the study of enzyme catalysis, effectively complementing 'structure-function' analyses with 'flexibility-function' investigations. In addition to offering quantitative, site-specific information to help characterize residue motion, these NMR methods are now being applied to enzyme engineering purposes, providing a powerful tool to help characterize the effects of controlling long-range networks of flexible residues affecting enzyme function. Recent advancements in this emerging field are presented here, with particular attention to mutagenesis reports highlighting the relevance of NMR relaxation dispersion tools in enzyme engineering.

Simulation assisted characterization of kaolinite-methanol intercalation complexes synthesized using cost-efficient homogenization method

NASA Astrophysics Data System (ADS)

Makó, Éva; Kovács, András; Ható, Zoltán; Kristóf, Tamás

2015-12-01

Recent experimental and simulation findings with kaolinite-methanol intercalation complexes raised the question of the existence of more stable structures in wet and dry state, which has not been fully cleared up yet. Experimental and molecular simulation analyses were used to investigate different types of kaolinite-methanol complexes, revealing their real structures. Cost-efficient homogenization methods were applied to synthesize the kaolinite-dimethyl sulfoxide and kaolinite-urea pre-intercalation complexes of the kaolinite-methanol ones. The tested homogenization method required an order of magnitude lower amount of reagents than the generally applied solution method. The influence of the type of pre-intercalated molecules and of the wetting or drying (at room temperature and at 150 °C) procedure on the intercalation was characterized experimentally by X-ray diffraction and thermal analysis. Consistent with the suggestion from the present simulations, 1.12-nm and 0.83-nm stable kaolinite-methanol complexes were identified. For these complexes, our molecular simulations predict either single-layered structures of mobile methanol/water molecules or non-intercalated structures of methoxy-functionalized kaolinite. We found that the methoxy-modified kaolinite can easily be intercalated by liquid methanol.

Structural characterization of sol-gel derived oxide nanostuctures using synchrotron x-ray techniques

NASA Astrophysics Data System (ADS)

Sun, Tao

Ceramic oxides possess extraordinarily rich functionalities. With the advent of nanofabrication techniques, it is now possible to grow nanostructured oxides with precise control of composition, morphology, and microstructure, which has re-vitalized the research in the field of traditional ceramics. The unexpected behavior and enhanced properties of oxide nanostructures have been extensively reported. However, knowledge about the underlying mechanisms as well as structural implications is still quite limited. Therefore, it is imperative to develop and employ sophisticated characterization tools for unraveling the structure-property relationships for oxide nanostructures. The present thesis work aims at addressing the critical issues associated with fabrication, and more importantly, structural characterization of functional oxide nanostructures. The dissertation starts with introducing the strategy for synthesizing phase-pure and highly controlled oxide nanostructures using sol-gel deposition and an innovative approach called "soft" electron beam lithography. Some specific oxides are chosen for the present study, such as BiFeO3, CoFe2O4, and SnO2, because of their scientific and technological significance. Subsequent to fabrication of tailored oxide nanostructures, advanced synchrotron x-ray scattering techniques have been applied for structural characterization. The nucleation and growth behavior of BiFeO3 thin film was investigated using in situ grazing-incidence small-angle x-ray scattering (GISAXS) technique. The results reveal that the kinetics for early-stage nuclei growth are governed by the oriented-attachment model. Moreover, the porous structures of undoped and Pd-doped semiconducting SnOx thin films were quantitatively characterized using GISAXS. By correlating the structural parameters with H2 sensitivity of SnOx films, it is found out that the microstructure of doped film is favorable for gas sensing, but it is not the major reason for the overall property enhancement arising from the dopant. Furthermore, a novel method based on scanning x-ray microdiffraction technique is proposed and applied for probing the strain distribution around individual CoFe2O4 nanoline epitaxially grown on MgO substrate. It is demonstrated that x-ray diffuse scattering intensity can be used to gauge the edge-induced subtle strain variation. The dissertation underscores the need for quantitative understanding of structural underpinning in the mechanisms and behavior of oxide nanostructures, and highlights the role of advanced synchrotron x-ray scattering approaches.

Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation

PubMed Central

Sanderson, Jean; Sudoyo, Herawati; Karafet, Tatiana M.; Hammer, Michael F.; Cox, Murray P.

2015-01-01

Admixture between long-separated populations is a defining feature of the genomes of many species. The mosaic block structure of admixed genomes can provide information about past contact events, including the time and extent of admixture. Here, we describe an improved wavelet-based technique that better characterizes ancestry block structure from observed genomic patterns. principal components analysis is first applied to genomic data to identify the primary population structure, followed by wavelet decomposition to develop a new characterization of local ancestry information along the chromosomes. For testing purposes, this method is applied to human genome-wide genotype data from Indonesia, as well as virtual genetic data generated using genome-scale sequential coalescent simulations under a wide range of admixture scenarios. Time of admixture is inferred using an approximate Bayesian computation framework, providing robust estimates of both admixture times and their associated levels of uncertainty. Crucially, we demonstrate that this revised wavelet approach, which we have released as the R package adwave, provides improved statistical power over existing wavelet-based techniques and can be used to address a broad range of admixture questions. PMID:25852078

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms

PubMed Central

Olson, Wilma K.

2014-01-01

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides. PMID:24791158

Structural, optical and field emission properties of urchin-shaped ZnO nanostructures.

PubMed

Al-Heniti, Saleh; Umar, Ahmad

2013-01-01

In this work, well-crystallized urchin-shaped ZnO structures were synthesized on silicon substrate by simple non-catalytic thermal evaporation process by using metallic zinc powder in the presence of oxygen as source materials for zinc and oxygen, respectively. The synthesized ZnO structures were characterized in detail in terms of their morphological, structural, optical and field emission properties. The detailed morphological investigations revealed that the synthesized structures possess urchin-shape and grown in high-density over the substrate surface. The detailed structural and optical characterizations revealed that the synthesized urchin-shaped ZnO structures are well-crystallized and exhibiting good optical properties. The field emission analysis for urchin-shaped ZnO structures exhibits a turn-on field of 4.6 V/microm. The emission current density reached to 0.056 mA/cm2 at an applied electrical field of 6.4 V/microm and shows no saturation. The calculated field enhancement factor 'beta', from the F-N plot, was found to be approximately 2.2 x 10(3).

Thermal Analysis by Structural Characterization as a Method for Assessing Heterogeneity in Complex Solid Pharmaceutical Dosage Forms.

PubMed

Alhijjaj, Muqdad; Reading, Mike; Belton, Peter; Qi, Sheng

2015-11-03

Characterizing inter- and intrasample heterogeneity of solid and semisolid pharmaceutical products is important both for rational design of dosage forms and subsequent quality control during manufacture; however, most pharmaceutical products are multicomponent formulations that are challenging in this regard. Thermal analysis, in particular differential scanning calorimetry, is commonly used to obtain structural information, such as degree of crystallinity, or identify the presence of a particular polymorph, but the results are an average over the whole sample; it cannot directly provide information about the spatial distribution of phases. This study demonstrates the use of a new thermo-optical technique, thermal analysis by structural characterization (TASC), that can provide spatially resolved information on thermal transitions by applying a novel algorithm to images acquired by hot stage microscopy. We determined that TASC can be a low cost, relatively rapid method of characterizing heterogeneity and other aspects of structure. In the examples studied, it was found that high heating rates enabled screening times of 3-5 min per sample. In addition, this study demonstrated the higher sensitivity of TASC for detecting the metastable form of polyethylene glycol (PEG) compared to conventional differential scanning calorimetry (DSC). This preliminary work suggests that TASC will be a worthwhile additional tool for characterizing a broad range of materials.

Characterizing the evolution of climate networks

NASA Astrophysics Data System (ADS)

Tupikina, L.; Rehfeld, K.; Molkenthin, N.; Stolbova, V.; Marwan, N.; Kurths, J.

2014-06-01

Complex network theory has been successfully applied to understand the structural and functional topology of many dynamical systems from nature, society and technology. Many properties of these systems change over time, and, consequently, networks reconstructed from them will, too. However, although static and temporally changing networks have been studied extensively, methods to quantify their robustness as they evolve in time are lacking. In this paper we develop a theory to investigate how networks are changing within time based on the quantitative analysis of dissimilarities in the network structure. Our main result is the common component evolution function (CCEF) which characterizes network development over time. To test our approach we apply it to several model systems, Erdős-Rényi networks, analytically derived flow-based networks, and transient simulations from the START model for which we control the change of single parameters over time. Then we construct annual climate networks from NCEP/NCAR reanalysis data for the Asian monsoon domain for the time period of 1970-2011 CE and use the CCEF to characterize the temporal evolution in this region. While this real-world CCEF displays a high degree of network persistence over large time lags, there are distinct time periods when common links break down. This phasing of these events coincides with years of strong El Niño/Southern Oscillation phenomena, confirming previous studies. The proposed method can be applied for any type of evolving network where the link but not the node set is changing, and may be particularly useful to characterize nonstationary evolving systems using complex networks.

Computer Simulations of Intrinsically Disordered Proteins

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Chatterjee, Prathit; Ham, Sihyun

2017-05-01

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

Laser-Induced Breakdown Spectroscopy (LIBS) for Monitoring the Formation of Hydroxyapatite Porous Layers

PubMed Central

Sola, Daniel; Paulés, Daniel; Grima, Lorena

2017-01-01

Laser-induced breakdown spectroscopy (LIBS) is applied to characterize the formation of porous hydroxyapatite layers on the surface of 0.8CaSiO3-0.2Ca3(PO4)2 biocompatible eutectic glass immersed in simulated body fluid (SBF). Compositional and structural characterization analyses were also conducted by field emission scanning electron microscopy (FESEM), energy dispersive X-ray spectroscopy (EDX), and micro-Raman spectroscopy. PMID:29211006

Metrology in health: a pilot study

NASA Astrophysics Data System (ADS)

Ferreira, M.; Matos, A.

2015-02-01

The purpose of this paper is to identify and analyze some relevant issues which arise when the concept of metrological traceability is applied to health care facilities. Discussion is structured around the results that were obtained through a characterization and comparative description of the practices applied in 45 different Portuguese health entities. Following a qualitative exploratory approach, the information collected was the support for the initial research hypotheses and the development of the questionnaire survey. It was also applied a quantitative methodology that included a descriptive and inferential statistical analysis of the experimental data set.

Fragmentation study of iridoid glycosides including epimers by liquid chromatography-diode array detection/electrospray ionization mass spectrometry and its application in metabolic fingerprint analysis of Gardenia jasminoides Ellis.

PubMed

Zhou, Tingting; Liu, Hua; Wen, Jun; Fan, Guorong; Chai, Yifeng; Wu, Yutian

2010-09-15

A high-performance liquid chromatography-diode array detection/electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS) method was applied to the characterization of ten iridoid glycosides in Gardenia jasminoides Ellis, a traditional Chinese medicine. During the process of structural elucidation, two groups of isomers including two epimers were structurally characterized and differentiated according to their distinctive fragmentation patterns which were closely related to their isomeric differentiations. Subsequently, the major compounds were purified by multi-dimensional chromatography and semi-preparative HPLC and the structure identification was confirmed with NMR techniques. The major fragmentation pathways of iridoid glycosides in Gardenia jasminoides Ellis obtained through the MS data were schemed systematically, which provided the best sensitivity and specificity for characterization of the iridoid glycosides especially the isomers so far. Based on the fragmentation patterns of iridoid glycosides concluded, seven major iridoid glycosides were characterized in rat plasma after intravenous administration of Gardenia jasminoides Ellis. Copyright 2010 John Wiley & Sons, Ltd.

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

PubMed Central

Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

2013-01-01

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

Structural analysis of cell wall polysaccharides using PACE

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

Mortimer, Jennifer C.

The plant cell wall is composed of many complex polysaccharides. The composition and structure of the polysaccharides affect various cell properties including cell shape, cell function and cell adhesion. Many techniques to characterize polysaccharide structure are complicated, requiring expensive equipment and specialized operators e.g. NMR, MALDI-MS. PACE (Polysaccharide Analysis using Carbohydrate gel Electrophoresis) uses a simple, rapid technique to analyze polysaccharide quantity and structure (Goubet et al. 2002). Whilst the method here describes xylan analysis, it can be applied (by use of the appropriate glycosyl hydrolase) to any cell wall polysaccharide.

A Novel Physical Sensing Principle for Liquid Characterization Using Paper-Based Hygro-Mechanical Systems (PB-HMS).

PubMed

Perez-Cruz, Angel; Stiharu, Ion; Dominguez-Gonzalez, Aurelio

2017-07-20

In recent years paper-based microfluidic systems have emerged as versatile tools for developing sensors in different areas. In this work; we report a novel physical sensing principle for the characterization of liquids using a paper-based hygro-mechanical system (PB-HMS). The PB-HMS is formed by the interaction of liquid droplets and paper-based mini-structures such as cantilever beams. The proposed principle takes advantage of the hygroscopic properties of paper to produce hygro-mechanical motion. The dynamic response of the PB-HMS reveals information about the tested liquid that can be applied to characterize certain properties of liquids. A suggested method to characterize liquids by means of the proposed principle is introduced. The experimental results show the feasibility of such a method. It is expected that the proposed principle may be applied to sense properties of liquids in different applications where both disposability and portability are of extreme importance.

Fabrication of submicron proteinaceous structures by direct laser writing

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

Serien, Daniela; Takeuchi, Shoji, E-mail: takeuchi@iis.u-tokyo.ac.jp; ERATO Takeuchi Biohybrid Innovation Project, Japan Science and Technology Agency, 4-6-1 Komaba, Meguro-ku, 153-8505 Tokyo

In this paper, we provide a characterization of truly free-standing proteinaceous structures with submicron feature sizes depending on the fabrication conditions by model-based analysis. Protein cross-linking of bovine serum albumin is performed by direct laser writing and two-photon excitation of flavin adenine dinucleotide. We analyze the obtainable fabrication resolution and required threshold energy for polymerization. The applied polymerization model allows prediction of fabrication conditions and resulting fabrication size, alleviating the application of proteinaceous structure fabrication.

Functional approximation using artificial neural networks in structural mechanics

NASA Technical Reports Server (NTRS)

Alam, Javed; Berke, Laszlo

1993-01-01

The artificial neural networks (ANN) methodology is an outgrowth of research in artificial intelligence. In this study, the feed-forward network model that was proposed by Rumelhart, Hinton, and Williams was applied to the mapping of functions that are encountered in structural mechanics problems. Several different network configurations were chosen to train the available data for problems in materials characterization and structural analysis of plates and shells. By using the recall process, the accuracy of these trained networks was assessed.

Structural characterization of a first-generation articulated-truss joint for space crane application

NASA Technical Reports Server (NTRS)

Sutter, Thomas R.; Wu, K. Chauncey; Riutort, Kevin T.; Laufer, Joseph B.; Phelps, James E.

1992-01-01

A first-generation space crane articulated-truss joint was statically and dynamically characterized in a configuration that approximated an operational environment. The articulated-truss joint was integrated into a test-bed for structural characterization. Static characterization was performed by applying known loads and measuring the corresponding deflections to obtain load-deflection curves. Dynamic characterization was performed using modal testing to experimentally determine the first six mode shapes, frequencies, and modal damping values. Static and dynamic characteristics were also determined for a reference truss that served as a characterization baseline. Load-deflection curves and experimental frequency response functions are presented for the reference truss and the articulated-truss joint mounted in the test-bed. The static and dynamic experimental results are compared with analytical predictions obtained from finite element analyses. Load-deflection response is also presented for one of the linear actuators used in the articulated-truss joint. Finally, an assessment is presented for the predictability of the truss hardware used in the reference truss and articulated-truss joint based upon hardware stiffness properties that were previously obtained during the Precision Segmented Reflector (PSR) Technology Development Program.

Application of X-ray micro-CT for micro-structural characterization of APCVD deposited SiC coatings on graphite conduit.

PubMed

Agrawal, A K; Sarkar, P S; Singh, B; Kashyap, Y S; Rao, P T; Sinha, A

2016-02-01

SiC coatings are commonly used as oxidation protective materials in high-temperature applications. The operational performance of the coating depends on its microstructure and uniformity. This study explores the feasibility of applying tabletop X-ray micro-CT for the micro-structural characterization of SiC coating. The coating is deposited over the internal surface of pipe structured graphite fuel tube, which is a prototype of potential components of compact high-temperature reactor (CHTR). The coating is deposited using atmospheric pressure chemical vapor deposition (APCVD) and properties such as morphology, porosity, thickness variation are evaluated. Micro-structural differences in the coating caused by substrate distance from precursor inlet in a CVD reactor are also studied. The study finds micro-CT a potential tool for characterization of SiC coating during its future course of engineering. We show that depletion of reactants at larger distances causes development of larger pores in the coating, which affects its morphology, density and thickness. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterization of applied fields for ion mobility in traveling wave based structures for lossless ion manipulations (SLIM)

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

Hamid, Ahmed M.; Prabhakaran Nair Syamala Amma, Aneesh; Garimella, Venkata BS

2018-03-21

Ion mobility (IM) is rapidly gaining attention for the analysis of biomolecules due to the ability to distinguish the shapes of ions. However, conventional constant electric field drift tube IM has limited resolving power, constrained by practical limitations on the path length and maximum applied voltage. The implementation of traveling waves (TW) in IM removes the latter limitation, allowing higher resolution to be achieved using extended path lengths. These can be readily obtainable in structures for lossless ion manipulations (SLIM), which are fabricated from electric fields that are generated by appropriate potentials applied to arrays of electrodes patterned on twomore » parallel surfaces. In this work we have investigated the relationship between the various SLIM variables, such as electrode dimensions, inter-surface gap, and the TW applied voltages, that directly impact the fields experienced by ions. Ion simulation and theoretical calculations have been utilized to understand the dependence of SLIM geometry and effective electric field. The variables explored impact both ion confinement and the observed IM resolution in Structures for Lossless Ion Manipulations (SLIM) modules.« less

Characterization of applied fields for ion mobility separations in traveling wave based structures for lossless ion manipulations (SLIM)

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

Hamid, Ahmed M.; Prabhakaran, Aneesh; Garimella, Sandilya V. B.

Ion mobility (IM) is rapidly gaining attention for the analysis of biomolecules due to the ability to distinguish the shapes of ions. However, conventional constant electric field drift tube IM has limited resolving power, constrained by practical limitations on the path length and maximum applied voltage. The implementation of traveling waves (TW) in IM removes the latter limitation, allowing higher resolution to be achieved using extended path lengths. These can be readily obtainable in structures for lossless ion manipulations (SLIM), which are fabricated from electric fields that are generated by appropriate potentials applied to arrays of electrodes patterned on twomore » parallel surfaces. In this work we have investigated the relationship between the various SLIM variables, such as electrode dimensions, inter-surface gap, and the TW applied voltages, that directly impact the fields experienced by ions. Ion simulation and theoretical calculations have been utilized to understand the dependence of SLIM geometry and effective electric field. The variables explored impact both ion confinement and the observed IM resolution in Structures for Lossless Ion Manipulations (SLIM) modules.« less

Comparative analysis of the structure of carbon materials relevant in combustion.

PubMed

Apicella, B; Barbella, R; Ciajolo, A; Tregrossi, A

2003-06-01

The determination of the structure of carbon materials is an analytical problem that join the research scientific communities involved in the chemical characterization of heavy fuel-derived products (heavy fuel oils, coal-derived fuels, shale oil, etc.) and of carbon materials (polycyclic aromatic compounds, tar, soot) produced in many combustion processes. The knowledge of the structure of these "difficult" fuels and of the carbon materials produced by incomplete combustion is relevant to research for the best low-environmental impact operation of combustion systems; but an array of many analytical and spectroscopic tools are necessary, and often not sufficient, to attempt the characterization of such complex products and in particular to determine the distribution of molecular masses. In this paper the size exclusion chromatography using N-methyl-pyrrolidinone as eluent has been applied for the characterization of different carbon materials starting from typical carbon species, commercially available like polyacenaphthylene, carbon black, naphthalene pitch up to combustion products like soot and soot extract collected in fuel-rich combustion systems. Two main fractions were detected, separated and molecular weights (MWs) determined by comparison with polystyrene standards: a first fraction consisted of particles with very large molecular masses (>100000 u); a second fraction consisted of species in a relatively small MW range (200-600 u). The distribution of these fractions changes in dependence on the carbon sample characteristics. Fluorescence spectroscopy applied on the fractions separated by size-exclusion chromatography has been used and comparatively interpreted giving indications on the differences and similarities in chemical structure of such different materials.

Quantitative analysis of nano-pore geomaterials and representative sampling for digital rock physics

NASA Astrophysics Data System (ADS)

Yoon, H.; Dewers, T. A.

2014-12-01

Geomaterials containing nano-pores (e.g., shales and carbonate rocks) have become increasingly important for emerging problems such as unconventional gas and oil resources, enhanced oil recovery, and geologic storage of CO2. Accurate prediction of coupled geophysical and chemical processes at the pore scale requires realistic representation of pore structure and topology. This is especially true for chalk materials, where pore networks are small and complex, and require characterization at sub-micron scale. In this work, we apply laser scanning confocal microscopy to characterize pore structures and microlithofacies at micron- and greater scales and dual focused ion beam-scanning electron microscopy (FIB-SEM) for 3D imaging of nanometer-to-micron scale microcracks and pore distributions. With imaging techniques advanced for nano-pore characterization, a problem of scale with FIB-SEM images is how to take nanometer scale information and apply it to the thin-section or larger scale. In this work, several texture characterization techniques including graph-based spectral segmentation, support vector machine, and principal component analysis are applied for segmentation clusters represented by 1-2 FIB-SEM samples per each cluster. Geometric and topological properties are analyzed and lattice-Boltzmann method (LBM) is used to obtain permeability at several different scales. Upscaling of permeability to the Darcy scale (e.g., the thin-section scale) with image dataset will be discussed with emphasis on understanding microfracture-matrix interaction, representative volume for FIB-SEM sampling, and multiphase flow and reactive transport. Funding from the DOE Basic Energy Sciences Geosciences Program is gratefully acknowledged. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.

PubMed

Kimura, S Roy; Hu, Hai Peng; Ruvinsky, Anatoly M; Sherman, Woody; Favia, Angelo D

2017-06-26

In recent years, molecular dynamics simulations of proteins in explicit mixed solvents have been applied to various problems in protein biophysics and drug discovery, including protein folding, protein surface characterization, fragment screening, allostery, and druggability assessment. In this study, we perform a systematic study on how mixtures of organic solvent probes in water can reveal cryptic ligand binding pockets that are not evident in crystal structures of apo proteins. We examine a diverse set of eight PDB proteins that show pocket opening induced by ligand binding and investigate whether solvent MD simulations on the apo structures can induce the binding site observed in the holo structures. The cosolvent simulations were found to induce conformational changes on the protein surface, which were characterized and compared with the holo structures. Analyses of the biological systems, choice of probes and concentrations, druggability of the resulting induced pockets, and application to drug discovery are discussed here.

Preparation and Characterization of Various Poly(ether ether ketone) Containing Imidazolium Moiety for Anion Exchange Membrane Fuel Cell Application.

PubMed

Lee, Byeol-Nim; Son, Tae Yang; Park, Chi Hoon; Kim, Tae Hyun; Nam, Sang Yong

2018-09-01

In this study, various poly(ether ether ketone) were synthesized using three different monomers and the imidazolium group was introduced into synthesized poly(ether ether ketone)s by using substitution reaction. Synthesized polymers were used to prepare anion exchange membranes and to evaluate its properties. Thermal, chemical and structural properties were carried out using thermogravimetric analysis, nuclear magnetic resonance. The anion exchange membranes with different imidazolium moieties were characterized by several different analytical techniques such as water up take, ion exchange capacity, hydroxide conductivity for checking the possibility to apply the anion exchange membrane fuel cell. Consequently, results of characterization were studied to understand the correlation between stabilities of the membrane and functional group and polymer backbone structures. And we confirm membrane performance was improved by increasing imidazolium cation groups.

Synthesis and structural characterization of bulk Sb2Te3 single crystal

NASA Astrophysics Data System (ADS)

Sultana, Rabia; Gahtori, Bhasker; Meena, R. S.; Awana, V. P. S.

2018-05-01

We report the growth and characterization of bulk Sb2Te3 single crystal synthesized by the self flux method via solid state reaction route from high temperature melt (850˚C) and slow cooling (2˚C/hour) of constituent elements. The single crystal X-ray diffraction pattern showed the 00l alignment and the high crystalline nature of the resultant sample. The rietveld fitted room temperature powder XRD revealed the phase purity and rhombohedral structure of the synthesized crystal. The formation and analysis of unit cell structure further verified the rhombohedral structure composed of three quintuple layers stacked one over the other. The SEM image showed the layered directional growth of the synthesized crystal carried out using the ZEISS-EVOMA-10 scanning electron microscope The electrical resistivity measurement was carried out using the conventional four-probe method on a quantum design Physical Property Measurement System (PPMS). The temperature dependent electrical resistivity plot for studied Sb2Te3 single crystal depicts metallic behaviour in the absence of any applied magnetic field. The synthesis as well as the structural characterization of as grown Sb2Te3 single crystal is reported and discussed in the present letter.

New Insights Toward Quantitative Relationships between Lignin Reactivity to Monomers and Their Structural Characteristics.

PubMed

Ma, Ruoshui; Zhang, Xiumei; Wang, Yi; Zhang, Xiao

2018-04-27

The heterogeneous and complex structural characteristics of lignin present a significant challenge to predict its processability (e.g. depolymerization, modifications etc) to valuable products. This study provides a detailed characterization and comparison of structural properties of seven representative biorefinery lignin samples derived from forest and agricultural residues, which were subjected to representative pretreatment methods. A range of wet chemistry and spectroscopy methods were applied to determine specific lignin structural characteristics such as functional groups, inter-unit linkages and peak molecular weight. In parallel, oxidative depolymerization of these lignin samples to either monomeric phenolic compounds or dicarboxylic acids were conducted, and the product yields were quantified. Based on these results (lignin structural characteristics and monomer yields), we demonstrated for the first time to apply multiple-variable linear estimations (MVLE) approach using R statistics to gain insight toward a quantitative correlation between lignin structural properties and their conversion reactivity toward oxidative depolymerization to monomers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantifying seascape structure: Extending terrestrial spatial pattern metrics to the marine realm

USGS Publications Warehouse

Wedding, L.M.; Christopher, L.A.; Pittman, S.J.; Friedlander, A.M.; Jorgensen, S.

2011-01-01

Spatial pattern metrics have routinely been applied to characterize and quantify structural features of terrestrial landscapes and have demonstrated great utility in landscape ecology and conservation planning. The important role of spatial structure in ecology and management is now commonly recognized, and recent advances in marine remote sensing technology have facilitated the application of spatial pattern metrics to the marine environment. However, it is not yet clear whether concepts, metrics, and statistical techniques developed for terrestrial ecosystems are relevant for marine species and seascapes. To address this gap in our knowledge, we reviewed, synthesized, and evaluated the utility and application of spatial pattern metrics in the marine science literature over the past 30 yr (1980 to 2010). In total, 23 studies characterized seascape structure, of which 17 quantified spatial patterns using a 2-dimensional patch-mosaic model and 5 used a continuously varying 3-dimensional surface model. Most seascape studies followed terrestrial-based studies in their search for ecological patterns and applied or modified existing metrics. Only 1 truly unique metric was found (hydrodynamic aperture applied to Pacific atolls). While there are still relatively few studies using spatial pattern metrics in the marine environment, they have suffered from similar misuse as reported for terrestrial studies, such as the lack of a priori considerations or the problem of collinearity between metrics. Spatial pattern metrics offer great potential for ecological research and environmental management in marine systems, and future studies should focus on (1) the dynamic boundary between the land and sea; (2) quantifying 3-dimensional spatial patterns; and (3) assessing and monitoring seascape change. ?? Inter-Research 2011.

Characterization of the Electric Double Layer Formation Dynamics of a Metal/Ionic Liquid/Metal Structure.

PubMed

Schmidt, Elliot; Shi, Sha; Ruden, P Paul; Frisbie, C Daniel

2016-06-15

Although ionic liquids (ILs) have been used extensively in recent years as a high-capacitance "dielectric" in electric double layer transistors, the dynamics of the double layer formation have remained relatively unexplored. Better understanding of the dynamics and relaxation processes involved in electric double layer formation will guide device optimization, particularly with regard to switching speed. In this paper, we explore the dynamical characteristics of an IL in a metal/ionic liquid/metal (M/IL/M) capacitor. In particular, we examine a Au/IL/Au structure where the IL is 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate. The experiments consist of frequency-dependent impedance measurements and time-dependent current vs voltage measurements for applied linear voltage ramps and abrupt voltage steps. The parameters of an equivalent circuit model are determined by fits to the impedance vs frequency data and subsequently verified by calculating the current vs voltage characteristics for the applied potential profiles. The data analysis indicates that the dynamics of the structure are characterized by a wide distribution of relaxation times spanning the range of less than microseconds to longer than seconds. Possible causes for these time scales are discussed.

Non-invasive dynamic measurement of helicopter blades

NASA Astrophysics Data System (ADS)

Serafini, J.; Bernardini, G.; Mattioni, L.; Vezzari, V.; Ficuciello, C.

2017-08-01

This paper presents the development and the application on helicopter blades of a measurement system based on FBG strain gauges. Here, the main goal is the structural characterization of the main rotor blades, with the aim of showing the potentialities of such a system in blades quality check applications, as well as in the development of structural health monitoring and rotor state feedback devices. The device has been used in both non-rotating and rotating tests, and does not require the presence of slip rings or optical joint since it is completely allocated in the rotating system. It has been successfully applied to characterize the frequency response of blades lead-lag, flap and torsion deformations, up to 250 Hz.

Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms

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

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalasemore » (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.« less

Methanol clusters (CH3OH)n, n = 3-6 in external electric fields: density functional theory approach.

PubMed

Rai, Dhurba; Kulkarni, Anant D; Gejji, Shridhar P; Pathak, Rajeev K

2011-07-14

Structural evolution of cyclic and branched-cyclic methanol clusters containing three to six molecules, under the influence of externally applied uniform static electric field is studied within the density functional theory. Akin to the situation for water clusters, the electric field is seen to stretch the intermolecular hydrogen bonds, and eventually break the H-bonded network at certain characteristic threshold field values of field strength in the range 0.009-0.016 a.u., yielding linear or branched structures with a lower energy. These structural transitions are characterized by an abrupt increase in the electric dipole moment riding over its otherwise steady nonlinear increase with the applied field. The field tends to rupture the H-bonded structure; consequently, the number of hydrogen bonds decreases with increasing field strength. Vibrational spectra analyzed for fields applied perpendicular to the cyclic ring structures bring out the shifts in the OH ring vibrations (blueshift) and the CO stretch vibrations (redshift). For a given field strength, the blueshifts increase with the number of molecules in the ring and are found to be generally larger than those in the corresponding water cluster counterparts.

Investigating Language and the Media: The Case of Newswriting

ERIC Educational Resources Information Center

Perrin, Daniel

2013-01-01

Drawing on a case study of newswriting, this article presents media linguistics as a subdiscipline of applied linguistics (AL), dealing with a distinctive field of language use. Language in the media is characterized by specific environments, functions, and structures. Medialinguistic research, however, tends to overcome disciplinary boundaries.…

Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using illumina sequencing

Treesearch

Sandra A. Owusu; Margaret Staton; Tara N. Jennings; Scott Schlarbaum; Mark V. Coggeshall; Jeanne Romero-Severson; John E. Carlson; Oliver Gailing

2013-01-01

Premise of the study: Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies.

High Resolution Imaging of the Sun with CORONAS-1

NASA Technical Reports Server (NTRS)

Karovska, Margarita

1998-01-01

We applied several image restoration and enhancement techniques, to CORONAS-I images. We carried out the characterization of the Point Spread Function (PSF) using the unique capability of the Blind Iterative Deconvolution (BID) technique, which recovers the real PSF at a given location and time of observation, when limited a priori information is available on its characteristics. We also applied image enhancement technique to extract the small scale structure imbeded in bright large scale structures on the disk and on the limb. The results demonstrate the capability of the image post-processing to substantially increase the yield from the space observations by improving the resolution and reducing noise in the images.

Vectorial strain gauge method using single flexible orthogonal polydimethylsiloxane gratings

NASA Astrophysics Data System (ADS)

Guo, Hao; Tang, Jun; Qian, Kun; Tsoukalas, Dimitris; Zhao, Miaomiao; Yang, Jiangtao; Zhang, Binzhen; Chou, Xiujian; Liu, Jun; Xue, Chenyang; Zhang, Wendong

2016-03-01

A vectorial strain gauge method using a single sensing element is reported based on the double-sided polydimethylsiloxane (PDMS) Fraunhofer diffraction gratings structures. Using O2 plasma treatment steps, orthogonal wrinkled gratings were fabricated on both sides of a pre-strained PDMS film. Diffracted laser spots from this structure have been used to experimentally demonstrate, that any applied strain can be quantitatively characterized in both the x and y directions with an error of less than 0.6% and with a gauge factor of approximately 10. This simple and low cost technology which is completely different from the traditional vectorial strain gauge method, can be applied to surface vectorial strain measurement and multi-axis integrated mechanical sensors.

Comparative advantages and limitations of the basic metrology methods applied to the characterization of nanomaterials.

PubMed

Linkov, Pavel; Artemyev, Mikhail; Efimov, Anton E; Nabiev, Igor

2013-10-07

Fabrication of modern nanomaterials and nanostructures with specific functional properties is both scientifically promising and commercially profitable. The preparation and use of nanomaterials require adequate methods for the control and characterization of their size, shape, chemical composition, crystalline structure, energy levels, pathways and dynamics of physical and chemical processes during their fabrication and further use. In this review, we discuss different instrumental methods for the analysis and metrology of materials and evaluate their advantages and limitations at the nanolevel.

Multifunctional Poro-Vascular Composites for UAV Performance Enhancement

DTIC Science & Technology

2012-07-31

structural “skin” materials with surface pores and internal vascular channels filled with an ionic- liquid whose height and shape at the pore exits is...2 V t e e q q          Intrinsic contact angle (zero voltage) Applied potential Interfacial tension (IFT) of ionic liquid Lippmann...Characterization flat plates  single (capillary) pore  PV pore arrays FTA 1000 Drop-Shape Characterization • Microscope lens : 0.5 to 12x magnification • Side

Top-down approach for the direct characterization of low molecular weight heparins using LC-FT-MS.

PubMed

Li, Lingyun; Zhang, Fuming; Zaia, Joseph; Linhardt, Robert J

2012-10-16

Low molecular heparins (LMWHs) are structurally complex, heterogeneous, polydisperse, and highly negatively charged mixtures of polysaccharides. The direct characterization of LMWH is a major challenge for currently available analytical technologies. Electrospray ionization (ESI) liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for the characterization complex biological samples in the fields of proteomics, metabolomics, and glycomics. LC-MS has been applied to the analysis of heparin oligosaccharides, separated by size exclusion, reversed phase ion-pairing chromatography, and chip-based amide hydrophilic interaction chromatography (HILIC). However, there have been limited applications of ESI-LC-MS for the direct characterization of intact LMWHs (top-down analysis) due to their structural complexity, low ionization efficiency, and sulfate loss. Here we present a simple and reliable HILIC-Fourier transform (FT)-ESI-MS platform to characterize and compare two currently marketed LMWH products using the top-down approach requiring no special sample preparation steps. This HILIC system relies on cross-linked diol rather than amide chemistry, affording highly resolved chromatographic separations using a relatively high percentage of acetonitrile in the mobile phase, resulting in stable and high efficiency ionization. Bioinformatics software (GlycReSoft 1.0) was used to automatically assign structures within 5-ppm mass accuracy.

Quantitative atomic-scale structure characterization of ordered mesoporous carbon materials by solid state NMR

DOE PAGES

Wang, Zhuoran; Opembe, Naftali; Kobayashi, Takeshi; ...

2018-02-03

In this study, solid-state (SS)NMR techniques were applied to characterize the atomic-scale structures of ordered mesoporous carbon (OMC) materials prepared using Pluronic F127 as template with resorcinol and formaldehyde as polymerizing precursors. A rigorous quantitative analysis was developed using a combination of 13C SSNMR spectra acquired with direct polarization and cross polarization on natural abundant and selectively 13C-enriched series of samples pyrolyzed at various temperatures. These experiments identified and counted the key functional groups present in the OMCs at various stages of preparation and thermal treatment. Lastly, the chemical evolution of molecular networks, the average sizes of aromatic clusters andmore » the extended molecular structures of OMCs were then inferred by coupling this information with the elemental analysis results.« less

Quantitative atomic-scale structure characterization of ordered mesoporous carbon materials by solid state NMR

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

Wang, Zhuoran; Opembe, Naftali; Kobayashi, Takeshi

In this study, solid-state (SS)NMR techniques were applied to characterize the atomic-scale structures of ordered mesoporous carbon (OMC) materials prepared using Pluronic F127 as template with resorcinol and formaldehyde as polymerizing precursors. A rigorous quantitative analysis was developed using a combination of 13C SSNMR spectra acquired with direct polarization and cross polarization on natural abundant and selectively 13C-enriched series of samples pyrolyzed at various temperatures. These experiments identified and counted the key functional groups present in the OMCs at various stages of preparation and thermal treatment. Lastly, the chemical evolution of molecular networks, the average sizes of aromatic clusters andmore » the extended molecular structures of OMCs were then inferred by coupling this information with the elemental analysis results.« less

A Lagrangian cylindrical coordinate system for characterizing dynamic surface geometry of tubular anatomic structures.

PubMed

Lundh, Torbjörn; Suh, Ga-Young; DiGiacomo, Phillip; Cheng, Christopher

2018-03-03

Vascular morphology characterization is useful for disease diagnosis, risk stratification, treatment planning, and prediction of treatment durability. To quantify the dynamic surface geometry of tubular-shaped anatomic structures, we propose a simple, rigorous Lagrangian cylindrical coordinate system to monitor well-defined surface points. Specifically, the proposed system enables quantification of surface curvature and cross-sectional eccentricity. Using idealized software phantom examples, we validate the method's ability to accurately quantify longitudinal and circumferential surface curvature, as well as eccentricity and orientation of eccentricity. We then apply the method to several medical imaging data sets of human vascular structures to exemplify the utility of this coordinate system for analyzing morphology and dynamic geometric changes in blood vessels throughout the body. Graphical abstract Pointwise longitudinal curvature of a thoracic aortic endograft surface for systole and diastole, with their absolute difference.

Characterization and manipulation of individual defects in insulating hexagonal boron nitride using scanning tunnelling microscopy.

PubMed

Wong, Dillon; Velasco, Jairo; Ju, Long; Lee, Juwon; Kahn, Salman; Tsai, Hsin-Zon; Germany, Chad; Taniguchi, Takashi; Watanabe, Kenji; Zettl, Alex; Wang, Feng; Crommie, Michael F

2015-11-01

Defects play a key role in determining the properties and technological applications of nanoscale materials and, because they tend to be highly localized, characterizing them at the single-defect level is of particular importance. Scanning tunnelling microscopy has long been used to image the electronic structure of individual point defects in conductors, semiconductors and ultrathin films, but such single-defect electronic characterization remains an elusive goal for intrinsic bulk insulators. Here, we show that individual native defects in an intrinsic bulk hexagonal boron nitride insulator can be characterized and manipulated using a scanning tunnelling microscope. This would typically be impossible due to the lack of a conducting drain path for electrical current. We overcome this problem by using a graphene/boron nitride heterostructure, which exploits the atomically thin nature of graphene to allow the visualization of defect phenomena in the underlying bulk boron nitride. We observe three different defect structures that we attribute to defects within the bulk insulating boron nitride. Using scanning tunnelling spectroscopy we obtain charge and energy-level information for these boron nitride defect structures. We also show that it is possible to manipulate the defects through voltage pulses applied to the scanning tunnelling microscope tip.

Characterization method for relative Raman enhancement for surface-enhanced Raman spectroscopy using gold nanoparticle dimer array

NASA Astrophysics Data System (ADS)

Sugano, Koji; Ikegami, Kohei; Isono, Yoshitada

2017-06-01

In this paper, a characterization method for Raman enhancement for highly sensitive and quantitative surface-enhanced Raman spectroscopy (SERS) is reported. A particle dimer shows a marked electromagnetic enhancement when the particle connection direction is matched to the polarization direction of incident light. In this study, dimers were arrayed by nanotrench-guided self-assembly for a marked total Raman enhancement. By measuring acetonedicarboxylic acid, the fabricated structures were characterized for SERS depending on the polarization angle against the particle connection direction. This indicates that the fabricated structures cause an effective SERS enhancement, which is dominated by the electromagnetic enhancement. Then, we measured 4,4‧-bipyridine, which is a pesticide material, for quantitative analysis. In advance, we evaluated the enhancement of the particle structure by the Raman measurement of acetonedicarboxylic acid. Finally, we compared the Raman intensities of acetonedicarboxylic acid and 4,4‧-bipyridine. Their intensities showed good correlation. The advantage of this method for previously evaluating the enhancement of the substrate was demonstrated. This developed SERS characterization method is expected to be applied to various quantitative trace analyses of molecules with high sensitivity.

Characterization of Slosh Damping for Ortho-Grid and Iso-Grid Internal Tank Structures

NASA Technical Reports Server (NTRS)

Westra, Douglas G.; Sansone, Marco D.; Eberhart, Chad J.; West, Jeffrey S.

2016-01-01

Grid stiffened tank structures such as Ortho-Grid and Iso-Grid are widely used in cryogenic tanks for providing stiffening to the tank while reducing mass, compared to tank walls of constant cross-section. If the structure is internal to the tank, it will positively affect the fluid dynamic behavior of the liquid propellant, in regard to fluid slosh damping. As NASA and commercial companies endeavor to explore the solar system, vehicles will by necessity become more mass efficient, and design margin will be reduced where possible. Therefore, if the damping characteristics of the Ortho-Grid and Iso-Grid structure is understood, their positive damping effect can be taken into account in the systems design process. Historically, damping by internal structures has been characterized by rules of thumb and for Ortho-Grid, empirical design tools intended for slosh baffles of much larger cross-section have been used. There is little or no information available to characterize the slosh behavior of Iso-Grid internal structure. Therefore, to take advantage of these structures for their positive damping effects, there is much need for obtaining additional data and tools to characterize them. Recently, the NASA Marshall Space Flight Center conducted both sub-scale testing and computational fluid dynamics (CFD) simulations of slosh damping for Ortho-Grid and Iso-Grid tanks for cylindrical tanks containing water. Enhanced grid meshing techniques were applied to the geometrically detailed and complex Ortho-Grid and Iso-Grid structures. The Loci-STREAM CFD program with the Volume of Fluid Method module for tracking and locating the water-air fluid interface was used to conduct the simulations. The CFD simulations were validated with the test data and new empirical models for predicting damping and frequency of Ortho-Grid and Iso-Grid structures were generated.

Characterization of newly synthesized pyrimidine derivatives for corrosion inhibition as inferred from computational chemical analysis

NASA Astrophysics Data System (ADS)

El-Taib Heakal, F.; Rizk, S. A.; Elkholy, A. E.

2018-01-01

Corrosion of metallic constructions is a serious problem in most industries worldwide that can be controlled via addition of special chemicals having adsorption capability on metal surfaces and hence isolating it from the aggressive environment. These chemicals are characterized by being rich in functional groups containing free lone pairs of electrons and/or π-electrons. In the present study four newly imidazole-pyrimidine based ionic derivatives have been synthesized and their structures were characterized by means of elemental analysis and different spectroscopic techniques. Quantum chemical calculations were carried out to give insights into the structural and electronic characteristics of these fabricated compounds. Monte Carlo simulation was also applied to shed the light on our prepared corrosion inhibitor molecules by examining their aptitude to adsorb on iron surface. Our ultimate goal is to help industries in fighting corrosion by providing them with a cheap and efficient anti-corrosion molecules.

Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain.

PubMed

Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Petitjean, Michel; Flatters, Delphine; Camproux, Anne-Claude

2017-10-01

While recent literature focuses on drug promiscuity, the characterization of promiscuous binding sites (ability to bind several ligands) remains to be explored. Here, we present a proteochemometric modeling approach to analyze diverse ligands and corresponding multiple binding sub-pockets associated with one promiscuous binding site to characterize protein-ligand recognition. We analyze both geometrical and physicochemical profile correspondences. This approach was applied to examine the well-studied druggable urokinase catalytic domain inhibitor binding site, which results in a large number of complex structures bound to various ligands. This approach emphasizes the importance of jointly characterizing pocket and ligand spaces to explore the impact of ligand diversity on sub-pocket properties and to establish their main profile correspondences. This work supports an interest in mining available 3D holo structures associated with a promiscuous binding site to explore its main protein-ligand recognition tendency. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interfacial ionic 'liquids': connecting static and dynamic structures

DOE PAGES

Uysal, Ahmet; Zhou, Hua; Feng, Guang; ...

2014-12-05

It is well known that room temperature ionic liquids (RTILs) often adopt a charge-separated layered structure, i.e. with alternating cation- and anion-rich layers, at electrified interfaces. However, the dynamic response of the layered structure to temporal variations in applied potential is not well understood. For this research, we used in situ, real-time x-ray reflectivity to study the potential-dependent electric double layer (EDL) structure of an imidazolium-based RTIL on charged epitaxial graphene during potential cycling as a function of temperature. The results suggest that the graphene–RTIL interfacial structure is bistable in which the EDL structure at any intermediate potential can bemore » described by the combination of two extreme-potential structures whose proportions vary depending on the polarity and magnitude of the applied potential. This picture is supported by the EDL structures obtained by fully atomistic molecular dynamics simulations at various static potentials. Lastly, the potential-driven transition between the two structures is characterized by an increasing width but with an approximately fixed hysteresis magnitude as a function of temperature. The results are consistent with the coexistence of distinct anion- and cation-adsorbed structures separated by an energy barrier (~0.15 eV).« less

Interfacial ionic 'liquids': connecting static and dynamic structures.

PubMed

Uysal, Ahmet; Zhou, Hua; Feng, Guang; Lee, Sang Soo; Li, Song; Cummings, Peter T; Fulvio, Pasquale F; Dai, Sheng; McDonough, John K; Gogotsi, Yury; Fenter, Paul

2015-01-28

It is well known that room temperature ionic liquids (RTILs) often adopt a charge-separated layered structure, i.e. with alternating cation- and anion-rich layers, at electrified interfaces. However, the dynamic response of the layered structure to temporal variations in applied potential is not well understood. We used in situ, real-time x-ray reflectivity to study the potential-dependent electric double layer (EDL) structure of an imidazolium-based RTIL on charged epitaxial graphene during potential cycling as a function of temperature. The results suggest that the graphene-RTIL interfacial structure is bistable in which the EDL structure at any intermediate potential can be described by the combination of two extreme-potential structures whose proportions vary depending on the polarity and magnitude of the applied potential. This picture is supported by the EDL structures obtained by fully atomistic molecular dynamics simulations at various static potentials. The potential-driven transition between the two structures is characterized by an increasing width but with an approximately fixed hysteresis magnitude as a function of temperature. The results are consistent with the coexistence of distinct anion- and cation-adsorbed structures separated by an energy barrier (∼0.15 eV).

Nano-architecture of metal-organic frameworks

NASA Astrophysics Data System (ADS)

Milichko, Valentin A.; Zalogina, Anastasiia; Mingabudinova, Leila R.; Vinogradov, Alexander V.; Ubyivovk, Evgeniy; Krasilin, Andrei A.; Mukhin, Ivan; Zuev, Dmitry A.; Makarov, Sergey V.; Pidko, Evgeny A.

2017-09-01

Change the shape and size of materials supports new functionalities never found in the sources. This strategy has been recently applied for porous crystalline materials - metal-organic frameworks (MOFs) to create hollow nanoscale structures or mesostructures with improved functional properties. However, such structures are characterized by amorphous state or polycrystallinity which limits their applicability. Here we follow this strategy to create such nano- and mesostructures with perfect crystallinity and new photonics functionalities by laser or focused ion beam fabrication.

Evaluation of the influence of acquisition parameters of microtomography in image quality applied by carbonate rocks

NASA Astrophysics Data System (ADS)

Santos, T. M. P.; Machado, A. S.; Araújo, O. M. O.; Ferreira, C. G.; Lopes, R. T.

2018-03-01

X-ray computed microtomography is a powerful nondestructive technique for 2D and 3D structure analysis. However, parameters used in acquisition promote directs influence in qualitative and quantitative results in characterization of samples, due image resolution. The aim of this study is value the influence of theses parameters in results through of tests changing these parameters in different situations and system characterization. Results demonstrate those pixel size and detector matrixes are the main parameters that influence in resolution and image quality. Microtomography was considered an excellent technique for characterization using the best image resolution possible.

Multiscale tomography of buried magnetic structures: its use in the localization and characterization of archaeological structures

NASA Astrophysics Data System (ADS)

Saracco, Ginette; Moreau, Frédérique; Mathé, Pierre-Etienne; Hermitte, Daniel; Michel, Jean-Marie

2007-10-01

We have previously developed a method for characterizing and localizing `homogeneous' buried sources, from the measure of potential anomalies at a fixed height above ground (magnetic, electric and gravity). This method is based on potential theory and uses the properties of the Poisson kernel (real by definition) and the continuous wavelet theory. Here, we relax the assumption on sources and introduce a method that we call the `multiscale tomography'. Our approach is based on the harmonic extension of the observed magnetic field to produce a complex source by use of a complex Poisson kernel solution of the Laplace equation for complex potential field. A phase and modulus are defined. We show that the phase provides additional information on the total magnetic inclination and the structure of sources, while the modulus allows us to characterize its spatial location, depth and `effective degree'. This method is compared to the `complex dipolar tomography', extension of the Patella method that we previously developed. We applied both methods and a classical electrical resistivity tomography to detect and localize buried archaeological structures like antique ovens from magnetic measurements on the Fox-Amphoux site (France). The estimates are then compared with the results of excavations.

Preparation and Characterization of Fluorescent SiO2 Microspheres

NASA Astrophysics Data System (ADS)

Xu, Cui; Zhang, Hao; Guan, Ruifang

2018-01-01

Fluorescent compound without typical fluorophores was synthesized with citric acid (CA) and aminopropyltriethoxysilane (APTS) firstly, and then it was grafted to the surface of the prepared SiO2 microspheres by chemical reaction. The fluorescent SiO2 microspheres with good fluorescent properties were obtained by optimizing the reaction conditions. And the morphology and structure of the fluorescent SiO2 microspheres have been characterized by scanning electron microscopy (SEM) and fourier transform infrared (FTIR) spectroscopy. The results showed that the preparation of fluorescent SiO2 microspheres have good monodispersity and narrow particle size distribution. Moreover, the fluorescent SiO2 microspheres can be applied to detect Fe3+ in aqueous solution, prepare fluorescent SiO2 rubber, and have potential to be applied in the fluorescent labeling and fingerprint appearing technique fields.

Quantitative analysis of pulse thermography data for degradation assessment of historical buildings

NASA Astrophysics Data System (ADS)

Di Maio, Rosa; Piegari, Ester; Mancini, Cecilia; Chiapparino, Antonella

2015-06-01

In the last decades, infrared thermography has been successfully applied to various materials and structures for the assessment of their state of conservation and planning suitable restoration works. To this aim, mathematical models are required to characterize thermal anomaly sources, such as detachments, water infiltration and material decomposition processes. In this paper, an algorithm based on the conservative finite difference method is used to analyse pulse thermography data acquired on an ancient building in the Pompeii archaeological site (Naples, Italy). The numerical study is applied to both broad and narrow elongated thermal anomalies. In particular, from the comparison between simulated and experimental thermal decays, the plaster thickness was characterized in terms of thermal properties and areas of possible future detachments, and moisture infiltration depths were identified.

Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

NASA Astrophysics Data System (ADS)

Qin, W.; Yang, L.

2004-05-01

Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study and the current multi-spectral and multi-angular satellite data (MODIS, MISR), a robust retrieval system to estimate woody vegetation structural/biophysical parameters is proposed.

Electrical Characterization of Amorphous Silicon MIS-Based Structures for HIT Solar Cell Applications.

PubMed

García, Héctor; Castán, Helena; Dueñas, Salvador; Bailón, Luis; García-Hernansanz, Rodrigo; Olea, Javier; Del Prado, Álvaro; Mártil, Ignacio

2016-12-01

A complete electrical characterization of hydrogenated amorphous silicon layers (a-Si:H) deposited on crystalline silicon (c-Si) substrates by electron cyclotron resonance chemical vapor deposition (ECR-CVD) was carried out. These structures are of interest for photovoltaic applications. Different growth temperatures between 30 and 200 °C were used. A rapid thermal annealing in forming gas atmosphere at 200 °C during 10 min was applied after the metallization process. The evolution of interfacial state density with the deposition temperature indicates a better interface passivation at higher growth temperatures. However, in these cases, an important contribution of slow states is detected as well. Thus, using intermediate growth temperatures (100-150 °C) might be the best choice.

Electrical Characterization of Amorphous Silicon MIS-Based Structures for HIT Solar Cell Applications

NASA Astrophysics Data System (ADS)

García, Héctor; Castán, Helena; Dueñas, Salvador; Bailón, Luis; García-Hernansanz, Rodrigo; Olea, Javier; del Prado, Álvaro; Mártil, Ignacio

2016-07-01

A complete electrical characterization of hydrogenated amorphous silicon layers (a-Si:H) deposited on crystalline silicon (c-Si) substrates by electron cyclotron resonance chemical vapor deposition (ECR-CVD) was carried out. These structures are of interest for photovoltaic applications. Different growth temperatures between 30 and 200 °C were used. A rapid thermal annealing in forming gas atmosphere at 200 °C during 10 min was applied after the metallization process. The evolution of interfacial state density with the deposition temperature indicates a better interface passivation at higher growth temperatures. However, in these cases, an important contribution of slow states is detected as well. Thus, using intermediate growth temperatures (100-150 °C) might be the best choice.

Characterization of wafer-level bonded hermetic packages using optical leak detection

NASA Astrophysics Data System (ADS)

Duan, Ani; Wang, Kaiying; Aasmundtveit, Knut; Hoivik, Nils

2009-07-01

For MEMS devices required to be operated in a hermetic environment, one of the main reliability issues is related to the packaging methods applied. In this paper, an optical method for testing low volume hermetic cavities formed by anodic bonding between glass and SOI (silicon on insulator) wafer is presented. Several different cavity-geometry structures have been designed, fabricated and applied to monitor the hermeticity of wafer level anodic bonding. SOI wafer was used as the cap wafer on which the different-geometry structures were fabricated using standard MEMS technology. The test cavities were bonded using SOI wafers to glass wafers at 400C and 1000mbar pressure inside a vacuum bonding chamber. The bonding voltage varies from 200V to 600V. The bonding strength between glass and SOI wafer was mechanically tested using shear tester. The deformation amplitudes of the cavity cap surface were monitored by using an optical interferometer. The hermeticity of the glass-to-SOI wafer level bonding was characterized through observing the surface deformation in a 6 months period in atmospheric environment. We have observed a relatively stable micro vacuum-cavity.

Hopf algebras of rooted forests, cocyles, and free Rota-Baxter algebras

NASA Astrophysics Data System (ADS)

Zhang, Tianjie; Gao, Xing; Guo, Li

2016-10-01

The Hopf algebra and the Rota-Baxter algebra are the two algebraic structures underlying the algebraic approach of Connes and Kreimer to renormalization of perturbative quantum field theory. In particular, the Hopf algebra of rooted trees serves as the "baby model" of Feynman graphs in their approach and can be characterized by certain universal properties involving a Hochschild 1-cocycle. Decorated rooted trees have also been applied to study Feynman graphs. We will continue the study of universal properties of various spaces of decorated rooted trees with such a 1-cocycle, leading to the concept of a cocycle Hopf algebra. We further apply the universal properties to equip a free Rota-Baxter algebra with the structure of a cocycle Hopf algebra.

Polymorphs of Theophylline Characterized by DNP Enhanced Solid-State NMR

PubMed Central

2015-01-01

We show how dynamic nuclear polarization (DNP) enhanced solid-state NMR spectroscopy can be used to characterize polymorphs and solvates of organic solids. We applied DNP to three polymorphs and one hydrated form of the asthma drug molecule theophylline. For some forms of theophylline, sample grinding and impregnation with the radical-containing solution, which are necessary to prepare the samples for DNP, were found to induce polymorphic transitions or desolvation between some forms. We present protocols for sample preparation for solid-state magic-angle spinning (MAS) DNP experiments that avoid the polymorphic phase transitions in theophylline. These protocols include cryogrinding, grinding under inert atmosphere, and the appropriate choice of the impregnating liquid. By applying these procedures, we subsequently demonstrate that two-dimensional correlation experiments, such as 1H–13C and 1H–15N HETCOR or 13C–13C INADEQUATE, can be obtained at natural isotopic abundance in reasonable times, thus enabling more advanced structural characterization of polymorphs. PMID:26393368

Fault-tolerant control of large space structures using the stable factorization approach

NASA Technical Reports Server (NTRS)

Razavi, H. C.; Mehra, R. K.; Vidyasagar, M.

1986-01-01

Large space structures are characterized by the following features: they are in general infinite-dimensional systems, and have large numbers of undamped or lightly damped poles. Any attempt to apply linear control theory to large space structures must therefore take into account these features. Phase I consisted of an attempt to apply the recently developed Stable Factorization (SF) design philosophy to problems of large space structures, with particular attention to the aspects of robustness and fault tolerance. The final report on the Phase I effort consists of four sections, each devoted to one task. The first three sections report theoretical results, while the last consists of a design example. Significant results were obtained in all four tasks of the project. More specifically, an innovative approach to order reduction was obtained, stabilizing controller structures for plants with an infinite number of unstable poles were determined under some conditions, conditions for simultaneous stabilizability of an infinite number of plants were explored, and a fault tolerance controller design that stabilizes a flexible structure model was obtained which is robust against one failure condition.

Influence of Thunderstorms on the Structure of the Ionosphere using Composite Analysis

NASA Astrophysics Data System (ADS)

Nava, O.; Sutherland, E.

2017-12-01

It is well known in the amateur (ham) radio community that thunderstorms have a significant influence on local and long-distance high-frequency (HF) communications. This study aims to characterize the structure of the ionosphere in response to strong convective activity and cloud electrification. Superposed Epoch Analysis is applied to surface weather observations and ionosonde data at Eglin Air Force Base, Florida from August 2014 to July 2017. Preliminary results indicate that thunderstorms significantly modify the structure of the ionosphere, generating statistically different measurements of several key parameters (e.g., foEs, hmF2, ITEC) compared to clear-sky observations. Seasonal and diurnal influences between the thunderstorm and clear sky cases are also explored. Accurate characterization of the ionosphere in response to thunderstorms has important implications for the effective use of HF communications in civilian and military operations, to include emergency services, aviation, amateur radio, and over-the-horizon radar.

Multi-scale integration and predictability in resting state brain activity

PubMed Central

Kolchinsky, Artemy; van den Heuvel, Martijn P.; Griffa, Alessandra; Hagmann, Patric; Rocha, Luis M.; Sporns, Olaf; Goñi, Joaquín

2014-01-01

The human brain displays heterogeneous organization in both structure and function. Here we develop a method to characterize brain regions and networks in terms of information-theoretic measures. We look at how these measures scale when larger spatial regions as well as larger connectome sub-networks are considered. This framework is applied to human brain fMRI recordings of resting-state activity and DSI-inferred structural connectivity. We find that strong functional coupling across large spatial distances distinguishes functional hubs from unimodal low-level areas, and that this long-range functional coupling correlates with structural long-range efficiency on the connectome. We also find a set of connectome regions that are both internally integrated and coupled to the rest of the brain, and which resemble previously reported resting-state networks. Finally, we argue that information-theoretic measures are useful for characterizing the functional organization of the brain at multiple scales. PMID:25104933

Characterization of structural and electrical properties of ZnO tetrapods

NASA Astrophysics Data System (ADS)

Gu, Yu-Dong; Mai, Wen-Jie; Jiang, Peng

2011-12-01

ZnO tetrapods were synthesized by a typical thermal vapor-solid deposition method in a horizontal tube furnace. Structural characterization was carried out by transmission electron microscopy (TEM) and select-area electron diffraction (SAED), which shows the presence of zinc blende nucleus in the center of tetrapods while the four branches taking hexagonal wurtzite structure. The electrical transport property of ZnO tetrapods was investigated through an in-situ nanoprobe system. The three branches of a tetrapod serve as source, drain, and "gate", respectively; while the fourth branch pointing upward works as the force trigger by vertically applying external force downward. The conductivity of each branch of ZnO-tetrapods increases 3-4 times under pressure. In such situation, the electrical current through the branches of ZnO tetrapods can be tuned by external force, and therefore a simple force sensor based on ZnO tetrapods has been demonstrated for the first time.

Structural and compositional characterization of the adhesive produced by reef building oysters.

PubMed

Alberts, Erik M; Taylor, Stephen D; Edwards, Stephanie L; Sherman, Debra M; Huang, Chia-Ping; Kenny, Paul; Wilker, Jonathan J

2015-04-29

Oysters have an impressive ability to overcome difficulties of life within the stressful intertidal zone. These shellfish produce an adhesive for attaching to each other and building protective reef communities. With their reefs often exceeding kilometers in length, oysters play a major role in balancing the health of coastal marine ecosystems. Few details are available to describe oyster adhesive composition or structure. Here several characterization methods were applied to describe the nature of this material. Microscopy studies indicated that the glue is comprised of organic fiber-like and sheet-like structures surrounded by an inorganic matrix. Phospholipids, cross-linking chemistry, and conjugated organics were found to differentiate this adhesive from the shell. Symbiosis in material synthesis could also be present, with oysters incorporating bacterial polysaccharides into their adhesive. Oyster glue shows that an organic-inorganic composite material can provide adhesion, a property especially important when constructing a marine ecosystem.

Spectroscopic characterization of charge-transfer complexes of morpholine with chloranilic and picric acids in organic media: crystal structure of bis(morpholinium 2,4,6-trinitrocyclohexanolate).

PubMed

Refat, Moamen S; El-Zayat, Lamia A; Yeşilel, Okan Zafer

2010-02-01

Electron donor-acceptor interaction of morpholine (morp) with chloranilic acid (cla) and picric acid (pa) as pi-acceptors was investigated spectrophotometrically and found to form stable charge-transfer (CT) complexes (n-pi*) of [(Hmorp)(2)(cla)] and [(Hmorp)(pa)](2). The donor site involved in CT interaction is morpholine nitrogen. These complexes are easily synthesized from the reaction of morp with cla and pa within MeOH and CHCl(3) solvents, respectively. (1)HNMR, IR, elemental analyses, and UV-vis techniques characterize the two morpholinium charge-transfer complexes. Benesi-Hildebrand and its modification methods were applied to the determination of association constant (K), molar extinction coefficient (epsilon). The X-ray crystal structure was carried out for the interpretation the predict structure of the [(Hmorp)(pa)](2) complex. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Spectroscopic characterization of charge-transfer complexes of morpholine with chloranilic and picric acids in organic media: Crystal structure of bis(morpholinium 2,4,6-trinitrocyclohexanolate)

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; El-Zayat, Lamia A.; Yeşilel, Okan Zafer

2010-02-01

Electron donor-acceptor interaction of morpholine (morp) with chloranilic acid (cla) and picric acid (pa) as π-acceptors was investigated spectrophotometrically and found to form stable charge-transfer (CT) complexes (n-π*) of [(Hmorp) 2(cla)] and [(Hmorp)(pa)] 2. The donor site involved in CT interaction is morpholine nitrogen. These complexes are easily synthesized from the reaction of morp with cla and pa within MeOH and CHCl 3 solvents, respectively. 1HNMR, IR, elemental analyses, and UV-vis techniques characterize the two morpholinium charge-transfer complexes. Benesi-Hildebrand and its modification methods were applied to the determination of association constant ( K), molar extinction coefficient ( ɛ). The X-ray crystal structure was carried out for the interpretation the predict structure of the [(Hmorp)(pa)] 2 complex.

Discrete shaped strain sensors for intelligent structures

NASA Technical Reports Server (NTRS)

Andersson, Mark S.; Crawley, Edward F.

1992-01-01

Design of discrete, highly distributed sensor systems for intelligent structures has been studied. Data obtained indicate that discrete strain-averaging sensors satisfy the functional requirements for distributed sensing of intelligent structures. Bartlett and Gauss-Hanning sensors, in particular, provide good wavenumber characteristics while meeting the functional requirements. They are characterized by good rolloff rates and positive Fourier transforms for all wavenumbers. For the numerical integration schemes, Simpson's rule is considered to be very simple to implement and consistently provides accurate results for five sensors or more. It is shown that a sensor system that satisfies the functional requirements can be applied to a structure that supports mode shapes with purely sinusoidal curvature.

Assessing Structure and Condition of Temperate And Tropical Forests: Fusion of Terrestrial Lidar and Airborne Multi-Angle and Lidar Remote Sensing

NASA Astrophysics Data System (ADS)

Saenz, Edward J.

Forests provide vital ecosystem functions and services that maintain the integrity of our natural and human environment. Understanding the structural components of forests (extent, tree density, heights of multi-story canopies, biomass, etc.) provides necessary information to preserve ecosystem services. Increasingly, remote sensing resources have been used to map and monitor forests globally. However, traditional satellite and airborne multi-angle imagery only provide information about the top of the canopy and little about the forest structure and understory. In this research, we investigative the use of rapidly evolving lidar technology, and how the fusion of aerial and terrestrial lidar data can be utilized to better characterize forest stand information. We further apply a novel terrestrial lidar methodology to characterize a Hemlock Woolly Adelgid infestation in Harvard Forest, Massachusetts, and adapt a dynamic terrestrial lidar sampling scheme to identify key structural vegetation profiles of tropical rainforests in La Selva, Costa Rica.

Effect of Pd substitution for Ni on magnetism in UNiAl

NASA Astrophysics Data System (ADS)

Dremov, R. V.; Andreev, A. V.; Šebek, J.; Mushnikov, N. V.; Goto, T.; Havela, L.; Sechovský, V.; Shiokawa, Y.; Homma, Y.

1999-01-01

Itinerant 5f-electron antiferromagnet UNiAl ( TN=19.3 K) undergoes a metamagnetic transition in fields ( Bc≈11 T) applied along the c-axis of the hexagonal ZrNiAl-type structure. The same structure is preserved in the UNi 1- xPd xAl solid solutions x⩽0.4 characterized by isotropic lattice expansion with increasing x. The gradual increase of Bc and TN due to the Pd doping can be tentatively attributed to enhancement of antiferromagnetic exchange interactions.

To the theory of hybrid modes of the discrete spectrum in finite structures with nanocrystalline films

NASA Astrophysics Data System (ADS)

Kireeva, Anastassiya I.; Rudenok, Igor P.

2018-04-01

The profound research and physical applications of interactions of different types of waves with medium are very important. Particularly the most interesting sphere is for complex environments, which may be characterized by the increasing number of methods. Their objective analysis increased because of great applied significance. For the optical range it comes to considering the structure, the dimensions of the spatial inhomogeneity of which are comparable to the wavelength of the radiation.

Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

PubMed Central

D'Atri, Valentina; Porrini, Massimiliano; Rosu, Frédéric; Gabelica, Valérie

2015-01-01

Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting ΩCALC are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with ΩEXP determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26259654

Electric-field-induced structural modulation of epitaxial BiFeO3 multiferroic thin films as studied using x-ray microdiffraction

NASA Astrophysics Data System (ADS)

Bark, Chung W.; Ryu, Sangwoo; Koo, Yang M.; Jang, Hyun M.; Youn, Hwa S.

2007-01-01

An in situ method, called synchrotron x-ray microdiffraction, was introduced to examine the electric-field-induced structural modulation of the epitaxially grown pseudotetragonal BiFeO3 thin film. To evaluate the d spacing (d001) from the measured intensity contour in the 2θ-χ space, the peak position in each diffraction profile was determined by applying two-dimensional Lorentzian fitting. By tracing the change of d spacing as a function of the applied electric field and by examining the Landau free energy function for P4mm symmetry, the authors were able to estimate the two important parameters that characterize the field-induced structural modulation. The estimated linear piezoelectric coefficient (d33) at zero-field limit is 15pm /V, and the effective nonlinear electrostrictive coefficient (Qeff) is as low as ˜8.0×10-3m4/C2.

Foamability and structure analysis of foams in Hele-Shaw cell

NASA Astrophysics Data System (ADS)

Caps, H.; Vandewalle, N.; Broze, G.; Zocchi, G.

2007-05-01

The authors have generated two-dimensional foams by imposing an intermittent drainage in a Hele-Shaw cell partially filled with a detergent/water mixture. The foam generation associated with this process is reproducible and depends on the surfactant molecules composing the solution. A kinetic model can be proposed for the foam evolution. The structure of the foam is also investigated: the average bubble side number and correlation functions are measured. Distinguishable behaviors are observed for different surfactant molecules. This way of producing a foam is thus adequate for applied foam structure characterizations and fundamental studies.

Characterization and manufacture of braided composites for large commercial aircraft structures

NASA Technical Reports Server (NTRS)

Fedro, Mark J.; Willden, Kurtis

1992-01-01

Braided composite materials has been recognized as a potential cost effective material form for fuselage structural elements. Consequently, there is a strong need for more knowledge in the design, manufacture, test, and analysis of textile structural composites. Advance braided composite technology is advanced towards applications to a large commercial transport fuselage. The mechanics are summarized of materials and manufacturing demonstration results which were obtained in order to acquire an understanding of how braided composites can be applied to a commercial fuselage. Textile composites consisting of 2-D, 2-D triaxial, and 3-D braid patterns with thermoplastic and two resin transfer molding resin systems were studied. The structural performance of braided composites was evaluated through an extensive mechanical test program. Analytical methods were also developed and applied to predict the following: internal fiber architecture; stiffness; fiber stresses; failure mechanisms; notch effects; and the history of failure of the braided composite specimens. The applicability of braided composites to a commercial transport fuselage was further assessed through a manufacturing demonstration.

Utilization of protein intrinsic disorder knowledge in structural proteomics

PubMed Central

Oldfield, Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A. Keith; Uversky, Vladimir N.

2014-01-01

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed. PMID:23232152

Fabrication and characterization of dichroic fine crystals by the reprecipitation method

NASA Astrophysics Data System (ADS)

Iino, Tatsuya; Mori, Shunsuke; Shito, Keiji; Kimura, Ayaka; Morishita, Yoshii; Chiba, Takayuki; Katagiri, Hiroshi; Okada, Shuji; Masuhara, Akito

2018-06-01

Suspended particle devices can rapidly switch from a dark blue state to a clear state by applying AC voltage, but their maximum transmittance has to be improved. In this work, we have targeted dichroic dyes and applied the reprecipitation method to KPD-503, a trisazo dye showing little dichroism in bulk crystals despite the dye molecules having large dichroism. As a result, microcrystals showing large dichroism were obtained. These microcrystals were considered to have a kinetically stable structure and oriented by voltage in a dispersing medium.

Surveillance theory applied to virus detection: a case for targeted discovery

USGS Publications Warehouse

Bogich, Tiffany L.; Anthony, Simon J.; Nichols, James D.

2013-01-01

Virus detection and mathematical modeling have gone through rapid developments in the past decade. Both offer new insights into the epidemiology of infectious disease and characterization of future risk; however, modeling has not yet been applied to designing the best surveillance strategies for viral and pathogen discovery. We review recent developments and propose methods to integrate viral and pathogen discovery and mathematical modeling through optimal surveillance theory, arguing for a more targeted approach to novel virus detection guided by the principles of adaptive management and structured decision-making.

Population activity structure of excitatory and inhibitory neurons

PubMed Central

Doiron, Brent

2017-01-01

Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure. PMID:28817581

Fabrication and characterization of self-folding thermoplastic sheets using unbalanced thermal shrinkage.

PubMed

Danielson, Christian; Mehrnezhad, Ali; YekrangSafakar, Ashkan; Park, Kidong

2017-06-14

Self-folding or micro-origami technologies are actively investigated as a novel manufacturing process to fabricate three-dimensional macro/micro-structures. In this paper, we present a simple process to produce a self-folding structure with a biaxially oriented polystyrene sheet (BOPS) or Shrinky Dinks. A BOPS sheet is known to shrink to one-third of its original size in plane, when it is heated above 160 °C. A grid pattern is engraved on one side of the BOPS film with a laser engraver to decrease the thermal shrinkage of the engraved side. The thermal shrinkage of the non-engraved side remains the same and this unbalanced thermal shrinkage causes folding of the structure as the structure shrinks at high temperature. We investigated the self-folding mechanism and characterized how the grid geometry, the grid size, and the power of the laser engraver affect the bending curvature. The developed fabrication process to locally modulate thermomechanical properties of the material by engraving the grid pattern and the demonstrated design methodology to harness the unbalanced thermal shrinkage can be applied to develop complicated self-folding macro/micro structures.

Identification and structural characterization of serobactins, a suite of lipopeptide siderophores produced by the grass endophyte Herbaspirillum seropedicae.

PubMed

Rosconi, Federico; Davyt, Danilo; Martínez, Verónica; Martínez, Marcela; Abin-Carriquiry, Juan Andrés; Zane, Hannah; Butler, Alison; de Souza, Emanuel M; Fabiano, Elena

2013-03-01

Herbaspirillum seropedicae Z67 is a diazotrophic endophyte able to colonize the interior of many economically relevant crops such as rice, wheat, corn and sorghum. Structures of siderophores produced by bacterial endophytes have not yet been elucidated. The aim of this work was to identify and characterize the siderophores produced by this bacterium. In a screening for mutants unable to produce siderophores we found a mutant that had a transposon insertion in a non-ribosomal peptide synthase (NRPS) gene coding for a putative siderophore biosynthetic enzyme. The chemical structure of the siderophore was predicted using computational genomic tools. The predicted structure was confirmed by chemical analysis. We found that siderophores produced by H. seropedicae Z67 are a suite of amphiphilic lipopeptides, named serobactin A, B and C, which vary by the length of the fatty acid chain. We also demonstrated the biological activity of serobactins as nutritional iron sources for H. seropedicae. These are the first structurally described siderophores produced by endophytic bacteria. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Talent Development as an Ecology of Games: A Case Study of Norwegian Handball

ERIC Educational Resources Information Center

Bjørndal, Christian Thue; Ronglan, Lars Tore; Andersen, Svein S.

2017-01-01

Structured talent identification and development, it has been argued, is one of the foundations of international sporting success and many modern elite sport systems have applied normative talent development (TD) models. The success of Norwegian handball, however, is based on an alternative approach to TD. Norwegian handball is characterized by a…

Efficiency vs. Effectiveness: Can W. Edwards Deming's Principles of Quality Management Be Applied Successfully to American Education.

ERIC Educational Resources Information Center

Petry, John R.

The field of education has been slow to recognize the Total Quality Management (TQM) concept. This resistance may result from entrenched management styles characterized by hierarchical decision-making structures. TQM emphasizes management based on leadership instead of management by objective, command, and coercion. The TQM concept consists of…

Characterization of Aggregation Propensity of a Human Fc-Fusion Protein Therapeutic by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; Iacob, Roxana E.; Krystek, Stanley R.; Jin, Mi; Wei, Hui; Tao, Li; Das, Tapan K.; Tymiak, Adrienne A.; Engen, John R.; Chen, Guodong

2017-05-01

Aggregation of protein therapeutics has long been a concern across different stages of manufacturing processes in the biopharmaceutical industry. It is often indicative of aberrant protein therapeutic higher-order structure. In this study, the aggregation propensity of a human Fc-fusion protein therapeutic was characterized. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to examine the conformational dynamics of dimers collected from a bioreactor. HDX-MS data combined with spatial aggregation propensity calculations revealed a potential aggregation interface in the Fc domain. This study provides a general strategy for the characterization of the aggregation propensity of Fc-fusion proteins at the molecular level.

Characterization of Low-Molecular-Weight Heparins by Strong Anion-Exchange Chromatography.

PubMed

Sadowski, Radosław; Gadzała-Kopciuch, Renata; Kowalkowski, Tomasz; Widomski, Paweł; Jujeczka, Ludwik; Buszewski, Bogusław

2017-11-01

Currently, detailed structural characterization of low-molecular-weight heparin (LMWH) products is an analytical subject of great interest. In this work, we carried out a comprehensive structural analysis of LMWHs and applied a modified pharmacopeial method, as well as methods developed by other researchers, to the analysis of novel biosimilar LMWH products; and, for the first time, compared the qualitative and quantitative composition of commercially available drugs (enoxaparin, nadroparin, and dalteparin). For this purpose, we used strong anion-exchange (SAX) chromatography with spectrophotometric detection because this method is more helpful, easier, and faster than other separation techniques for the detailed disaccharide analysis of new LMWH drugs. In addition, we subjected the obtained results to statistical analysis (factor analysis, t-test, and Newman-Keuls post hoc test).

Synthesis and characterization of a novel schiff base of 1,2-diaminopropane with substituted salicyaldehyde and its transition metal complexes: Single crystal structures and biological activities

NASA Astrophysics Data System (ADS)

Tadavi, Samina K.; Yadav, Abhijit A.; Bendre, Ratnamala S.

2018-01-01

A novel schiff base H2L derived from simple condensation of 2-hydroxy-6-isopropyl-3-methyl benzaldehyde and 1,2-diaminopropane in 2:1 M ratio and its [MnL], [CoL] and [NiL]2 complexes have been prepared and characterized by spectroscopic technique, elemental analysis, SEM-EDX analysis, and cyclic voltammetry. Additionally, single crystal X-ray diffraction technique has been applied to the schiff base ligand H2L and its nickel complex. The structure of nickel complex exhibited dimeric form with formula [NiL]2 with distorted square planar geometry around each nickel center. Furthermore, all the synthesized compounds were screened for their antimicrobial and antioxidant and DNA cleavage activities.

Structural Health Monitoring Using Textile Reinforcement Structures with Integrated Optical Fiber Sensors

PubMed Central

Bremer, Kort; Weigand, Frank; Zheng, Yulong; Alwis, Lourdes Shanika; Helbig, Reinhard; Roth, Bernhard

2017-01-01

Optical fiber-based sensors “embedded” in functionalized carbon structures (FCSs) and textile net structures (TNSs) based on alkaline-resistant glass are introduced for the purpose of structural health monitoring (SHM) of concrete-based structures. The design aims to monitor common SHM parameters such as strain and cracks while at the same time acting as a structural strengthening mechanism. The sensor performances of the two systems are characterized in situ using Mach-Zehnder interferometric (MZI) and optical attenuation measurement techniques, respectively. For this purpose, different FCS samples were subjected to varying elongation using a tensile testing machine by carefully incrementing the applied force, and good correlation between the applied force and measured length change was observed. For crack detection, the functionalized TNSs were embedded into a concrete block which was then exposed to varying load using the three-point flexural test until destruction. Promising results were observed, identifying that the location of the crack can be determined using the conventional optical time domain reflectometry (OTDR) technique. The embedded sensors thus evaluated show the value of the dual achievement of the schemes proposed in obtaining strain/crack measurement while being utilized as strengthening agents as well. PMID:28208636

Side-Chain Liquid Crystalline Poly(meth)acrylates with Bent-Core Mesogens

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

Chen,X.; Tenneti, K.; Li, C.

2007-01-01

We report the design, synthesis, and characterization of side-chain liquid crystalline (LC) poly(meth)acrylates with end-on bent-core liquid crystalline (BCLC) mesogens. Both conventional free radical polymerization and atom transfer radical polymerization have been used to synthesize these liquid crystalline polymers (LCP). The resulting polymers exhibit thermotropic LC behavior. Differential scanning calorimetry, thermopolarized light microscopy, wide-angle X-ray diffraction, and small-angle X-ray scattering were used to characterize the LC structure of both monomers and polymers. The electro-optic (EO) measurement was carried out by applying a triangular wave and measuring the LC EO response. SmCP (Smectic C indicates the LC molecules are tilted withmore » respect to the layer normal; P denotes polar ordering) phases were observed for both monomers and polymers. In LC monomers, typical antiferroelectric switching was observed. In the ground state, SmCP{sub A} (A denotes antiferroelectric) was observed which switched to SmCP{sub F} (F denotes ferroelectric) upon applying an electric field. In the corresponding LCP, a unique bilayer structure was observed, which is different from the reported BCLC bilayer SmCG (G denotes generated) phase. Most of the LCPs did not switch upon applying electric field while weak AF switching was observed in a low molecular weight poly{l_brace}3'-[4-(4-n-dodecyloxybenzoyloxy)benzoyloxy]-4-(12-acryloyloxydodecyloxy)benzoyloxybiphenyl{r_brace} sample.« less

Electroluminescent devices formed using semiconductor nanocrystals as an electron transport media and method of making such electroluminescent devices

DOEpatents

Alivisatos, A. Paul; Colvin, Vickie

1996-01-01

An electroluminescent device is described, as well as a method of making same, wherein the device is characterized by a semiconductor nanocrystal electron transport layer capable of emitting visible light in response to a voltage applied to the device. The wavelength of the light emitted by the device may be changed by changing either the size or the type of semiconductor nanocrystals used in forming the electron transport layer. In a preferred embodiment the device is further characterized by the capability of emitting visible light of varying wavelengths in response to changes in the voltage applied to the device. The device comprises a hole processing structure capable of injecting and transporting holes, and usually comprising a hole injecting layer and a hole transporting layer; an electron transport layer in contact with the hole processing structure and comprising one or more layers of semiconductor nanocrystals; and an electron injecting layer in contact with the electron transport layer for injecting electrons into the electron transport layer. The capability of emitting visible light of various wavelengths is principally based on the variations in voltage applied thereto, but the type of semiconductor nanocrystals used and the size of the semiconductor nanocrystals in the layers of semiconductor nanometer crystals may also play a role in color change, in combination with the change in voltage.

Effects of alginate hydrogel cross-linking density on mechanical and biological behaviors for tissue engineering.

PubMed

Jang, Jinah; Seol, Young-Joon; Kim, Hyeon Ji; Kundu, Joydip; Kim, Sung Won; Cho, Dong-Woo

2014-09-01

An effective cross-linking of alginate gel was made through reaction with calcium carbonate (CaCO3). We used human chondrocytes as a model cell to study the effects of cross-linking density. Three different pore size ranges of cross-linked alginate hydrogels were fabricated. The morphological, mechanical, and rheological properties of various alginate hydrogels were characterized and responses of biosynthesis of cells encapsulated in each gel to the variation in cross-linking density were investigated. Desired outer shape of structure was maintained when the alginate solution was cross-linked with the applied method. The properties of alginate hydrogel could be tailored through applying various concentrations of CaCO3. The rate of synthesized GAGs and collagens was significantly higher in human chondrocytes encapsulated in the smaller pore structure than that in the larger pore structure. The expression of chondrogenic markers, including collagen type II and aggrecan, was enhanced in the smaller pore structure. It was found that proper structural morphology is a critical factor to enhance the performance and tissue regeneration. Copyright © 2014 Elsevier Ltd. All rights reserved.

An electromagnetic induction method for underground target detection and characterization

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

Bartel, L.C.; Cress, D.H.

1997-01-01

An improved capability for subsurface structure detection is needed to support military and nonproliferation requirements for inspection and for surveillance of activities of threatening nations. As part of the DOE/NN-20 program to apply geophysical methods to detect and characterize underground facilities, Sandia National Laboratories (SNL) initiated an electromagnetic induction (EMI) project to evaluate low frequency electromagnetic (EM) techniques for subsurface structure detection. Low frequency, in this case, extended from kilohertz to hundreds of kilohertz. An EMI survey procedure had already been developed for borehole imaging of coal seams and had successfully been applied in a surface mode to detect amore » drug smuggling tunnel. The SNL project has focused on building upon the success of that procedure and applying it to surface and low altitude airborne platforms. Part of SNL`s work has focused on improving that technology through improved hardware and data processing. The improved hardware development has been performed utilizing Laboratory Directed Research and Development (LDRD) funding. In addition, SNL`s effort focused on: (1) improvements in modeling of the basic geophysics of the illuminating electromagnetic field and its coupling to the underground target (partially funded using LDRD funds) and (2) development of techniques for phase-based and multi-frequency processing and spatial processing to support subsurface target detection and characterization. The products of this project are: (1) an evaluation of an improved EM gradiometer, (2) an improved gradiometer concept for possible future development, (3) an improved modeling capability, (4) demonstration of an EM wave migration method for target recognition, and a demonstration that the technology is capable of detecting targets to depths exceeding 25 meters.« less

Biophysical characterization of the structural change of Nopp140, an intrinsically disordered protein, in the interaction with CK2α

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

Na, Jung-Hyun; Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792; Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760

2016-08-19

Nucleolar phosphoprotein 140 (Nopp140) is a nucleolar protein, more than 80% of which is disordered. Previous studies have shown that the C-terminal region of Nopp140 (residues 568–596) interacts with protein kinase CK2α, and inhibits the catalytic activity of CK2. Although the region of Nopp140 responsible for the interaction with CK2α was identified, the structural features and the effect of this interaction on the structure of Nopp140 have not been defined due to the difficulty of structural characterization of disordered protein. In this study, the disordered feature of Nopp140 and the effect of CK2α on the structure of Nopp140 were examinedmore » using single-molecule fluorescence resonance energy transfer (smFRET) and electron paramagnetic resonance (EPR). The interaction with CK2α was increased conformational rigidity of the CK2α-interacting region of Nopp140 (Nopp140C), suggesting that the disordered and flexible conformation of Nopp140C became more rigid conformation as it binds to CK2α. In addition, site specific spin labeling and EPR analysis confirmed that the residues 574–589 of Nopp140 are critical for binding to CK2α. Similar technical approaches can be applied to analyze the conformational changes in other IDPs during their interactions with binding partners. - Highlights: • Nopp140 is intrinsically disordered protein (IDP). • Conformation of Nopp140 became more rigid conformation due to interaction with CK2α. • smFRET and EPR could be applied to analyze the structural changes of IDPs.« less

Information Theory Applied to Animal Communication Systems and Its Possible Application to SETI

NASA Astrophysics Data System (ADS)

Hanser, Sean F.; Doyle, Laurance R.; McCowan, Brenda; Jenkins, Jon M.

2004-06-01

Information theory, as first introduced by Claude Shannon (Shannon &Weaver 1949) quantitatively evaluates the organizational complexity of communication systems. At the same time George Zipf was examining linguistic structure in a way that was mathematically similar to the components of the Shannon first-order entropy (Zipf 1949). Both Shannon's and Zipf's mathematical procedures have been applied to animal communication and recently have been providing insightful results. The Zipf plot is a useful tool for a first estimate of the characterization of a communication system's complexity (which can later be examined for complex structure at deeper levels using Shannon entropic analysis). In this paper we shall discuss some of the applications and pitfalls of using the Zipf distribution as a preliminary evaluator of the communication complexity of a signaling system.

Structural characterization and aging of glassy pharmaceuticals made using acoustic levitation.

PubMed

Benmore, Chris J; Weber, J K R; Tailor, Amit N; Cherry, Brian R; Yarger, Jeffery L; Mou, Qiushi; Weber, Warner; Neuefeind, Joerg; Byrn, Stephen R

2013-04-01

Here, we report the structural characterization of several amorphous drugs made using the method of quenching molten droplets suspended in an acoustic levitator. (13) C NMR, X-ray, and neutron diffraction results are discussed for glassy cinnarizine, carbamazepine, miconazole nitrate, probucol, and clotrimazole. The (13) C NMR results did not find any change in chemical bonding induced by the amorphization process. High-energy X-ray diffraction results were used to characterize the ratio of crystalline to amorphous material present in the glasses over a period of 8 months. All the glasses were stable for at least 6 months except carbamazepine, which has a strong tendency to crystallize within a few months. Neutron and X-ray pair distribution function analyses were applied to the glassy materials, and the results were compared with their crystalline counterparts. The two diffraction techniques yielded similar results in most cases and identified distinct intramolecular and intermolecular correlations. The intramolecular scattering was calculated based on the crystal structure and fit to the measured X-ray structure factor. The resulting intermolecular pair distribution functions revealed broad-nearest and next-nearest neighbor molecule-molecule correlations. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 102:1290-1300, 2013. Copyright © 2013 Wiley Periodicals, Inc.

Offdiagonal complexity: A computationally quick complexity measure for graphs and networks

NASA Astrophysics Data System (ADS)

Claussen, Jens Christian

2007-02-01

A vast variety of biological, social, and economical networks shows topologies drastically differing from random graphs; yet the quantitative characterization remains unsatisfactory from a conceptual point of view. Motivated from the discussion of small scale-free networks, a biased link distribution entropy is defined, which takes an extremum for a power-law distribution. This approach is extended to the node-node link cross-distribution, whose nondiagonal elements characterize the graph structure beyond link distribution, cluster coefficient and average path length. From here a simple (and computationally cheap) complexity measure can be defined. This offdiagonal complexity (OdC) is proposed as a novel measure to characterize the complexity of an undirected graph, or network. While both for regular lattices and fully connected networks OdC is zero, it takes a moderately low value for a random graph and shows high values for apparently complex structures as scale-free networks and hierarchical trees. The OdC approach is applied to the Helicobacter pylori protein interaction network and randomly rewired surrogates.

Information diffusion in structured online social networks

NASA Astrophysics Data System (ADS)

Li, Pei; Zhang, Yini; Qiao, Fengcai; Wang, Hui

2015-05-01

Nowadays, due to the word-of-mouth effect, online social networks have been considered to be efficient approaches to conduct viral marketing, which makes it of great importance to understand the diffusion dynamics in online social networks. However, most research on diffusion dynamics in epidemiology and existing social networks cannot be applied directly to characterize online social networks. In this paper, we propose models to characterize the information diffusion in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and study the diffusion threshold, above which the user influence of generating a message will approach infinity. We conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly. These results are of use in understanding the diffusion dynamics in online social networks and also critical for advertisers in viral marketing who want to estimate the user influence before posting an advertisement.

Mode extraction on wind turbine blades via phase-based video motion estimation

NASA Astrophysics Data System (ADS)

Sarrafi, Aral; Poozesh, Peyman; Niezrecki, Christopher; Mao, Zhu

2017-04-01

In recent years, image processing techniques are being applied more often for structural dynamics identification, characterization, and structural health monitoring. Although as a non-contact and full-field measurement method, image processing still has a long way to go to outperform other conventional sensing instruments (i.e. accelerometers, strain gauges, laser vibrometers, etc.,). However, the technologies associated with image processing are developing rapidly and gaining more attention in a variety of engineering applications including structural dynamics identification and modal analysis. Among numerous motion estimation and image-processing methods, phase-based video motion estimation is considered as one of the most efficient methods regarding computation consumption and noise robustness. In this paper, phase-based video motion estimation is adopted for structural dynamics characterization on a 2.3-meter long Skystream wind turbine blade, and the modal parameters (natural frequencies, operating deflection shapes) are extracted. Phase-based video processing adopted in this paper provides reliable full-field 2-D motion information, which is beneficial for manufacturing certification and model updating at the design stage. The phase-based video motion estimation approach is demonstrated through processing data on a full-scale commercial structure (i.e. a wind turbine blade) with complex geometry and properties, and the results obtained have a good correlation with the modal parameters extracted from accelerometer measurements, especially for the first four bending modes, which have significant importance in blade characterization.

Steel bridge retrofit evaluation

NASA Astrophysics Data System (ADS)

Prine, David W.

1998-03-01

The development of a retrofit design aimed at retarding or eliminating fatigue crack growth in a large bridge can be a very difficult and expensive procedure. Analytical techniques frequently do not provide sufficient accuracy when applied to complex structural details. The Infrastructure Technology Institute (ITI) of Northwestern University, under contract to the California Department of Transportation (Caltrans), recently applied experimental state-of-the-art NDE technology to the Interstate 80 bridge over the Sacramento River near Sacramento, California (Bryte Bend). Acoustic emission monitoring was applied in conjunction with strain gage monitoring to aid in characterizing the retrofits' effect on existing active fatigue cracks. The combined test results clearly showed that one retrofit design was superior to the other.

Unified constitutive models for high-temperature structural applications

NASA Technical Reports Server (NTRS)

Lindholm, U. S.; Chan, K. S.; Bodner, S. R.; Weber, R. M.; Walker, K. P.

1988-01-01

Unified constitutive models are characterized by the use of a single inelastic strain rate term for treating all aspects of inelastic deformation, including plasticity, creep, and stress relaxation under monotonic or cyclic loading. The structure of this class of constitutive theory pertinent for high temperature structural applications is first outlined and discussed. The effectiveness of the unified approach for representing high temperature deformation of Ni-base alloys is then evaluated by extensive comparison of experimental data and predictions of the Bodner-Partom and the Walker models. The use of the unified approach for hot section structural component analyses is demonstrated by applying the Walker model in finite element analyses of a benchmark notch problem and a turbine blade problem.

Parametric modelling design applied to weft knitted surfaces and its effects in their physical properties

NASA Astrophysics Data System (ADS)

Oliveira, N. P.; Maciel, L.; Catarino, A. P.; Rocha, A. M.

2017-10-01

This work proposes the creation of models of surfaces using a parametric computer modelling software to obtain three-dimensional structures in weft knitted fabrics produced on single needle system machines. Digital prototyping, another feature of digital modelling software, was also explored in three-dimensional drawings generated using the Rhinoceros software. With this approach, different 3D structures were developed and produced. Physical characterization tests were then performed on the resulting 3D weft knitted structures to assess their ability to promote comfort. From the obtained results, it is apparent that the developed structures have potential for application in different market segments, such as clothing and interior textiles.

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

Li, Shuning; Roy, Amitava; Lichtenberg, Henning

The micro-segmented flow technique was applied for continuous synthesis of ZnO micro- and nanoparticles with short residence times of 9.4 s and 21.4 s, respectively. The obtained particles were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Small angle X-ray scattering (SAXS) and photoluminescence spectroscopy were used to determine the size and optical properties of ZnO nanoparticles. In addition, extended X-ray absorption fine structure (EXAFS) spectroscopy was employed to investigate local structural properties. The EXAFS measurements reveal a larger degree of structural disorder in the nanoparticles than the microparticles. These structural changes should be taken into considerationmore » while evaluating the size-dependent visible emission of ZnO nanoparticles.« less

Determination of the structural phase and octahedral rotation angle in halide perovskites

NASA Astrophysics Data System (ADS)

dos Reis, Roberto; Yang, Hao; Ophus, Colin; Ercius, Peter; Bizarri, Gregory; Perrodin, Didier; Shalapska, Tetiana; Bourret, Edith; Ciston, Jim; Dahmen, Ulrich

2018-02-01

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurement of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). The approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.

Learning and Information Approaches for Inference in Dynamic Data-Driven Geophysical Applications

NASA Astrophysics Data System (ADS)

Ravela, S.

2015-12-01

Many Geophysical inference problems are characterized by non-linear processes, high-dimensional models and complex uncertainties. A dynamic coupling between models, estimation, and sampling is typically sought to efficiently characterize and reduce uncertainty. This process is however fraught with several difficulties. Among them, the key difficulties are the ability to deal with model errors, efficacy of uncertainty quantification and data assimilation. In this presentation, we present three key ideas from learning and intelligent systems theory and apply them to two geophysical applications. The first idea is the use of Ensemble Learning to compensate for model error, the second is to develop tractable Information Theoretic Learning to deal with non-Gaussianity in inference, and the third is a Manifold Resampling technique for effective uncertainty quantification. We apply these methods, first to the development of a cooperative autonomous observing system using sUAS for studying coherent structures. We apply this to Second, we apply this to the problem of quantifying risk from hurricanes and storm surges in a changing climate. Results indicate that learning approaches can enable new effectiveness in cases where standard approaches to model reduction, uncertainty quantification and data assimilation fail.

Characterization of Viscoelastic Materials Through an Active Mixer by Direct-Ink Writing

NASA Astrophysics Data System (ADS)

Drake, Eric

The goal of this thesis is two-fold: First, to determine mixing effectiveness of an active mixer attachment to a three-dimensional (3D) printer by characterizing actively-mixed, three-dimensionally printed silicone elastomers. Second, to understand mechanical properties of a printed lattice structure with varying geometry and composition. Ober et al defines mixing effectiveness as a measureable quantity characterized by two key variables: (i) a dimensionless impeller parameter (O ) that depends on mixer geometry as well as Peclet number (Pe) and (ii) a coefficient of variation (COV) that describes the mixer effectiveness based upon image intensity. The first objective utilizes tungsten tracer particles distributed throughout a batch of Dow Corning SE1700 (two parts silicone) - ink "A". Ink "B" is made from pure SE1700. Using the in-site active mixer, both ink "A" and "B" coalesce to form a hybrid ink just before extrusion. Two samples of varying mixer speeds and composition ratios are printed and analyzed by microcomputed tomography (MicroCT). A continuous stirred tank reactor (CSTR) model is applied to better understand mixing behavior. Results are then compared with computer models to verify the hypothesis. Data suggests good mixing for the sample with higher impeller speed. A Radial Distrubtion Function (RDF) macro is used to provide further qualitative analysis of mixing efficiency. The second objective of this thesis utilized three-dimensionally printed samples of varying geometry and composition to ascertain mechanical properties. Samples were printed using SE1700 provided by Lawrence Livermore National Laboratory with a face-centered tetragonal (FCT) structure. Hardness testing is conducted using a Shore OO durometer guided by a computer-controlled, three-axis translation stage to provide precise movements. Data is collected across an 'x-y' plane of the specimen. To explain the data, a simply supported beam model is applied to a single unit cell which yields basic structural behavior per cell. Characterizing the sample as a whole requires a more rigorous approach and non-trivial complexities due to varying geometries and compositions exist. The data demonstrates a uniform change in hardness as a function of position. Additionally, the data indicates periodicities in the lattice structure.

Detection and characterization of defects in moving parts of wind turbines

NASA Astrophysics Data System (ADS)

Forero, E.; Tibaduiza, D.; Anaya, M.; Castro, R.

2016-07-01

The detection, localization and characterization of defects in a material or a part that conform a structure is possible by using the transmission and reception of ultrasonic signals. Different strategies are used to achieve extract information from the part under evaluation. For this, it is then possible to use a distributed sensors arrays on the surface of the material and using scanning techniques such as are A-scan or B-scan, where it is possible to increase the level of detail regarding location, orientation and size of defects found, according to the strategy used. However, the systems and inspection techniques are often limited by the geometries and access to different types of structures. Due to these reasons, the acquisition of the returned signals, for identification and attenuation time, can suppress valuable information for accurate characterization of imperfections found in shape and location. In this paper, the use of spectral analysis of the collected signals is proposed as a tool for detection and characterization of defects in a structure. This analysis allows to determining the power distribution in a frequency range. This methodology is useful in non-destructive evaluation when it is not possible to have full access to the structure under inspection. In this case it is applied on a wind turbine operating to make the study of different echoes captured according to the geometry of the part and comparing said conducting analysis with previously established patterns of shapes, orientations, and sizes of defects found.

Three Dimensional Urban Characterization by IFSAR Measurements

NASA Technical Reports Server (NTRS)

Gamba, P.; Houshmand, B.

1998-01-01

In this paper a machine vision approach is applied to Interferometric Synthetic Aperture Radars (IFSAR) data to extract the most relevant built structures in a dense urban environment. The algorithm tries to cluster primitives (line segments) into more complex surfaces (planes) to approximate the 3D shape of these objects. Very interesting results starting from TOPSAR data recorded over S, Monica are presented.

LC-MS and MS/MS in the analysis of recombinant proteins

NASA Astrophysics Data System (ADS)

Coulot, M.; Domon, B.; Grossenbacher, H.; Guenat, C.; Maerki, W.; Müller, D. R.; Richter, W. J.

1993-03-01

Applicability and performance of electrospray ionization mass spectrometry (ESIMS) is demonstrated for protein analysis. ESIMS is applied in conjunction with on-line HPLC (LC-ESlMS) and direct tandem mass spectrometry (positive and negative ion mode ESlMS/MS) to the structural characterization of a recombinant protein (r-hirudin variant 1) and a congener phosphorylated at threonine 45 (RP-1).

Calculation and visualization of free energy barriers for several VOCs and TNT in HKUST-1.

PubMed

Sarkisov, Lev

2012-11-28

A simple protocol based on a lattice representation of the porous space is proposed to locate and characterize the free energy bottle-necks in rigid metal organic frameworks. As an illustration we apply this method to HKUST-1 to demonstrate that there are impassable free energy barriers for molecules of trinitrotoluene in this structure.

Zwitterionic-hydrophilic interaction capillary liquid chromatography coupled to tandem mass spectrometry for the characterization of human alpha-acid-glycoprotein N-glycan isomers.

PubMed

Mancera-Arteu, Montserrat; Giménez, Estela; Barbosa, José; Peracaula, Rosa; Sanz-Nebot, Victòria

2017-10-23

In this work, a μZIC-HILIC-MS/MS methodology was established in negative ion mode for the characterization of glycan isomers. The possibility to separate the glycan isomers by the μZIC-HILIC strategy coupled to a high resolution tandem mass spectrometry detection permitted us to obtain valuable information about each glycan structure. The most important diagnostic ion fragments previously described to characterize structural features of glycans, were evaluated in this study using hAGP as model glycoprotein. The assignation of hAGP glycan isomers performed in our previous work using the GRIL strategy in combination with exoglycosidase digestion [1] was used in this paper to confirm or discard some ion fragments reported in the literature and delve into the structural characterization of glycan isomers. Sialic acid as well as fucose linkage-type glycan isomers were assigned using this approach and daughter ions with higher diagnostic value were determined. The location of α2-3/α2-6 sialic acids on antennas and a deeper characterization of several highly sialylated tri- and tetraantennary glycans was also possible using the established MS/MS method. Moreover, relying on the characterization performed in Ref. [1], core and antenna fucosylation were differentiated in this work using specific ion fragments obtained in the tandem mass spectra. This methodology was also applied to hAGP purified from control and pathological serum samples, which corroborated its robustness and its potential for finding novel glycan-based biomarkers in patho-glycomic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthesis and characterization of new complexes of nickel (II), palladium (II) and platinum(II) with derived sulfonamide ligand: Structure, DFT study, antibacterial and cytotoxicity activities

NASA Astrophysics Data System (ADS)

Bouchoucha, Afaf; Zaater, Sihem; Bouacida, Sofiane; Merazig, Hocine; Djabbar, Safia

2018-06-01

The synthesis, characterization and biological study of new nickel (II), palladium (II), and platinum (II) complexes with sulfamethoxazole ligand used in pharmaceutical field, were reported. [MLCl2].nH2O is the general formula obtained for Pd(II) and Pt(II) complexes. These complexes have been prepared and characterized by elemental analysis, FTIR, 1HNMR spectral, magnetic measurements, UV-Visible spectra, and conductivity. The DFT calculation was applied to optimize the geometric structure of the Pd(II) and Pt(II) complexes. A new single-crystal X-ray structure of the Ni(II) complex has been determined. It crystallized in monoclinic system with P 21/c space group and Z = 8. The invitro antibacterial activity of ligand and complexes against Escherichia coli, P. aeruginosa, Klebsiella pneumoniae, S. aureus, Bacillus subtilis species has been carried out and compared using agar-diffusion method. The Pd(II) and Pt(II) complexes showed a remarkable inhibition against bacteria tested. The invitro cytotoxicity assay of the complexes against three cell lines chronic myelogenous leukaemia (K562), human colon adenocarcinoma (HT-29) and breast cancer (MCF-7) was also reported.

Wideband Single-Crystal Transducer for Bone Characterization

NASA Technical Reports Server (NTRS)

Liang, Yu; Snook, Kevin

2012-01-01

The microgravity conditions of space travel result in unique physiological demands on the human body. In particular, the absence of the continual mechanical stresses on the skeletal system that are present on Earth cause the bones to decalcify. Trabecular structure decreases in thickness and increases in spacing, resulting in decreased bone strength and increased risk of injury. Thus, monitoring bone health is a high priority for long-term space travel. A single probe covering all frequency bands of interest would be ideal for such measurements, and this would also minimize storage space and eliminate the complexity of integrating multiple probes. This invention is an ultrasound transducer for the structural characterization of bone. Such characterization measures features of reflected and transmitted ultrasound signals, and correlates these signals with bone structure metrics such as bone mineral density, trabecular spacing, and thickness, etc. The techniques used to determine these various metrics require measurements over a broad range of ultrasound frequencies, and therefore, complete characterization requires the use of several narrowband transducers. This is a single transducer capable of making these measurements in all the required frequency bands. The device achieves this capability through a unique combination of a broadband piezoelectric material; a design incorporating multiple resonator sizes with distinct, overlapping frequency spectra; and a micromachining process for producing the multiple-resonator pattern with common electrode surfaces between the resonators. This device consists of a pattern of resonator bars with common electrodes that is wrapped around a central mandrel such that the radiating faces of the resonators are coplanar and can be simultaneously applied to the sample to be measured. The device operates as both a source and receiver of acoustic energy. It is operated by connection to an electronic system capable of both providing an excitation signal to the transducer and amplifying the signal received from the transducer. The excitation signal may be either a wide-bandwidth signal to excite the transducer across its entire operational spectrum, or a narrow-bandwidth signal optimized for a particular measurement technique. The transducer face is applied to the skin covering the bone to be characterized, and may be operated in through transmission mode using two transducers, or in pulse-echo mode.

Estimation of in-situ stresses in concrete members using polarized ultrasonic shear waves

NASA Astrophysics Data System (ADS)

Chen, Andrew; Schumacher, Thomas

2014-02-01

Ultrasonic testing is commonly used to detect flaws, estimate geometries, and characterize properties of materials and structures. Acoustoelasticity refers to the dependency of stress wave velocity with applied stresses and is a phenomenon that has been known by geophysicists since the 1960s. A way to capitalize on this effect for concrete applications is by using ultrasonic shear waves which are particularly sensitive to applied stresses when polarized in the direction of the applied stress. The authors conducted an experiment on a 150 mm (6 in.) diameter concrete cylinder specimen with a length of 305 mm (12 in.) that was loaded in discrete load steps to failure. At each load step two ultrasonic shear waves were transmitted through the specimen, one with the polarization perpendicular and the other transverse to the applied stress. The velocity difference between the two sets of polarized shear waves was found to correlate with the applied stress in the specimen. Two potential applications for this methodology include estimation of stresses in pre-stressed concrete bridge girders and investigation of load redistribution in structural support elements after extreme events. This paper introduces the background of the methodology, presents an analysis of the collected data, and discusses the relationship between the recorded signals and the applied stress.

Multiple-step preparation and physicochemical characterization of crystalline α-germanium hydrogenphosphate

NASA Astrophysics Data System (ADS)

Romano, Ricardo; Ruiz, Ana I.; Alves, Oswaldo L.

2004-04-01

The reaction between germanium oxide and phosphoric acid has previously been described and led to impure germanium hydrogenphosphate samples with low crystallinity. A new multiple-step route involving the same reaction under refluxing and soft hydrothermal conditions is described for the preparation of pure and crystalline α-GeP. The physicochemical characterization of the samples allows accompaniment of the reaction evolution as well as determining short- and long-range structural organization. The phase purity of the α-GeP sample was confirmed by applying Rietveld's profile analysis, which also determined the cell parameters of its crystals.

The Application of Fractal and Multifractal Theory in Hydraulic-Flow-Unit Characterization and Permeability Estimation

NASA Astrophysics Data System (ADS)

Chen, X.; Yao, G.; Cai, J.

2017-12-01

Pore structure characteristics are important factors in influencing the fluid transport behavior of porous media, such as pore-throat ratio, pore connectivity and size distribution, moreover, wettability. To accurately characterize the diversity of pore structure among HFUs, five samples selected from different HFUs (porosities are approximately equal, however permeability varies widely) were chosen to conduct micro-computerized tomography test to acquire direct 3D images of pore geometries and to perform mercury injection experiments to obtain the pore volume-radii distribution. To characterize complex and high nonlinear pore structure of all samples, three classic fractal geometry models were applied. Results showed that each HFU has similar box-counting fractal dimension and generalized fractal dimension in the number-area model, but there are significant differences in multifractal spectrums. In the radius-volume model, there are three obvious linear segments, corresponding to three fractal dimension values, and the middle one is proved as the actual fractal dimension according to the maximum radius. In the number-radius model, the spherical-pore size distribution extracted by maximum ball algorithm exist a decrease in the number of small pores compared with the fractal power rate rather than the traditional linear law. Among the three models, only multifractal analysis can classify the HFUs accurately. Additionally, due to the tightness and low-permeability in reservoir rocks, connate water film existing in the inner surface of pore channels commonly forms bound water. The conventional model which is known as Yu-Cheng's model has been proved to be typically not applicable. Considering the effect of irreducible water saturation, an improved fractal permeability model was also deduced theoretically. The comparison results showed that the improved model can be applied to calculate permeability directly and accurately in such unconventional rocks.

Measuring the bending of asymmetric planar EAP structures

NASA Astrophysics Data System (ADS)

Weiss, Florian M.; Zhao, Xue; Thalmann, Peter; Deyhle, Hans; Urwyler, Prabitha; Kovacs, Gabor; Müller, Bert

2013-04-01

The geometric characterization of low-voltage dielectric electro-active polymer (EAP) structures, comprised of nanometer thickness but areas of square centimeters, for applications such as artificial sphincters requires methods with nanometer precision. Direct optical detection is usually restricted to sub-micrometer resolution because of the wavelength of the light applied. Therefore, we propose to take advantage of the cantilever bending system with optical readout revealing a sub-micrometer resolution at the deflection of the free end. It is demonstrated that this approach allows us to detect bending of rather conventional planar asymmetric, dielectric EAP-structures applying voltages well below 10 V. For this purpose, we built 100 μm-thin silicone films between 50 nm-thin silver layers on a 25 μm-thin polyetheretherketone (PEEK) substrate. The increase of the applied voltage in steps of 50 V until 1 kV resulted in a cantilever bending that exhibits only in restricted ranges the expected square dependence. The mean laser beam displacement on the detector corresponded to 6 nm per volt. The apparatus will therefore become a powerful mean to analyze and thereby improve low-voltage dielectric EAP-structures to realize nanometer-thin layers for stack actuators to be incorporated into artificial sphincter systems for treating severe urinary and fecal incontinence.

Preparation of refractory cermet structures for lithium compatibility testing

NASA Technical Reports Server (NTRS)

Heestand, R. L.; Jones, R. A.; Wright, T. R.; Kizer, D. E.

1973-01-01

High-purity nitride and carbide cermets were synthesized for compatability testing in liquid lithium. A process was developed for the preparation of high-purity hafnium nitride powder, which was subsequently blended with tungsten powder or tantalum nitride and tungsten powders and fabricated into 3 in diameter billets by uniaxial hot pressing. Specimens were then cut from the billets for compatability testing. Similar processing techniques were applied to produce hafnium carbide and zirconium carbide cermets for use in the testing program. All billets produced were characterized with respect to chemistry, structure, density, and strength properties.

An investigation of hydrogenized amorphous Si structures with Doppler broadening positron annihilation techniques

NASA Astrophysics Data System (ADS)

Petkov, M. P.; Marek, T.; Asoka-Kumar, P.; Lynn, K. G.; Crandall, R. S.; Mahan, A. H.

1998-07-01

In this letter, we examine the feasibility of applying positron annihilation spectroscopy to the study of hydrogenized amorphous silicon (a-Si:H)-based structures produced by chemical vapor deposition techniques. The positron probe, sensitive to open volume formations, is used to characterize neutral and negatively charged silicon dangling bonds, typical for undoped and n-doped a-Si:H, respectively. Using depth profiling along the growth direction a difference was observed in the electronic environment of these defects, which enables their identification in a p-i-n device.

Biological materials: a materials science approach.

PubMed

Meyers, Marc A; Chen, Po-Yu; Lopez, Maria I; Seki, Yasuaki; Lin, Albert Y M

2011-07-01

The approach used by Materials Science and Engineering is revealing new aspects in the structure and properties of biological materials. The integration of advanced characterization, mechanical testing, and modeling methods can rationalize heretofore unexplained aspects of these structures. As an illustration of the power of this methodology, we apply it to biomineralized shells, avian beaks and feathers, and fish scales. We also present a few selected bioinspired applications: Velcro, an Al2O3-PMMA composite inspired by the abalone shell, and synthetic attachment devices inspired by gecko. Copyright © 2010 Elsevier Ltd. All rights reserved.

Pultruded Rod/Overwrap Testing for Various Stitched Stringer Configurations

NASA Technical Reports Server (NTRS)

Leone, Frank A., Jr.

2016-01-01

The unidirectional carbon pultruded rod running through the tops of the stringers is a key design feature of the Pultruded Rod Efficient Unitized Structure (PRSEUS) concept as applied to aircraft fuselage structure. Reported herein are the test methods and results from a test campaign in which the strength of the rod/overwrap interface of various PRSEUS stringer configurations were characterized. The different stringer configurations included different materials and stacking sequences for the stringer overwrap and whether or not an additional layer of adhesive was included between the rod and the overwrap.

Thermodynamic characterization of networks using graph polynomials

NASA Astrophysics Data System (ADS)

Ye, Cheng; Comin, César H.; Peron, Thomas K. DM.; Silva, Filipi N.; Rodrigues, Francisco A.; Costa, Luciano da F.; Torsello, Andrea; Hancock, Edwin R.

2015-09-01

In this paper, we present a method for characterizing the evolution of time-varying complex networks by adopting a thermodynamic representation of network structure computed from a polynomial (or algebraic) characterization of graph structure. Commencing from a representation of graph structure based on a characteristic polynomial computed from the normalized Laplacian matrix, we show how the polynomial is linked to the Boltzmann partition function of a network. This allows us to compute a number of thermodynamic quantities for the network, including the average energy and entropy. Assuming that the system does not change volume, we can also compute the temperature, defined as the rate of change of entropy with energy. All three thermodynamic variables can be approximated using low-order Taylor series that can be computed using the traces of powers of the Laplacian matrix, avoiding explicit computation of the normalized Laplacian spectrum. These polynomial approximations allow a smoothed representation of the evolution of networks to be constructed in the thermodynamic space spanned by entropy, energy, and temperature. We show how these thermodynamic variables can be computed in terms of simple network characteristics, e.g., the total number of nodes and node degree statistics for nodes connected by edges. We apply the resulting thermodynamic characterization to real-world time-varying networks representing complex systems in the financial and biological domains. The study demonstrates that the method provides an efficient tool for detecting abrupt changes and characterizing different stages in network evolution.

Kinetics and mechanism of catalytic hydroprocessing of components of coal-derived liquids. Sixteenth quarterly report, February 16, 1983-May 15, 1983.

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

Gates, B. C.; Olson, H. H.; Schuit, G. C.A.

1983-08-22

A new method of structural analysis is applied to a group of hydroliquefied coal samples. The method uses elemental analysis and NMR data to estimate the concentrations of functional groups in the samples. The samples include oil and asphaltene fractions obtained in a series of hydroliquefaction experiments, and a set of 9 fractions separated from a coal-derived oil. The structural characterization of these samples demonstrates that estimates of functional group concentrations can be used to provide detailed structural profiles of complex mixtures and to obtain limited information about reaction pathways. 11 references, 1 figure, 7 tables.

Market structure and the role of consumer information in the physician services industry: an empirical test.

PubMed

Wong, H S

1996-04-01

This paper applies Panzar and Rosse's (1987) econometric test of market structure to examine two long-debated issues: What is the market structure for physician services? Do more physicians in a market area raise the search cost of obtaining consumer information and increase prices (Satterthwaite, 1979, 1985)? For primary care and general and family practice physicians, the monopolistically competitive model prevailed over the competing hypotheses--monopoly, perfect competition, and monopolistic competition characterized by consumer informational confusion. Although less conclisive, there is some evidence to support the monopolistically competitive model for surgeons and the consumer informational confusion model for internal medicine physicians.

Fabrication and characterization of Gd2O2SO4:Tb3+ phosphors by sol-gel method

NASA Astrophysics Data System (ADS)

Aritman, I.; Yildirim, S.; Kisa, A.; Guleryuz, L. F.; Yurddaskal, M.; Dikici, T.; Celik, E.

2017-02-01

The objective of the innovative approaches of the scintillation materials to be used in the digital portal imaging systems in the radiotherapy applications is to research the GOS material production that has been activated with the rare earth elements (RE), to produce the scintillation detectors that have a rapid imaging process with a lesser radiation and higher image quality from these materials and to apply the radiographic imaging systems. The GOS: Tb3+ showed high emission peak and high x-ray absorption properties which have been determined for application to mammography and dental radiography. In this study, Gd2O2SO4:Tb3+ phosphors were fabricated by the sol-gel method that is a unique technique and not previously applied. Besides, the structural characterization of GOS: Tb3+ has been investigated. The strongest emission peak located at 549 nm under 312 nm UV light excitation was appeared on the GOS: Tb3+ phosphor particles. The characterization processing optimized by using FTIR, DTA-TG, XRD, XPS, SEM and the luminescence spectroscopy.

Characterizing Exterior and Interior Tropical Forest Structure Variability with Full-Waveform Airborne LIDAR Data in Lopé, Gabon

NASA Astrophysics Data System (ADS)

Marselis, S.; Tang, H.; Blair, J. B.; Hofton, M. A.; Armston, J.; Dubayah, R.

2017-12-01

Terrestrial ecotones, transition zones between ecological systems, have been identified as important regions to monitor the effects of environmental and human pressures on ecosystems. To observe such changes, the variability in vegetation horizontal and vertical structure must be characterized. The objective of this study is to quantify changes in vegetation structure in a tropical forest-savanna mosaic using airborne waveform lidar data. The study area is located in the northern part of the Lopé National Park in Gabon and is comprised of the vegetation types: savanna, colonizing forest, monodominant Okoumé forest, young Marantaceae forest and mixed Marantaceae forest. The lidar data were collected by the Land Vegetation and Ice Sensor (LVIS) in early March 2016, during the AfriSAR campaign. Metrics derived from the LVIS waveforms were then used to classify the five main vegetation types and characterize observed structural variability within types and across ecotones. Several supervised and unsupervised classification alogrithms, in combination with statistical analysis, were applied. The investigated methods are promising in their use to directly describe the structural variability within and between different vegetation types, map these vegetation types and the extent and location of their transition zones, and to characterize, among other attributes, the sharpness and width of such ecotones. These results provide important information in ecosystem studies as these methods can be used to study changes in vegetation structure, species-specific habitat, or the effects of deforestation and other human and natural pressures on the exterior and interior forest structure. These methods thus provide ample opportunity to assess the vegetation structure in degraded and second growth tropical forests to explore effects of e.g. grazing, logging or fragmentation. From this study we can conclude that lidar waveform remote sensing is highly useful in distinguishing vegetation types and their transition zones which will be increasingly important when assessing the impact of natural and human pressures on the world's tropical forests.

Electrical resistivity imaging in transmission between surface and underground tunnel for fault characterization

NASA Astrophysics Data System (ADS)

Lesparre, N.; Boyle, A.; Grychtol, B.; Cabrera, J.; Marteau, J.; Adler, A.

2016-05-01

Electrical resistivity images supply information on sub-surface structures and are classically performed to characterize faults geometry. Here we use the presence of a tunnel intersecting a regional fault to inject electrical currents between surface and the tunnel to improve the image resolution at depth. We apply an original methodology for defining the inversion parametrization based on pilot points to better deal with the heterogeneous sounding of the medium. An increased region of high spatial resolution is shown by analysis of point spread functions as well as inversion of synthetics. Such evaluations highlight the advantages of using transmission measurements by transferring a few electrodes from the main profile to increase the sounding depth. Based on the resulting image we propose a revised structure for the medium surrounding the Cernon fault supported by geological observations and muon flux measurements.

Numerical Characterization of a Composite Bonded Wing-Box

NASA Technical Reports Server (NTRS)

Smeltzer, Stanley S., III; Lovejoy, Andrew E.; Satyanarayana, Arunkumar

2008-01-01

The development of composite wing structures has focused on the use of mechanical fasteners to join heavily-loaded areas, while bonded joints have been used only for select locations. The focus of this paper is the examination of the adhesive layer in a generic bonded wing box that represents a "fastenerless" or unitized structure in order to characterize the general behavior and failure mechanisms. A global/local approach was applied to study the response of the adhesive layer using a global shell model and a local shell/solid model. The wing box was analyzed under load to represent a high-g up-bending condition such that the strains in the composite sandwich face sheets are comparable to an expected design allowable. The global/local analysis indicates that at these wing load levels the strains in the adhesive layer are well within the adhesive's elastic region, such that yielding would not be expected in the adhesive layer. The global/local methodology appears to be a promising approach to evaluate the structural integrity of the adhesively bonded structures.

Effective mass and Fermi surface complexity factor from ab initio band structure calculations

NASA Astrophysics Data System (ADS)

Gibbs, Zachary M.; Ricci, Francesco; Li, Guodong; Zhu, Hong; Persson, Kristin; Ceder, Gerbrand; Hautier, Geoffroy; Jain, Anubhav; Snyder, G. Jeffrey

2017-02-01

The effective mass is a convenient descriptor of the electronic band structure used to characterize the density of states and electron transport based on a free electron model. While effective mass is an excellent first-order descriptor in real systems, the exact value can have several definitions, each of which describe a different aspect of electron transport. Here we use Boltzmann transport calculations applied to ab initio band structures to extract a density-of-states effective mass from the Seebeck Coefficient and an inertial mass from the electrical conductivity to characterize the band structure irrespective of the exact scattering mechanism. We identify a Fermi Surface Complexity Factor: Nv*K* from the ratio of these two masses, which in simple cases depends on the number of Fermi surface pockets (Nv* ) and their anisotropy K*, both of which are beneficial to high thermoelectric performance as exemplified by the high values found in PbTe. The Fermi Surface Complexity factor can be used in high-throughput search of promising thermoelectric materials.

SAXS Combined with UV-vis Spectroscopy and QELS: Accurate Characterization of Silver Sols Synthesized in Polymer Matrices.

PubMed

Bulavin, Leonid; Kutsevol, Nataliya; Chumachenko, Vasyl; Soloviov, Dmytro; Kuklin, Alexander; Marynin, Andrii

2016-12-01

The present work demonstrates a validation of small-angle X-ray scattering (SAXS) combining with ultra violet and visible (UV-vis) spectroscopy and quasi-elastic light scattering (QELS) analysis for characterization of silver sols synthesized in polymer matrices. Polymer matrix internal structure and polymer chemical nature actually controlled the sol size characteristics. It was shown that for precise analysis of nanoparticle size distribution these techniques should be used simultaneously. All applied methods were in good agreement for the characterization of size distribution of small particles (less than 60 nm) in the sols. Some deviations of the theoretical curves from the experimental ones were observed. The most probable cause is that nanoparticles were not entirely spherical in form.

Femtosecond Pulse Characterization as Applied to One-Dimensional Photonic Band Edge Structures

NASA Technical Reports Server (NTRS)

Fork, Richard L.; Gamble, Lisa J.; Diffey, William M.

1999-01-01

The ability to control the group velocity and phase of an optical pulse is important to many current active areas of research. Electronically addressable one-dimensional photonic crystals are an attractive candidate to achieve this control. This report details work done toward the characterization of photonic crystals and improvement of the characterization technique. As part of the work, the spectral dependence of the group delay imparted by a GaAs/AlAs photonic crystal was characterized. Also, a first generation an electrically addressable photonic crystal was tested for the ability to electronically control the group delay. The measurement technique, using 100 femtosecond continuum pulses was improved to yield high spectral resolution (1.7 nanometers) and concurrently with high temporal resolution (tens of femtoseconds). Conclusions and recommendations based upon the work done are also presented.

Characterization of fossil remains using XRF, XPS and XAFS spectroscopies

NASA Astrophysics Data System (ADS)

Zougrou, I. M.; Katsikini, M.; Pinakidou, F.; Brzhezinskaya, M.; Papadopoulou, L.; Vlachos, E.; Tsoukala, E.; Paloura, E. C.

2016-05-01

Synchrotron radiation micro-X-Ray Fluorescence (μ-XRF), X-ray photoelectron (XPS) and X-ray Absorption Fine Structure (XAFS) spectroscopies are applied for the study of paleontological findings. More specifically the costal plate of a gigantic terrestrial turtle Titanochelon bacharidisi and a fossilized coprolite of the cave spotted hyena Crocuta crocuta spelaea are studied. Ca L 2,3-edge NEXAFS and Ca 2p XPS are applied for the identification and quantification of apatite and Ca containing minerals. XRF mapping and XAFS are employed for the study of the spatial distribution and speciation of the minerals related to the deposition environment.

Potential and Limitations of the Modal Characterization of a Spacecraft Bus Structure by Means of Active Structure Elements

NASA Technical Reports Server (NTRS)

Grillenbeck, Anton M.; Dillinger, Stephan A.; Elliott, Kenny B.

1998-01-01

Theoretical and experimental studies have been performed to investigate the potential and limitations of the modal characterization of a typical spacecraft bus structure by means of active structure elements. The aim of these studies has been test and advance tools for performing an accurate on-orbit modal identification which may be characterized by the availability of a generally very limited test instrumentation, autonomous excitation capabilities by active structure elements and a zero-g environment. The NASA LARC CSI Evolutionary Testbed provided an excellent object for the experimental part of this study program. The main subjects of investigation were: (1) the selection of optimum excitation and measurement to unambiguously identify modes of interest; (2) the applicability of different types of excitation means with focus on active structure elements; and (3) the assessment of the modal identification potential of different types of excitation functions and modal analysis tools. Conventional as well as dedicated modal analysis tools were applied to determine modal parameters and mode shapes. The results will be presented and discussed based on orthogonality checks as well as on suitable indicators for the quality of the acquired modes with respect to modal purity. In particular, the suitability for modal analysis of the acquired frequency response functions as obtained by excitation with active structure elements will be demonstrated with the help of reciprocity checks. Finally, the results will be summarized in a procedure to perform an on-orbit modal identification, including an indication of limitation to be observed.

[Studies on separation, purification and structure characteristics of a polysaccharide LTC-II from Pyrola corbieri].

PubMed

Mo, Zhengchang; Wu, Lanfang; Yang, Juan; Wang, Daoping

2011-06-01

To characterize the structure of polysaccharide LTC-II obtained from Pyrola corbieri. The polysaccharide was extracted from P. corbieri by hot water and ethanol precipitation. Crude polysaccharide was purified by DEAE-Cellulose chromatography and Sephacryl S-300 HR column chromatography. The purity and molecular weight of polysaccharide was determined by gel permeation chromatography. UV, IR, optical rotation, complete acid hydrolysis, periodate oxydation, Smith degradation, partial acid hydrolysis and methylation analysis were applied to determine the structural features. A homogeneous fraction LTC-II was obtained and its relative molecular mass was 22 000 Da. It consisted of arabinose, mannose, glucose, galactose in the molar ratio of 35. 2: 1.0: 13. 4: 4. 2. LTC-II had a backbone consisting glucose, mannose, galactose and mainly contained (1 --> 6)-linkaged glucose. The side chain possessed arabinose, glucose, galactose and mainly contained (1 --> 5)-linkaged arabinose. The terminal sugar were mainly glucose and galactose. Studies on the preliminary characterization of polysaccharide LTC-II from P. corbieri for the first time.

Non-contact tensile viscoelastic characterization of microscale biological materials

NASA Astrophysics Data System (ADS)

Li, Yuhui; Hong, Yuan; Xu, Guang-Kui; Liu, Shaobao; Shi, Qiang; Tang, Deding; Yang, Hui; Genin, Guy M.; Lu, Tian Jian; Xu, Feng

2018-06-01

Many structures and materials in nature and physiology have important "meso-scale" structures at the micron length-scale whose tensile responses have proven difficult to characterize mechanically. Although techniques such as atomic force microscopy and micro- and nano-identation are mature for compression and indentation testing at the nano-scale, and standard uniaxial and shear rheometry techniques exist for the macroscale, few techniques are applicable for tensile-testing at the micrometre-scale, leaving a gap in our understanding of hierarchical biomaterials. Here, we present a novel magnetic mechanical testing (MMT) system that enables viscoelastic tensile testing at this critical length scale. The MMT system applies non-contact loading, avoiding gripping and surface interaction effects. We demonstrate application of the MMT system to the first analyses of the pure tensile responses of several native and engineered tissue systems at the mesoscale, showing the broad potential of the system for exploring micro- and meso-scale analysis of structured and hierarchical biological systems.

Non-contact tensile viscoelastic characterization of microscale biological materials

NASA Astrophysics Data System (ADS)

Li, Yuhui; Hong, Yuan; Xu, Guang-Kui; Liu, Shaobao; Shi, Qiang; Tang, Deding; Yang, Hui; Genin, Guy M.; Lu, Tian Jian; Xu, Feng

2018-01-01

Many structures and materials in nature and physiology have important "meso-scale" structures at the micron length-scale whose tensile responses have proven difficult to characterize mechanically. Although techniques such as atomic force microscopy and micro- and nano-identation are mature for compression and indentation testing at the nano-scale, and standard uniaxial and shear rheometry techniques exist for the macroscale, few techniques are applicable for tensile-testing at the micrometre-scale, leaving a gap in our understanding of hierarchical biomaterials. Here, we present a novel magnetic mechanical testing (MMT) system that enables viscoelastic tensile testing at this critical length scale. The MMT system applies non-contact loading, avoiding gripping and surface interaction effects. We demonstrate application of the MMT system to the first analyses of the pure tensile responses of several native and engineered tissue systems at the mesoscale, showing the broad potential of the system for exploring micro- and meso-scale analysis of structured and hierarchical biological systems.

Learning to classify wakes from local sensory information

NASA Astrophysics Data System (ADS)

Alsalman, Mohamad; Colvert, Brendan; Kanso, Eva; Kanso Team

2017-11-01

Aquatic organisms exhibit remarkable abilities to sense local flow signals contained in their fluid environment and to surmise the origins of these flows. For example, fish can discern the information contained in various flow structures and utilize this information for obstacle avoidance and prey tracking. Flow structures created by flapping and swimming bodies are well characterized in the fluid dynamics literature; however, such characterization relies on classical methods that use an external observer to reconstruct global flow fields. The reconstructed flows, or wakes, are then classified according to the unsteady vortex patterns. Here, we propose a new approach for wake identification: we classify the wakes resulting from a flapping airfoil by applying machine learning algorithms to local flow information. In particular, we simulate the wakes of an oscillating airfoil in an incoming flow, extract the downstream vorticity information, and train a classifier to learn the different flow structures and classify new ones. This data-driven approach provides a promising framework for underwater navigation and detection in application to autonomous bio-inspired vehicles.

Structural characterization of humic-like substances with conventional and surface-enhanced spectroscopic techniques

NASA Astrophysics Data System (ADS)

Carletti, Paolo; Roldán, Maria Lorena; Francioso, Ornella; Nardi, Serenella; Sanchez-Cortes, Santiago

2010-10-01

Emission-excitation, synchronous fluorescence spectroscopy and surface-enhanced Raman scattering (SERS) combined with surface-enhanced fluorescence (SEF) were applied to aqueous solutions of a humic-like substance (HLS) extracted from earthworm faeces. All measurements were acquired in a wide range of pH (4-12) and analysed by the linear regression analysis. Diffuse Reflectance Infrared Fourier Transform (DRIFT) spectra were also acquired to assist in the structural characterization of this HLS. The emission and excitation spectra allowed the identification of two main fluorophores in the analysed sample. Moreover, a close correlation between fluorescence intensities of each fluorophore with pH variation was observed. SERS and SEF, in agreement with the fluorescence spectroscopy, showed that the HLS at low pH values exists in an aggregated and coiled molecular structure while it is dispersed and uncoiled at alkaline conditions. The obtained spectra also evidenced that different conditions modify the functional groups exposed to the surrounding aqueous environment.

The centrality of RNA for engineering gene expression

PubMed Central

Chappell, James; Takahashi, Melissa K; Meyer, Sarai; Loughrey, David; Watters, Kyle E; Lucks, Julius

2013-01-01

Synthetic biology holds promise as both a framework for rationally engineering biological systems and a way to revolutionize how we fundamentally understand them. Essential to realizing this promise is the development of strategies and tools to reliably and predictably control and characterize sophisticated patterns of gene expression. Here we review the role that RNA can play towards this goal and make a case for why this versatile, designable, and increasingly characterizable molecule is one of the most powerful substrates for engineering gene expression at our disposal. We discuss current natural and synthetic RNA regulators of gene expression acting at key points of control – transcription, mRNA degradation, and translation. We also consider RNA structural probing and computational RNA structure predication tools as a way to study RNA structure and ultimately function. Finally, we discuss how next-generation sequencing methods are being applied to the study of RNA and to the characterization of RNA's many properties throughout the cell. PMID:24124015

Design, Fabrication and Characterization of Thin Film Structures through Oxidation Kinetics

NASA Astrophysics Data System (ADS)

Diaz Leon, Juan Jose

Materials science and engineering is devoted to the understanding of the physics and chemistry of materials at the mesoscale and to applying that knowledge into real-life applications. In this work, different oxide materials and different oxidation methods are studied from a materials science point of view and for specific applications. First, the deposition of complex metal oxides is explored for solar energy concentration. This requires a number of multi-cation oxide structures such as thin-film dielectric barriers, low loss waveguides or the use of continuously graded composition oxides for antireflection coatings and light concentration. Then, oxidation via Joule heating is used for the self-alignment of a selector on top of a memristor structure on a nanovia. Simulations are used to explore the necessary voltage for the insulator-to-metal transition temperature of NbO2 using finite element analysis, followed by the fabrication and the characterization of such a device. Finally, long-term copper oxidation at room temperature and pressure is studied using optical techniques. Alternative characterization techniques are used to confirm the growth rate and phase change, and an application of copper oxide as a volatile conductive bridge is shown. All these examples show how the combination of novel simulation, fabrication and characterization techniques can be used to understand physical mechanisms and enable disruptive technologies in fields such as solar cells, light emitting diodes, photodetectors or memory devices.

Spectroscopic Ellipsometry Studies of Ag and ZnO Thin Films and Their Interfaces for Thin Film Photovoltaics

NASA Astrophysics Data System (ADS)

Sainju, Deepak

Many modern optical and electronic devices, including photovoltaic devices, consist of multilayered thin film structures. Spectroscopic ellipsometry (SE) is a critically important characterization technique for such multilayers. SE can be applied to measure key parameters related to the structural, optical, and electrical properties of the components of multilayers with high accuracy and precision. One of the key advantages of this non-destructive technique is its capability of monitoring the growth dynamics of thin films in-situ and in real time with monolayer level precision. In this dissertation, the techniques of SE have been applied to study the component layer materials and structures used as back-reflectors and as the transparent contact layers in thin film photovoltaic technologies, including hydrogenated silicon (Si:H), copper indium-gallium diselenide (CIGS), and cadmium telluride (CdTe). The component layer materials, including silver and both intrinsic and doped zinc oxide, are fabricated on crystalline silicon and glass substrates using magnetron sputtering techniques. These thin films are measured in-situ and in real time as well as ex-situ by spectroscopic ellipsometry in order to extract parameters related to the structural properties, such as bulk layer thickness and surface roughness layer thickness and their time evolution, the latter information specific to real time measurements. The index of refraction and extinction coefficient or complex dielectric function of a single unknown layer can also be obtained from the measurement versus photon energy. Applying analytical expressions for these optical properties versus photon energy, parameters that describe electronic transport, such as electrical resistivity and electron scattering time, can be extracted. The SE technique is also performed as the sample is heated in order to derive the effects of annealing on the optical properties and derived electrical transport parameters, as well as the intrinsic temperature dependence of these properties and parameters. One of the major achievements of this dissertation research is the characterization of the thickness and optical properties of the interface layer formed between the silver and zinc oxide layers in a back-reflector structure used in thin film photovoltaics. An understanding of the impact of these thin film material properties on solar cell device performance has been complemented by applying reflectance and transmittance spectroscopy as well as simulations of cell performance.

In-situ electrical, mechanical and electrochemical characterizations of one-dimensional nanostructures

NASA Astrophysics Data System (ADS)

Mir Shah Ghassemi, Seyyed Hessam

One-dimensional nanostructures initiated new aspects to the materials applications due to their superior properties compared to the bulk materials. Properties of nanostructures have been characterized by many techniques and used for various device applications. However, simultaneous correlation between the physical and structural properties of these nanomaterials has not been widely investigated. Therefore, it is necessary to perform in-situ study on the physical and structural properties of nanomaterials to understand their relation. In this work, we will use a unique instrument to perform real time atomic force microscopy (AFM) and scanning tunneling microscopy (STM) of nanomaterials inside a transmission electron microscopy (TEM) system. This AFM/STM-TEM system is used to investigate the mechanical, electrical, and electrochemical properties of boron nitride nanotubes (BNNTs) and Silicon nanorods (SiNRs). BNNTs are one of the subjects of this PhD research due to their comparable, and in some cases superior, properties compared to carbon nanotubes. Therefore, to further develop their applications, it is required to investigate these characteristics in atomic level. In this research, the mechanical properties of multi-walled BNNTs were first studied. Several tests were designed to study and characterize their real-time deformation behavior to the applied force. Observations revealed that BNNTs possess highly flexible structures under applied force. Detailed studies were then conducted to understand the bending mechanism of the BNNTs. Formations of reversible ripples were observed and described in terms of thermodynamic energy of the system. Fracture failure of BNNTs were initiated at the outermost walls and characterized to be brittle. Second, the electrical properties of individual BNNTs were studied. Results showed that the bandgap and electronic properties of BNNTs can be engineered by means of applied strain. It was found that the conductivity, electron concentration and carrier mobility of BNNTs can be tuned as a function of applied stress. Although, BNNTs are considered to be candidate for field emission applications, observations revealed that their properties degrade upon cycles of emissions. Results showed that due to the high emission current density, the temperature of the sample was increased and reached to the decomposition temperature at which the B-N bonds start to break. In addition to BNNTs, we have also performed in-situ study on the electrochemical properties of silicon nanorods (SiNRs). Specifically, lithiation and delithiation of SiNRs were studied by our STM-TEM system. Our observations showed the direct formation of Li22Si 5 phases as a result of lithium intercalation. Radial expansion of the anode materials were observed and characterized in terms of size-scale. Later, the formation and growth of the lithium fibers on the surface of the anode materials were observed and studied. Results revealed the formation of lithium islands inside the ionic liquid electrolyte which then grew as Li dendrite toward the cathode material.

Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays.

PubMed

Michailidou, S; Tsangaris, G; Fthenakis, G C; Tzora, A; Skoufos, I; Karkabounas, S C; Banos, G; Argiriou, A; Arsenos, G

2018-06-01

In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (F GRM ) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.

Soil structural quality assessment for soil protection regulation

NASA Astrophysics Data System (ADS)

Johannes, Alice; Boivin, Pascal

2017-04-01

Soil quality assessment is rapidly developing worldwide, though mostly focused on the monitoring of arable land and soil fertility. Soil protection regulations assess soil quality differently, focusing on priority pollutants and threshold values. The soil physical properties are weakly considered, due to lack of consensus and experimental difficulties faced with characterization. Non-disputable, easy to perform and inexpensive methods should be available for environmental regulation to be applied, which is unfortunately not the case. As a consequence, quantitative soil physical protection regulation is not applied, and inexpensive soil physical quality indicators for arable soil management are not available. Overcoming these limitations was the objective of a research project funded by the Swiss federal office for environment (FOEN). The main results and the perspectives of application are given in this presentation. A first step of the research was to characterize soils in a good structural state (reference soils) under different land use. The structural quality was assessed with field expertise and Visual Evaluation of the Soil Structure (VESS), and the physical properties were assessed with Shrinkage analysis. The relationships between the physical properties and the soil constituents were linear and highly determined. They represent the reference properties of the corresponding soils. In a second step, the properties of physically degraded soils were analysed and compared to the reference properties. This allowed defining the most discriminant parameters departing the different structure qualities and their threshold limits. Equivalent properties corresponding to these parameters but inexpensive and easy to determine were defined and tested. More than 90% of the samples were correctly classed with this method, which meets, therefore, the requirements for practical application in regulation. Moreover, result-oriented agri-environmental schemes for soil quality are now proposed to farmers based on these indicators.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS.

PubMed

van Erven, Gijs; de Visser, Ries; Merkx, Donny W H; Strolenberg, Willem; de Gijsel, Peter; Gruppen, Harry; Kabel, Mirjam A

2017-10-17

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13 C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12 C and 13 C lignin were isolated from nonlabeled and uniformly 13 C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13 C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12 C lignin analogue and was shown to be extremely accurate (>99.9%, R 2 > 0.999) and precise (RSD < 1.5%). Third, 13 C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS

PubMed Central

2017-01-01

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12C and 13C lignin were isolated from nonlabeled and uniformly 13C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12C lignin analogue and was shown to be extremely accurate (>99.9%, R2 > 0.999) and precise (RSD < 1.5%). Third, 13C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin. PMID:28926698

A new approach for crystallization of copper(ii) oxide hollow nanostructures with superior catalytic and magnetic response

NASA Astrophysics Data System (ADS)

Singh, Inderjeet; Landfester, Katharina; Chandra, Amreesh; Muñoz-Espí, Rafael

2015-11-01

We report the synthesis of copper(ii) oxide hollow nanostructures at ambient pressure and close to room temperature by applying the soft templating effect provided by the confinement of droplets in miniemulsion systems. Particle growth can be explained by considering a mechanism that involves both diffusion and reaction control. The catalytic reduction of p-nitrophenol in aqueous media is used as a model reaction to prove the catalytic activity of the materials: the synthesized hollow structures show nearly 100 times higher rate constants than solid CuO microspheres. The kinetic behavior and the order of the reduction reaction change due to the increase of the surface area of the hollow structures. The synthesis also leads to modification of physical properties such as magnetism.We report the synthesis of copper(ii) oxide hollow nanostructures at ambient pressure and close to room temperature by applying the soft templating effect provided by the confinement of droplets in miniemulsion systems. Particle growth can be explained by considering a mechanism that involves both diffusion and reaction control. The catalytic reduction of p-nitrophenol in aqueous media is used as a model reaction to prove the catalytic activity of the materials: the synthesized hollow structures show nearly 100 times higher rate constants than solid CuO microspheres. The kinetic behavior and the order of the reduction reaction change due to the increase of the surface area of the hollow structures. The synthesis also leads to modification of physical properties such as magnetism. Electronic supplementary information (ESI) available: Associated structural and morphological analysis, XPS characterization, BET surface area, catalytic measurements, recycle tests of the catalyst, and magnetic characterizations. See DOI: 10.1039/c5nr05579b

Turbulence modeling and combustion simulation in porous media under high Peclet number

NASA Astrophysics Data System (ADS)

Moiseev, Andrey A.; Savin, Andrey V.

2018-05-01

Turbulence modelling in porous flows and burning still remains not completely clear until now. Undoubtedly, conventional turbulence models must work well under high Peclet numbers when porous channels shape is implemented in details. Nevertheless, the true turbulent mixing takes place at micro-scales only, and the dispersion mixing works at macro-scales almost independent from true turbulence. The dispersion mechanism is characterized by the definite space scale (scale of the porous structure) and definite velocity scale (filtration velocity). The porous structure is stochastic one usually, and this circumstance allows applying the analogy between space-time-stochastic true turbulence and the dispersion flow which is stochastic in space only, when porous flow is simulated at the macro-scale level. Additionally, the mentioned analogy allows applying well-known turbulent combustion models in simulations of porous combustion under high Peclet numbers.

Method of forming structural heliostat

DOEpatents

Anderson, Alfred J.

1984-06-26

In forming a heliostat having a main support structure and pivoting and tilting motors and gears and a mirror module for reflecting solar energy onto a collector, the improvement characterized by a method of forming the mirror module in which the mirror is laid upon a solid rigid supporting bed in one or more sections, with or without focusing; a mirror backing sheet is applied by first applying respective thin layers of silicone grease and, thereafter, progressively rolling application to eliminate air bubbles; followed by affixing of a substrate assembly to the mirror backing sheet to form a mirror module that does not curve because of thermally induced stresses and differential thermal expansion or contraction effects. The silicone grease also serves to dampen fluttering of the mirror and protect the mirror backside against adverse effects of the weather. Also disclosed are specific details of preferred embodiments.

A programmable nanoreplica molding for the fabrication of nanophotonic devices.

PubMed

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-03-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively.

A programmable nanoreplica molding for the fabrication of nanophotonic devices

PubMed Central

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-01-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively. PMID:26925828

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

PubMed Central

Huang, Ruili; Xia, Menghang; Sakamuru, Srilatha; Zhao, Jinghua; Shahane, Sampada A.; Attene-Ramos, Matias; Zhao, Tongan; Austin, Christopher P.; Simeonov, Anton

2016-01-01

Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure–activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing. PMID:26811972

Hierarchical organization of functional connectivity in the mouse brain: a complex network approach.

PubMed

Bardella, Giampiero; Bifone, Angelo; Gabrielli, Andrea; Gozzi, Alessandro; Squartini, Tiziano

2016-08-18

This paper represents a contribution to the study of the brain functional connectivity from the perspective of complex networks theory. More specifically, we apply graph theoretical analyses to provide evidence of the modular structure of the mouse brain and to shed light on its hierarchical organization. We propose a novel percolation analysis and we apply our approach to the analysis of a resting-state functional MRI data set from 41 mice. This approach reveals a robust hierarchical structure of modules persistent across different subjects. Importantly, we test this approach against a statistical benchmark (or null model) which constrains only the distributions of empirical correlations. Our results unambiguously show that the hierarchical character of the mouse brain modular structure is not trivially encoded into this lower-order constraint. Finally, we investigate the modular structure of the mouse brain by computing the Minimal Spanning Forest, a technique that identifies subnetworks characterized by the strongest internal correlations. This approach represents a faster alternative to other community detection methods and provides a means to rank modules on the basis of the strength of their internal edges.

Hierarchical organization of functional connectivity in the mouse brain: a complex network approach

NASA Astrophysics Data System (ADS)

Bardella, Giampiero; Bifone, Angelo; Gabrielli, Andrea; Gozzi, Alessandro; Squartini, Tiziano

2016-08-01

This paper represents a contribution to the study of the brain functional connectivity from the perspective of complex networks theory. More specifically, we apply graph theoretical analyses to provide evidence of the modular structure of the mouse brain and to shed light on its hierarchical organization. We propose a novel percolation analysis and we apply our approach to the analysis of a resting-state functional MRI data set from 41 mice. This approach reveals a robust hierarchical structure of modules persistent across different subjects. Importantly, we test this approach against a statistical benchmark (or null model) which constrains only the distributions of empirical correlations. Our results unambiguously show that the hierarchical character of the mouse brain modular structure is not trivially encoded into this lower-order constraint. Finally, we investigate the modular structure of the mouse brain by computing the Minimal Spanning Forest, a technique that identifies subnetworks characterized by the strongest internal correlations. This approach represents a faster alternative to other community detection methods and provides a means to rank modules on the basis of the strength of their internal edges.

Method for detecting damage in carbon-fibre reinforced plastic-steel structures based on eddy current pulsed thermography

NASA Astrophysics Data System (ADS)

Li, Xuan; Liu, Zhiping; Jiang, Xiaoli; Lodewijks, Gabrol

2018-01-01

Eddy current pulsed thermography (ECPT) is well established for non-destructive testing of electrical conductive materials, featuring the advantages of contactless, intuitive detecting and efficient heating. The concept of divergence characterization of the damage rate of carbon fibre-reinforced plastic (CFRP)-steel structures can be extended to ECPT thermal pattern characterization. It was found in this study that the use of ECPT technology on CFRP-steel structures generated a sizeable amount of valuable information for comprehensive material diagnostics. The relationship between divergence and transient thermal patterns can be identified and analysed by deploying mathematical models to analyse the information about fibre texture-like orientations, gaps and undulations in these multi-layered materials. The developed algorithm enabled the removal of information about fibre texture and the extraction of damage features. The model of the CFRP-glue-steel structures with damage was established using COMSOL Multiphysics® software, and quantitative non-destructive damage evaluation from the ECPT image areas was derived. The results of this proposed method illustrate that damaged areas are highly affected by available information about fibre texture. This proposed work can be applied for detection of impact induced damage and quantitative evaluation of CFRP structures.

Peptide interfaces with graphene: an emerging intersection of analytical chemistry, theory, and materials.

PubMed

Russell, Shane R; Claridge, Shelley A

2016-04-01

Because noncovalent interface functionalization is frequently required in graphene-based devices, biomolecular self-assembly has begun to emerge as a route for controlling substrate electronic structure or binding specificity for soluble analytes. The remarkable diversity of structures that arise in biological self-assembly hints at the possibility of equally diverse and well-controlled surface chemistry at graphene interfaces. However, predicting and analyzing adsorbed monolayer structures at such interfaces raises substantial experimental and theoretical challenges. In contrast with the relatively well-developed monolayer chemistry and characterization methods applied at coinage metal surfaces, monolayers on graphene are both less robust and more structurally complex, levying more stringent requirements on characterization techniques. Theory presents opportunities to understand early binding events that lay the groundwork for full monolayer structure. However, predicting interactions between complex biomolecules, solvent, and substrate is necessitating a suite of new force fields and algorithms to assess likely binding configurations, solvent effects, and modulations to substrate electronic properties. This article briefly discusses emerging analytical and theoretical methods used to develop a rigorous chemical understanding of the self-assembly of peptide-graphene interfaces and prospects for future advances in the field.

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

dos Reis, Roberto; Yang, Hao; Ophus, Colin

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr 3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr 3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurementmore » of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). Finally, the approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.« less

A model-updating procedure to stimulate piezoelectric transducers accurately.

PubMed

Piranda, B; Ballandras, S; Steichen, W; Hecart, B

2001-09-01

The use of numerical calculations based on finite element methods (FEM) has yielded significant improvements in the simulation and design of piezoelectric transducers piezoelectric transducer utilized in acoustic imaging. However, the ultimate precision of such models is directly controlled by the accuracy of material characterization. The present work is dedicated to the development of a model-updating technique adapted to the problem of piezoelectric transducer. The updating process is applied using the experimental admittance of a given structure for which a finite element analysis is performed. The mathematical developments are reported and then applied to update the entries of a FEM of a two-layer structure (a PbZrTi-PZT-ridge glued on a backing) for which measurements were available. The efficiency of the proposed approach is demonstrated, yielding the definition of a new set of constants well adapted to predict the structure response accurately. Improvement of the proposed approach, consisting of the updating of material coefficients not only on the admittance but also on the impedance data, is finally discussed.

Design and implementation of handheld and desktop software for the structured reporting of hepatic masses using the LI-RADS schema.

PubMed

Clark, Toshimasa J; McNeeley, Michael F; Maki, Jeffrey H

2014-04-01

The Liver Imaging Reporting and Data System (LI-RADS) can enhance communication between radiologists and clinicians if applied consistently. We identified an institutional need to improve liver imaging report standardization and developed handheld and desktop software to serve this purpose. We developed two complementary applications that implement the LI-RADS schema. A mobile application for iOS devices written in the Objective-C language allows for rapid characterization of hepatic observations under a variety of circumstances. A desktop application written in the Java language allows for comprehensive observation characterization and standardized report text generation. We chose the applications' languages and feature sets based on the computing resources of target platforms, anticipated usage scenarios, and ease of application installation, deployment, and updating. Our primary results are the publication of the core source code implementing the LI-RADS algorithm and the availability of the applications for use worldwide via our website, http://www.liradsapp.com/. The Java application is free open-source software that can be integrated into nearly any vendor's reporting system. The iOS application is distributed through Apple's iTunes App Store. Observation categorizations of both programs have been manually validated to be correct. The iOS application has been used to characterize liver tumors during multidisciplinary conferences of our institution, and several faculty members, fellows, and residents have adopted the generated text of Java application into their diagnostic reports. Although these two applications were developed for the specific reporting requirements of our liver tumor service, we intend to apply this development model to other diseases as well. Through semiautomated structured report generation and observation characterization, we aim to improve patient care while increasing radiologist efficiency. Published by Elsevier Inc.

Excitation of plane Lamb wave in plate-like structures under applied surface loading

NASA Astrophysics Data System (ADS)

Zhou, Kai; Xu, Xinsheng; Zhao, Zhen; Yang, Zhengyan; Zhou, Zhenhuan; Wu, Zhanjun

2018-02-01

Lamb waves play an important role in structure health monitoring (SHM) systems. The excitation of Lamb waves has been discussed for a long time with absorbing results. However, little effort has been made towards the precise characterization of Lamb wave excitation by various transducer models with mathematical foundation. In this paper, the excitation of plane Lamb waves with plane strain assumption in isotropic plate structures under applied surface loading is solved with the Hamiltonian system. The response of the Lamb modes excited by applied loading is expressed analytically. The effect of applied loading is divided into the product of two parts as the effect of direction and the effect of distribution, which can be changed by selecting different types of transducer and the corresponding transducer configurations. The direction of loading determines the corresponding displacement of each mode. The effect of applied loading on the in-plane and normal directions depends on the in-plane and normal displacements at the surface respectively. The effect of the surface loading distribution on the Lamb mode amplitudes is mainly reflected by amplitude versus frequency or wavenumber. The frequencies at which the maxima and minima of the S0 or A0 mode response occur depend on the distribution of surface loading. The numerical results of simulations conducted on an infinite aluminum plate verify the theoretical prediction of not only the direction but also the distribution of applied loading. A pure S0 or A0 mode can be excited by selecting the appropriate direction and distribution at the corresponding frequency.

Didactical suggestion for a Dynamic Hybrid Intelligent e-Learning Environment (DHILE) applying the PENTHA ID Model

NASA Astrophysics Data System (ADS)

dall'Acqua, Luisa

2011-08-01

The teleology of our research is to propose a solution to the request of "innovative, creative teaching", proposing a methodology to educate creative Students in a society characterized by multiple reference points and hyper dynamic knowledge, continuously subject to reviews and discussions. We apply a multi-prospective Instructional Design Model (PENTHA ID Model), defined and developed by our research group, which adopts a hybrid pedagogical approach, consisting of elements of didactical connectivism intertwined with aspects of social constructivism and enactivism. The contribution proposes an e-course structure and approach, applying the theoretical design principles of the above mentioned ID Model, describing methods, techniques, technologies and assessment criteria for the definition of lesson modes in an e-course.

Theoretical and conformational studies of a series of cannabinoids

NASA Astrophysics Data System (ADS)

Da Silva, Albérico B. F.; Trsic, Milan

1995-11-01

The MNDO semi-empirical method is applied to the study of a series of cannabinoids with the aim of providing an improved understanding of the structure-activity relationship (SAR). The conformation of some groups that seem important in the biological activity (psychoactivity) of these compounds is characterized. Some electronic properties, such as atomic net charges and HOMO and LUMO energies, are correlated with the psychoactive effect.

Robust estimation of fractal measures for characterizing the structural complexity of the human brain: optimization and reproducibility

PubMed Central

Goñi, Joaquín; Sporns, Olaf; Cheng, Hu; Aznárez-Sanado, Maite; Wang, Yang; Josa, Santiago; Arrondo, Gonzalo; Mathews, Vincent P; Hummer, Tom A; Kronenberger, William G; Avena-Koenigsberger, Andrea; Saykin, Andrew J.; Pastor, María A.

2013-01-01

High-resolution isotropic three-dimensional reconstructions of human brain gray and white matter structures can be characterized to quantify aspects of their shape, volume and topological complexity. In particular, methods based on fractal analysis have been applied in neuroimaging studies to quantify the structural complexity of the brain in both healthy and impaired conditions. The usefulness of such measures for characterizing individual differences in brain structure critically depends on their within-subject reproducibility in order to allow the robust detection of between-subject differences. This study analyzes key analytic parameters of three fractal-based methods that rely on the box-counting algorithm with the aim to maximize within-subject reproducibility of the fractal characterizations of different brain objects, including the pial surface, the cortical ribbon volume, the white matter volume and the grey matter/white matter boundary. Two separate datasets originating from different imaging centers were analyzed, comprising, 50 subjects with three and 24 subjects with four successive scanning sessions per subject, respectively. The reproducibility of fractal measures was statistically assessed by computing their intra-class correlations. Results reveal differences between different fractal estimators and allow the identification of several parameters that are critical for high reproducibility. Highest reproducibility with intra-class correlations in the range of 0.9–0.95 is achieved with the correlation dimension. Further analyses of the fractal dimensions of parcellated cortical and subcortical gray matter regions suggest robustly estimated and region-specific patterns of individual variability. These results are valuable for defining appropriate parameter configurations when studying changes in fractal descriptors of human brain structure, for instance in studies of neurological diseases that do not allow repeated measurements or for disease-course longitudinal studies. PMID:23831414

Equivalent-Continuum Modeling of Nano-Structured Materials

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Gates, Thomas S.; Nicholson, Lee M.; Wise, Kristopher E.

2001-01-01

A method has been developed for modeling structure-property relationships of nano-structured materials. This method serves as a link between computational chemistry and solid mechanics by substituting discrete molecular structures with an equivalent-continuum model. It has been shown that this substitution may be accomplished by equating the vibrational potential energy of a nano-structured material with the strain energy of representative truss and continuum models. As an important example with direct application to the development and characterization of single-walled carbon nanotubes, the model has been applied to determine the effective continuum geometry of a graphene sheet. A representative volume element of the equivalent-continuum model has been developed with an effective thickness. This effective thickness has been shown to be similar to, but slightly smaller than, the interatomic spacing of graphite.

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

PubMed

Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

2017-10-01

Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Probabilistic structural analysis of space propulsion system LOX post

NASA Technical Reports Server (NTRS)

Newell, J. F.; Rajagopal, K. R.; Ho, H. W.; Cunniff, J. M.

1990-01-01

The probabilistic structural analysis program NESSUS (Numerical Evaluation of Stochastic Structures Under Stress; Cruse et al., 1988) is applied to characterize the dynamic loading and response of the Space Shuttle main engine (SSME) LOX post. The design and operation of the SSME are reviewed; the LOX post structure is described; and particular attention is given to the generation of composite load spectra, the finite-element model of the LOX post, and the steps in the NESSUS structural analysis. The results are presented in extensive tables and graphs, and it is shown that NESSUS correctly predicts the structural effects of changes in the temperature loading. The probabilistic approach also facilitates (1) damage assessments for a given failure model (based on gas temperature, heat-shield gap, and material properties) and (2) correlation of the gas temperature with operational parameters such as engine thrust.

Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation.

PubMed

Naville, Magali; Gautheret, Daniel

2010-01-01

Bacterial transcription attenuation occurs through a variety of cis-regulatory elements that control gene expression in response to a wide range of signals. The signal-sensing structures in attenuators are so diverse and rapidly evolving that only a small fraction have been properly annotated and characterized to date. Here we apply a broad-spectrum detection tool in order to achieve a more complete view of the transcriptional attenuation complement of key bacterial species. Our protocol seeks gene families with an unusual frequency of 5' terminators found across multiple species. Many of the detected attenuators are part of annotated elements, such as riboswitches or T-boxes, which often operate through transcriptional attenuation. However, a significant fraction of candidates were not previously characterized in spite of their unmistakable footprint. We further characterized some of these new elements using sequence and secondary structure analysis. We also present elements that may control the expression of several non-homologous genes, suggesting co-transcription and response to common signals. An important class of such elements, which we called mobile attenuators, is provided by 3' terminators of insertion sequences or prophages that may be exapted as 5' regulators when inserted directly upstream of a cellular gene. We show here that attenuators involve a complex landscape of signal-detection structures spanning the entire bacterial domain. We discuss possible scenarios through which these diverse 5' regulatory structures may arise or evolve.

A characterization of clinical questions asked by rehabilitation therapists.

PubMed

Kloda, Lorie Andrea; Bartlett, Joan C

2014-04-01

This study explored the information needs of rehabilitation therapists (occupational therapists, physical therapists, and speech-language pathologists) working with patients who have had strokes in order to characterize their clinical questions, defined as their formalized information needs arising in the context of everyday clinical practice. The researchers took a constructivist, interpretive approach, in which fifteen rehabilitation therapists working in various settings were recruited. Data were gathered using diaries, followed by diary-guided interviews, and thematically analyzed using template analysis. Rehabilitation therapists' clinical questions were characterized as having one or more of twelve foci and containing one or more of eight possible structural elements. Findings demonstrate that the evidence-based practice framework currently applied for questions relating to rehabilitation is inadequate for representing rehabilitation therapists' clinical questions. A new framework that is more comprehensive and descriptive is proposed. Librarians working with students and clinicians in rehabilitation can employ knowledge of the twelve foci and the question structure for rehabilitation to guide the reference interview. Instruction on question formulation in evidence-based practice can employ the revised structure for rehabilitation, offering students and clinicians an alternative to the traditional patient, intervention, comparison, outcome (PICO) structure. Information products, including bibliographic databases and synopsis services, can tailor their interfaces according to question foci and prompt users to enter search terms corresponding to any of the eight possible elements found in rehabilitation therapists' clinical questions.

Wideband Single-Crystal Transducer for Bone Characterization

NASA Technical Reports Server (NTRS)

Liang, Yu; Snook, Kevin

2012-01-01

The microgravity conditions of space travel result in unique physiological demands on the human body. In particular, the absence of the continual mechanical stresses on the skeletal system that are present on Earth cause the bones to decalcify. Trabecular structure decreases in thickness and increases in spacing, resulting in decreased bone strength and increased risk of injury. Thus, monitoring bone health is a high priority for long-term space travel. A single probe covering all frequency bands of interest would be ideal for such measurements, and this would also minimize storage space and eliminate the complexity of integrating multiple probes. This invention is an ultrasound transducer for the structural characterization of bone. Such characterization measures features of reflected and transmitted ultrasound signals, and correlates these signals with bone structure metrics such as bone mineral density, trabecular spacing, and thickness, etc. The techniques used to determine these various metrics require measurements over a broad range of ultrasound frequencies, and therefore, complete characterization requires the use of several narrowband transducers. This is a single transducer capable of making these measurements in all the required frequency bands. The device achieves this capability through a unique combination of a broadband piezoelectric material; a design incorporating multiple resonator sizes with distinct, overlapping frequency spectra; and a micromachining process for producing the multiple-resonator pattern with common electrode surfaces between the resonators. This device consists of a pattern of resonator bars with common electrodes that is wrapped around a central mandrel such that the radiating faces of the resonators are coplanar and can be simultaneously applied to the sample to be measured. The device operates as both a source and receiver of acoustic energy. It is operated by connection to an electronic system capable of both providing an excitation signal to the transducer and amplifying the signal received from the transducer. The excitation signal may be either a wide-bandwidth signal to excite the transducer across its entire operational spectrum, or a narrow-bandwidth signal optimized for a particular measurement technique. The transducer face is applied to the skin covering the bone to be characterized, and may be operated in through-transmission mode using two transducers, or in pulse-echo mode. The transducer is a unique combination of material, design, and fabrication technique. It is based on single-crystal lead magnesium niobate lead titanate (PMN-PT) piezoelectric material. As compared to the commonly used piezoceramics, this piezocrystal has superior piezoelectric and elastic properties, which results in devices with superior bandwidth, source level, and power requirements. This design necessitates a single resonant frequency. However, by operating in a transverse length-extensional mode, with the electric field applied orthogonally to the extensional direction, resonators of different sizes can share common electrodes, resulting in a multiply-resonant structure. With carefully sized resonators, and the superior bandwidth of piezocrystal, the resonances can be made to overlap to form a smooth, wide-bandwidth characteristic.

Simulation of Human-induced Vibrations Based on the Characterized In-field Pedestrian Behavior

PubMed Central

Van Nimmen, Katrien; Lombaert, Geert; De Roeck, Guido; Van den Broeck, Peter

2016-01-01

For slender and lightweight structures, vibration serviceability is a matter of growing concern, often constituting the critical design requirement. With designs governed by the dynamic performance under human-induced loads, a strong demand exists for the verification and refinement of currently available load models. The present contribution uses a 3D inertial motion tracking technique for the characterization of the in-field pedestrian behavior. The technique is first tested in laboratory experiments with simultaneous registration of the corresponding ground reaction forces. The experiments include walking persons as well as rhythmical human activities such as jumping and bobbing. It is shown that the registered motion allows for the identification of the time variant pacing rate of the activity. Together with the weight of the person and the application of generalized force models available in literature, the identified time-variant pacing rate allows to characterize the human-induced loads. In addition, time synchronization among the wireless motion trackers allows identifying the synchronization rate among the participants. Subsequently, the technique is used on a real footbridge where both the motion of the persons and the induced structural vibrations are registered. It is shown how the characterized in-field pedestrian behavior can be applied to simulate the induced structural response. It is demonstrated that the in situ identified pacing rate and synchronization rate constitute an essential input for the simulation and verification of the human-induced loads. The main potential applications of the proposed methodology are the estimation of human-structure interaction phenomena and the development of suitable models for the correlation among pedestrians in real traffic conditions. PMID:27167309

Thermal Gradient During Vacuum-Deposition Dramatically Enhances Charge Transport in Organic Semiconductors: Toward High-Performance N-Type Organic Field-Effect Transistors.

PubMed

Kim, Joo-Hyun; Han, Singu; Jeong, Heejeong; Jang, Hayeong; Baek, Seolhee; Hu, Junbeom; Lee, Myungkyun; Choi, Byungwoo; Lee, Hwa Sung

2017-03-22

A thermal gradient distribution was applied to a substrate during the growth of a vacuum-deposited n-type organic semiconductor (OSC) film prepared from N,N'-bis(2-ethylhexyl)-1,7-dicyanoperylene-3,4:9,10-bis(dicarboxyimide) (PDI-CN2), and the electrical performances of the films deployed in organic field-effect transistors (OFETs) were characterized. The temperature gradient at the surface was controlled by tilting the substrate, which varied the temperature one-dimensionally between the heated bottom substrate and the cooled upper substrate. The vacuum-deposited OSC molecules diffused and rearranged on the surface according to the substrate temperature gradient, producing directional crystalline and grain structures in the PDI-CN2 film. The morphological and crystalline structures of the PDI-CN2 thin films grown under a vertical temperature gradient were dramatically enhanced, comparing with the structures obtained from either uniformly heated films or films prepared under a horizontally applied temperature gradient. The field effect mobilities of the PDI-CN2-FETs prepared using the vertically applied temperature gradient were as high as 0.59 cm 2 V -1 s -1 , more than a factor of 2 higher than the mobility of 0.25 cm 2 V -1 s -1 submitted to conventional thermal annealing and the mobility of 0.29 cm 2 V -1 s -1 from the horizontally applied temperature gradient.

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

Nelson, Stacy; English, Shawn; Briggs, Timothy

Fiber-reinforced composite materials offer light-weight solutions to many structural challenges. In the development of high-performance composite structures, a thorough understanding is required of the composite materials themselves as well as methods for the analysis and failure prediction of the relevant composite structures. However, the mechanical properties required for the complete constitutive definition of a composite material can be difficult to determine through experimentation. Therefore, efficient methods are necessary that can be used to determine which properties are relevant to the analysis of a specific structure and to establish a structure's response to a material parameter that can only be definedmore » through estimation. The objectives of this paper deal with demonstrating the potential value of sensitivity and uncertainty quantification techniques during the failure analysis of loaded composite structures; and the proposed methods are applied to the simulation of the four-point flexural characterization of a carbon fiber composite material. Utilizing a recently implemented, phenomenological orthotropic material model that is capable of predicting progressive composite damage and failure, a sensitivity analysis is completed to establish which material parameters are truly relevant to a simulation's outcome. Then, a parameter study is completed to determine the effect of the relevant material properties' expected variations on the simulated four-point flexural behavior as well as to determine the value of an unknown material property. This process demonstrates the ability to formulate accurate predictions in the absence of a rigorous material characterization effort. Finally, the presented results indicate that a sensitivity analysis and parameter study can be used to streamline the material definition process as the described flexural characterization was used for model validation.« less

Advanced analysis of complex seismic waveforms to characterize the subsurface Earth structure

NASA Astrophysics Data System (ADS)

Jia, Tianxia

2011-12-01

This thesis includes three major parts, (1) Body wave analysis of mantle structure under the Calabria slab, (2) Spatial Average Coherency (SPAC) analysis of microtremor to characterize the subsurface structure in urban areas, and (3) Surface wave dispersion inversion for shear wave velocity structure. Although these three projects apply different techniques and investigate different parts of the Earth, their aims are the same, which is to better understand and characterize the subsurface Earth structure by analyzing complex seismic waveforms that are recorded on the Earth surface. My first project is body wave analysis of mantle structure under the Calabria slab. Its aim is to better understand the subduction structure of the Calabria slab by analyzing seismograms generated by natural earthquakes. The rollback and subduction of the Calabrian Arc beneath the southern Tyrrhenian Sea is a case study of slab morphology and slab-mantle interactions at short spatial scale. I analyzed the seismograms traversing the Calabrian slab and upper mantle wedge under the southern Tyrrhenian Sea through body wave dispersion, scattering and attenuation, which are recorded during the PASSCAL CAT/SCAN experiment. Compressional body waves exhibit dispersion correlating with slab paths, which is high-frequency components arrivals being delayed relative to low-frequency components. Body wave scattering and attenuation are also spatially correlated with slab paths. I used this correlation to estimate the positions of slab boundaries, and further suggested that the observed spatial variation in near-slab attenuation could be ascribed to mantle flow patterns around the slab. My second project is Spatial Average Coherency (SPAC) analysis of microtremors for subsurface structure characterization. Shear-wave velocity (Vs) information in soil and rock has been recognized as a critical parameter for site-specific ground motion prediction study, which is highly necessary for urban areas located in seismic active zones. SPAC analysis of microtremors provides an efficient way to estimate Vs structure. Compared with other Vs estimating methods, SPAC is noninvasive and does not require any active sources, and therefore, it is especially useful in big cities. I applied SPAC method in two urban areas. The first is the historic city, Charleston, South Carolina, where high levels of seismic hazard lead to great public concern. Accurate Vs information, therefore, is critical for seismic site classification and site response studies. The second SPAC study is in Manhattan, New York City, where depths of high velocity contrast and soil-to-bedrock are different along the island. The two experiments show that Vs structure could be estimated with good accuracy using SPAC method compared with borehole and other techniques. SPAC is proved to be an effective technique for Vs estimation in urban areas. One important issue in seismology is the inversion of subsurface structures from surface recordings of seismograms. My third project focuses on solving this complex geophysical inverse problems, specifically, surface wave phase velocity dispersion curve inversion for shear wave velocity. In addition to standard linear inversion, I developed advanced inversion techniques including joint inversion using borehole data as constrains, nonlinear inversion using Monte Carlo, and Simulated Annealing algorithms. One innovative way of solving the inverse problem is to make inference from the ensemble of all acceptable models. The statistical features of the ensemble provide a better way to characterize the Earth model.

Determination of the structural phase and octahedral rotation angle in halide perovskites

DOE PAGES

dos Reis, Roberto; Yang, Hao; Ophus, Colin; ...

2018-02-12

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr 3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr 3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurementmore » of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). Finally, the approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.« less

Characterization of applied fields for ion mobility separations in traveling wave based structures for lossless ion manipulations (SLIM)

DOE PAGES

Hamid, Ahmed M.; Prabhakaran, Aneesh; Garimella, Sandilya V. B.; ...

2018-03-26

Ion mobility (IM) is rapidly gaining attention for the separation and analysis of biomolecules due to the ability to distinguish the shapes of ions. However, conventional constant electric field drift tube IM separations have limited resolving power, constrained by practical limitations on the path length and maximum applied voltage. The implementation of traveling waves (TW) in IM removes the latter limitation, allowing higher resolution to be achieved using extended path lengths. Both of these can be readily obtained in Structures for Lossless Ion Manipulations (SLIM), which are fabricated from arrays of electrodes patterned on two parallel surfaces where potentials aremore » applied to generate appropriate electric fields between the surfaces. Here we have investigated the relationship between the primary SLIM variables, such as electrode dimensions, inter-surface gap, and the applied TW voltages, that directly impact the fields experienced by ions. Ion trajectory simulations and theoretical calculations have been utilized to understand the dependence of SLIM geometry and effective electric fields on IM resolution. The variables explored impact both ion confinement and the observed IM resolution using SLIM modules.« less

Characterization of applied fields for ion mobility separations in traveling wave based structures for lossless ion manipulations (SLIM)

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

Hamid, Ahmed M.; Prabhakaran, Aneesh; Garimella, Sandilya V. B.

Ion mobility (IM) is rapidly gaining attention for the separation and analysis of biomolecules due to the ability to distinguish the shapes of ions. However, conventional constant electric field drift tube IM separations have limited resolving power, constrained by practical limitations on the path length and maximum applied voltage. The implementation of traveling waves (TW) in IM removes the latter limitation, allowing higher resolution to be achieved using extended path lengths. Both of these can be readily obtained in Structures for Lossless Ion Manipulations (SLIM), which are fabricated from arrays of electrodes patterned on two parallel surfaces where potentials aremore » applied to generate appropriate electric fields between the surfaces. Here we have investigated the relationship between the primary SLIM variables, such as electrode dimensions, inter-surface gap, and the applied TW voltages, that directly impact the fields experienced by ions. Ion trajectory simulations and theoretical calculations have been utilized to understand the dependence of SLIM geometry and effective electric fields on IM resolution. The variables explored impact both ion confinement and the observed IM resolution using SLIM modules.« less

J plots: a new method for characterizing structures in the interstellar medium

NASA Astrophysics Data System (ADS)

Jaffa, S. E.; Whitworth, A. P.; Clarke, S. D.; Howard, A. D. P.

2018-06-01

Large-scale surveys have brought about a revolution in astronomy. To analyse the resulting wealth of data, we need automated tools to identify, classify, and quantify the important underlying structures. We present here a method for classifying and quantifying a pixelated structure, based on its principal moments of inertia. The method enables us to automatically detect, and objectively compare, centrally condensed cores, elongated filaments, and hollow rings. We illustrate the method by applying it to (i) observations of surface density from Hi-GAL, and (ii) simulations of filament growth in a turbulent medium. We limit the discussion here to 2D data; in a future paper, we will extend the method to 3D data.

Spectral tuning of Amazon parrot feather coloration by psittacofulvin pigments and spongy structures.

PubMed

Tinbergen, Jan; Wilts, Bodo D; Stavenga, Doekele G

2013-12-01

The feathers of Amazon parrots are brightly coloured. They contain a unique class of pigments, the psittacofulvins, deposited in both barbs and barbules, causing yellow or red coloured feathers. In specific feather areas, spongy nanostructured barb cells exist, reflecting either in the blue or blue-green wavelength range. The blue-green spongy structures are partly enveloped by a blue-absorbing, yellow-colouring pigment acting as a spectral filter, thus yielding a green coloured barb. Applying reflection and transmission spectroscopy, we characterized the Amazons' pigments and spongy structures, and investigated how they contribute to the feather coloration. The reflectance spectra of Amazon feathers are presumably tuned to the sensitivity spectra of the visual photoreceptors.

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

Lami, L.; Giovannetti, V.

The set of Entanglement Saving (ES) quantum channels is introduced and characterized. These are completely positive, trace preserving transformations which when acting locally on a bipartite quantum system initially prepared into a maximally entangled configuration, preserve its entanglement even when applied an arbitrary number of times. In other words, a quantum channel ψ is said to be ES if its powers ψ{sup n} are not entanglement-breaking for all integers n. We also characterize the properties of the Asymptotic Entanglement Saving (AES) maps. These form a proper subset of the ES channels that is constituted by those maps that not onlymore » preserve entanglement for all finite n but which also sustain an explicitly not null level of entanglement in the asymptotic limit n → ∞. Structure theorems are provided for ES and for AES maps which yield an almost complete characterization of the former and a full characterization of the latter.« less

Synthesis of hybrid interfacial silica-based nanospheres composite as a support for ultra-small palladium nanoparticle and application of PdNPs/HSN in Mizoroki-Heck reaction

NASA Astrophysics Data System (ADS)

Rostamnia, Sadegh; Kholdi, Saba

2017-12-01

The silica based hollow nanosphere (silica-HNS) containing polymer of polyaniline was synthesized and chosen as a promising support for PdNPs. Then it was applied as a green catalyst in the reaction of Heck coupling with high yield. TEM and SEM-EDX/mapping images were used to study the structure and morphology. FT-IR spectroscopy, Thermal gravimetry analysis (TGA), and BET were used to characterize and investigate the catalyst. Also, the amounts of Pd loading were characterized by ICP-AES technique. Catalyst recyclability showed 5 successful runs for the reaction.

Positronics of subnanometer atomistic imperfections in solids as a high-informative structure characterization tool.

PubMed

Shpotyuk, Oleh; Filipecki, Jacek; Ingram, Adam; Golovchak, Roman; Vakiv, Mykola; Klym, Halyna; Balitska, Valentyna; Shpotyuk, Mykhaylo; Kozdras, Andrzej

2015-01-01

Methodological possibilities of positron annihilation lifetime (PAL) spectroscopy applied to characterize different types of nanomaterials treated within three-term fitting procedure are critically reconsidered. In contrast to conventional three-term analysis based on admixed positron- and positronium-trapping modes, the process of nanostructurization is considered as substitutional positron-positronium trapping within the same host matrix. Developed formalism allows estimate interfacial void volumes responsible for positron trapping and characteristic bulk positron lifetimes in nanoparticle-affected inhomogeneous media. This algorithm was well justified at the example of thermally induced nanostructurization occurring in 80GeSe2-20Ga2Se3 glass.

Preparation, characterization and catalytic properties of MCM-48 supported tungstophosphoric acid mesoporous materials for green synthesis of benzoic acid

NASA Astrophysics Data System (ADS)

Wu, Hai-Yan; Zhang, Xiao-Li; Chen, Xi; Chen, Ya; Zheng, Xiu-Cheng

2014-03-01

MCM-48 and tungstophosphoric acid (HPW) were prepared and applied for the synthesis of HPW/MCM-48 mesoporous materials. The characterization results showed that HPW/MCM-48 obtained retained the typical mesopore structure of MCM-48, and the textural parameters decreased with the increase loading of HPW. The catalytic oxidation results of benzyl alcohol and benzaldehyde with 30% H2O2 indicated that HPW/MCM-48 was an efficient catalyst for the green synthesis of benzoic acid. Furthermore, 35 wt% HPW/MCM-48 sample showed the highest activity under the reaction conditions.

Positronics of subnanometer atomistic imperfections in solids as a high-informative structure characterization tool

NASA Astrophysics Data System (ADS)

Shpotyuk, Oleh; Filipecki, Jacek; Ingram, Adam; Golovchak, Roman; Vakiv, Mykola; Klym, Halyna; Balitska, Valentyna; Shpotyuk, Mykhaylo; Kozdras, Andrzej

2015-02-01

Methodological possibilities of positron annihilation lifetime (PAL) spectroscopy applied to characterize different types of nanomaterials treated within three-term fitting procedure are critically reconsidered. In contrast to conventional three-term analysis based on admixed positron- and positronium-trapping modes, the process of nanostructurization is considered as substitutional positron-positronium trapping within the same host matrix. Developed formalism allows estimate interfacial void volumes responsible for positron trapping and characteristic bulk positron lifetimes in nanoparticle-affected inhomogeneous media. This algorithm was well justified at the example of thermally induced nanostructurization occurring in 80GeSe2-20Ga2Se3 glass.

Density Functional Theory Investigations of D-A-D' Structural Molecules as Donor Materials in Organic Solar Cell.

PubMed

Chen, Junxian; Liu, Qingyu; Li, Hao; Zhao, Zhigang; Lu, Zhiyun; Huang, Yan; Xu, Dingguo

2018-01-01

Squaraine core based small molecules in bulk heterojunction organic solar cells have received extensive attentions due to their distinguished photochemical properties in far red and infrared domain. In this paper, combining theoretical simulations and experimental syntheses and characterizations, three major factors (fill factor, short circuit and open-cirvuit voltage) have been carried out together to achieve improvement of power conversion efficiencies of solar cells. As model material systems with D-A-D' framework, two asymmetric squaraines (CNSQ and CCSQ-Tol) as donor materials in bulk heterojunction organic solar cell were synthesized and characterized. Intensive density functional theory computations were applied to identify some direct connections between three factors and corresponding molecular structural properties. It then helps us to predict one new molecule of CCSQ'-Ox that matches all the requirements to improve the power conversion efficiency.

Synthesis, characterization and computational chemical study of novel pyrazole derivatives as anticorrosion and antiscalant agents

NASA Astrophysics Data System (ADS)

El-Taib Heakal, F.; Attia, S. K.; Rizk, S. A.; Abou Essa, M. A.; Elkholy, A. E.

2017-11-01

Metals corrosion and scales deposition are two serious problems of heavy burden in most industries. Both problems can be mitigated by adding special chemicals capable of being adsorbed on metallic surfaces as well as on scale growing crystal surfaces. Efficient materials should be rich in functional groups containing heteroatoms and/or π bonds for supporting their adsorbability on surfaces. In the present work, four novel pyrazole derivatives were synthesized and characterized for their structures using elemental analysis and spectroscopic tools. The tested compounds were fabricated by treating 2,3-diaryloxirane-2,3-dicarbonitriles with different nitrogen nucleophiles. The density functional theory (DFT) was then applied to explore the structural and electronic characteristics of these materials. Molecular dynamics simulation was also run to scrutinize the ability of the prepared compounds to act as corrosion inhibitors and antiscalant agents by adsorbing on Fe and CaSO4 surfaces.

Characterization of hydrothermally synthesized SnS nanoparticles for solar cell application

NASA Astrophysics Data System (ADS)

Rajwar, Birendra Kumar; Sharma, Shailendra Kumar

2018-05-01

In the present study, SnS nanoparticles were synthesized by simple hydrothermal method using stannous chloride and thiourea as tin (Sn) and sulfur (S) precursor respectively. Synthesized nanoparticles were characterized by X-ray diffraction (XRD), Field Emission Scanning Electron Microscopy and UV-Vis Spectroscopy techniques. XRD pattern reveals that as-prepared nanoparticles exhibit orthorhombic structure. Average particles size was calculated using Scherrer's formula and found to be 23 nm. FESEM image shows that the as-prepared nanoparticles are in plate like structure. Direct optical band gap (Eg) of as-synthesized nanoparticles was calculated through UV-Vis Spectroscopy measurement and found to be 1.34 eV, which is near to optimum need for photovoltaic solar energy conversion (1.5 eV). Thus this SnS, narrowband gap semiconductor material can be applied as an alternative absorber material for solar cell application.

Electric potential and electric field imaging

NASA Astrophysics Data System (ADS)

Generazio, E. R.

2017-02-01

The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field made be used for "illuminating" volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e-Sensor enhancements (ephemeral e-Sensor) are discussed. Demonstrations for structural, electronic, human, and memory applications are shown. This new EFI capability is demonstrated to reveal characterization of electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, crime scene forensics, design and materials selection for advanced sensors, dielectric morphology of structures, tether integrity, organic molecular memory, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

Systems and methods for determining strength of cylindrical structures by internal pressure loading

DOEpatents

DeTeresa, Steven John; Groves, Scott Eric; Sanchez, Roberto Joseph; Andrade, William Andrew

2015-08-04

In one embodiment, an apparatus, includes: a mandrel; an expansion cylinder, comprising: opposite first and second ends; an inner circumferential surface extending between the ends and characterized by an inner diameter, the inner circumferential surface defining a hollow cavity; an outer circumferential surface extending between the ends and characterized by an outer diameter that is greater than the inner diameter; and a plurality of slots extending from the inner circumferential surface to the outer circumferential surface and latitudinally oriented between the ends; and one or more base plates configured to engage one of the ends of the expansion cylinder. In another embodiment, a method includes: arranging an expansion cylinder inside a test cylinder; arranging a mandrel inside the expansion cylinder; applying a force to the mandrel for exerting a radial force on the expansion cylinder; and detecting one or more indicia of structural failure of the test cylinder.

Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy.

PubMed

Jantschke, Anne; Koers, Eline; Mance, Deni; Weingarth, Markus; Brunner, Eike; Baldus, Marc

2015-12-07

Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP-supported ssNMR approach assisted by microscopy, MS, and MD simulations was applied to study the structural organization of intact biosilica. For the first time, the secondary structure elements of tightly biosilica-associated native proteins in diatom biosilica were characterized in situ. Our data suggest that these proteins are rich in a limited set of amino acids and adopt a mixture of random-coil and β-strand conformations. Furthermore, biosilica-associated long-chain polyamines and carbohydrates were characterized, thereby leading to a model for the supramolecular organization of intact biosilica. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Acoustic emission characterization of steel fibre reinforced concrete during bending

NASA Astrophysics Data System (ADS)

Aggelis, D. G.; Soulioti, D. V.; Sapouridis, N.; Barkoula, N. M.; Paipetis, A. S.; Matikas, T. E.

2010-04-01

The acoustic emission (AE) behaviour of steel fibre reinforced concrete is studied in this paper. The experiments were conducted in four-point bending with concurrent monitoring of AE signals. The sensors used, were of broadband response in order to capture a wide range of fracturing phenomena. The results indicate that AE parameters undergo significant changes much earlier than the final fracture of the specimens, even if the AE hit rate seems approximately constant. Specifically, the Ib-value which takes into account the amplitude distribution of the recent AE hits decreases when the load reaches about 60-70 % of its maximum value. Additionally, the average frequency of the signals decreases abruptly when a fracture incident occurs, indicating that matrix cracking events produce higher frequencies than fibre pull-out events. It is concluded that proper study of AE parameters enables the characterization of structural health of large structures in cases where remote monitoring is applied.

Modeling and characterization of double resonant tunneling diodes for application as energy selective contacts in hot carrier solar cells

NASA Astrophysics Data System (ADS)

Jehl, Zacharie; Suchet, Daniel; Julian, Anatole; Bernard, Cyril; Miyashita, Naoya; Gibelli, Francois; Okada, Yoshitaka; Guillemolles, Jean-Francois

2017-02-01

Double resonant tunneling barriers are considered for an application as energy selective contacts in hot carrier solar cells. Experimental symmetric and asymmetric double resonant tunneling barriers are realized by molecular beam epitaxy and characterized by temperature dependent current-voltage measurements. The negative differential resistance signal is enhanced for asymmetric heterostructures, and remains unchanged between low- and room-temperatures. Within Tsu-Esaki description of the tunnel current, this observation can be explained by the voltage dependence of the tunnel transmission amplitude, which presents a resonance under finite bias for asymmetric structures. This effect is notably discussed with respect to series resistance. Different parameters related to the electronic transmission of the structure and the influence of these parameters on the current voltage characteristic are investigated, bringing insights on critical processes to optimize in double resonant tunneling barriers applied to hot carrier solar cells.

Reprint of: Combining theory and experiment for X-ray absorption spectroscopy and resonant X-ray scattering characterization of polymers

DOE PAGES

Su, Gregory M.; Cordova, Isvar A.; Brady, Michael A.; ...

2016-11-01

An improved understanding of fundamental chemistry, electronic structure, morphology, and dynamics in polymers and soft materials requires advanced characterization techniques that are amenable to in situ and operando studies. Soft X-ray methods are especially useful in their ability to non-destructively provide information on specific materials or chemical moieties. Analysis of these experiments, which can be very dependent on X-ray energy and polarization, can quickly become complex. Complementary modeling and predictive capabilities are required to properly probe these critical features. Here in this paper, we present relevant background on this emerging suite of techniques. We focus on how the combination ofmore » theory and experiment has been applied and can be further developed to drive our understanding of how these methods probe relevant chemistry, structure, and dynamics in soft materials.« less

Combining theory and experiment for X-ray absorption spectroscopy and resonant X-ray scattering characterization of polymers

DOE PAGES

Su, Gregory M.; Cordova, Isvar A.; Brady, Michael A.; ...

2016-07-04

We present that an improved understanding of fundamental chemistry, electronic structure, morphology, and dynamics in polymers and soft materials requires advanced characterization techniques that are amenable to in situ and operando studies. Soft X-ray methods are especially useful in their ability to non-destructively provide information on specific materials or chemical moieties. Analysis of these experiments, which can be very dependent on X-ray energy and polarization, can quickly become complex. Complementary modeling and predictive capabilities are required to properly probe these critical features. Here, we present relevant background on this emerging suite of techniques. Finally, we focus on how the combinationmore » of theory and experiment has been applied and can be further developed to drive our understanding of how these methods probe relevant chemistry, structure, and dynamics in soft materials.« less

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.

PubMed

Guerette, Paul A; Hoon, Shawn; Seow, Yiqi; Raida, Manfred; Masic, Admir; Wong, Fong T; Ho, Vincent H B; Kong, Kiat Whye; Demirel, Melik C; Pena-Francesch, Abdon; Amini, Shahrouz; Tay, Gavin Z; Ding, Dawei; Miserez, Ali

2013-10-01

Efforts to engineer new materials inspired by biological structures are hampered by the lack of genomic data from many model organisms studied in biomimetic research. Here we show that biomimetic engineering can be accelerated by integrating high-throughput RNA-seq with proteomics and advanced materials characterization. This approach can be applied to a broad range of systems, as we illustrate by investigating diverse high-performance biological materials involved in embryo protection, adhesion and predation. In one example, we rapidly engineer recombinant squid sucker ring teeth proteins into a range of structural and functional materials, including nanopatterned surfaces and photo-cross-linked films that exceed the mechanical properties of most natural and synthetic polymers. Integrating RNA-seq with proteomics and materials science facilitates the molecular characterization of natural materials and the effective translation of their molecular designs into a wide range of bio-inspired materials.

Tertiary and Quaternary Ammonium-Phosphate Ionic Liquids as Lubricant Additives

DOE PAGES

Barnhill, William C.; Luo, Huimin; Meyer, III, Harry M; ...

2016-06-23

In this work we investigated the feasibility of five quaternary (aprotic) and four tertiary (protic) ammonium ionic liquids (ILs) with an identical organophosphate anion as lubricant antiwear additives. Viscosity, oil solubility, thermal stability, and corrosivity of the candidate ILs were characterized and correlated to the molecular structure. The protic group exhibits higher oil solubility than the aprotic group, and longer alkyl chains seem to provide better oil solubility and higher thermal stability. Selected ILs were applied as oil additives in steel-cast iron tribological tests and demonstrated promising anti-scuffing and anti-wear functionality. The thickness, nanostructure, coverage and composition of the tribofilmmore » formed by the besting performing IL were revealed by surface characterization for mechanistic understanding of the tribochemical interactions between the IL and metal surface. Results provide fundamental insights of the correlations among the molecular structure, physiochemical properties and lubricating performance for ammonium-phosphate ILs.« less

Tertiary and Quaternary Ammonium-Phosphate Ionic Liquids as Lubricant Additives

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

Barnhill, William C.; Luo, Huimin; Meyer, III, Harry M

In this work we investigated the feasibility of five quaternary (aprotic) and four tertiary (protic) ammonium ionic liquids (ILs) with an identical organophosphate anion as lubricant antiwear additives. Viscosity, oil solubility, thermal stability, and corrosivity of the candidate ILs were characterized and correlated to the molecular structure. The protic group exhibits higher oil solubility than the aprotic group, and longer alkyl chains seem to provide better oil solubility and higher thermal stability. Selected ILs were applied as oil additives in steel-cast iron tribological tests and demonstrated promising anti-scuffing and anti-wear functionality. The thickness, nanostructure, coverage and composition of the tribofilmmore » formed by the besting performing IL were revealed by surface characterization for mechanistic understanding of the tribochemical interactions between the IL and metal surface. Results provide fundamental insights of the correlations among the molecular structure, physiochemical properties and lubricating performance for ammonium-phosphate ILs.« less

Depth estimation of laser glass drilling based on optical differential measurements of acoustic response

NASA Astrophysics Data System (ADS)

Gorodesky, Niv; Ozana, Nisan; Berg, Yuval; Dolev, Omer; Danan, Yossef; Kotler, Zvi; Zalevsky, Zeev

2016-09-01

We present the first steps of a device suitable for characterization of complex 3D micro-structures. This method is based on an optical approach allowing extraction and separation of high frequency ultrasonic sound waves induced to the analyzed samples. Rapid, non-destructive characterization of 3D micro-structures are limited in terms of geometrical features and optical properties of the sample. We suggest a method which is based on temporal tracking of secondary speckle patterns generated when illuminating a sample with a laser probe while applying known periodic vibration using an ultrasound transmitter. In this paper we investigated lasers drilled through glass vias. The large aspect ratios of the vias possess a challenge for traditional microscopy techniques in analyzing depth and taper profiles of the vias. The correlation of the amplitude vibrations to the vias depths is experimentally demonstrated.

Atomic scale characterization of white etching area and its adjacent matrix in a martensitic 100Cr6 bearing steel

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

Li, Y.J., E-mail: y.li@mpie.de

Atom probe tomography was employed to characterize the microstructure and C distribution in the white etching area (WEA) of a martensitic 100Cr6 bearing steel subjected to rolling contact fatigue. Different from its surrounding matrix where a plate-like martensitic structure prevails, the WEA exhibits equiaxed grains with a uniform grain size of about 10 nm. Significant C grain boundary enrichment (>7.5at.%) and an overall higher C concentration than the nominal value are observed in the WEA. These results suggest that the formation of WEA results from severe local plastic deformation that causes dissolution of carbides and the redistribution of C. -more » Highlights: •APT has been applied to characterize the microstructure of white etching area (WEA). •Quantitative analyses of C distribution indicate that carbides are dissolved on the WEA. •WEA contains equiaxed grains with a uniform grain size of 10 nm. •C segregation at grain boundaries stabilizes the nanosized grain structure. •Formation of WEA is explained by severe local plastic deformation introduced by cyclic contact loading.« less

Defect and field-enhancement characterization through electron-beam-induced current analysis

NASA Astrophysics Data System (ADS)

Umezawa, Hitoshi; Gima, Hiroki; Driche, Khaled; Kato, Yukako; Yoshitake, Tsuyoshi; Mokuno, Yoshiaki; Gheeraert, Etienne

2017-05-01

To investigate the effects of defects and field enhancement in diamond power devices, a biased Schottky barrier diode was characterized by electron-beam-induced current (EBIC) analysis. The nonuniform distribution of the electrical field was revealed by bright spots on the laterally expanded depletion layer of the EBIC intensity map when the applied electrical field exceeded 0.95 MV/cm. The nonuniformity is partly due to a structural effect: the roughness at the edge of the Schottky electrode, induced by lithography and lift-off processes. A second family of spots was shown to increase the leakage current of the device. The time constant associated with this second spot family was 0.98 ms, which is three orders of magnitude shorter than that for defects previously characterized by deep-level transient spectroscopy.

High-throughput characterization of film thickness in thin film materials libraries by digital holographic microscopy.

PubMed

Lai, Yiu Wai; Krause, Michael; Savan, Alan; Thienhaus, Sigurd; Koukourakis, Nektarios; Hofmann, Martin R; Ludwig, Alfred

2011-10-01

A high-throughput characterization technique based on digital holography for mapping film thickness in thin-film materials libraries was developed. Digital holographic microscopy is used for fully automatic measurements of the thickness of patterned films with nanometer resolution. The method has several significant advantages over conventional stylus profilometry: it is contactless and fast, substrate bending is compensated, and the experimental setup is simple. Patterned films prepared by different combinatorial thin-film approaches were characterized to investigate and demonstrate this method. The results show that this technique is valuable for the quick, reliable and high-throughput determination of the film thickness distribution in combinatorial materials research. Importantly, it can also be applied to thin films that have been structured by shadow masking.

Structural analysis of hierarchically organized zeolites

PubMed Central

Mitchell, Sharon; Pinar, Ana B.; Kenvin, Jeffrey; Crivelli, Paolo; Kärger, Jörg; Pérez-Ramírez, Javier

2015-01-01

Advances in materials synthesis bring about many opportunities for technological applications, but are often accompanied by unprecedented complexity. This is clearly illustrated by the case of hierarchically organized zeolite catalysts, a class of crystalline microporous solids that has been revolutionized by the engineering of multilevel pore architectures, which combine unique chemical functionality with efficient molecular transport. Three key attributes, the crystal, the pore and the active site structure, can be expected to dominate the design process. This review examines the adequacy of the palette of techniques applied to characterize these distinguishing features and their catalytic impact. PMID:26482337

Dynamical simulation of electron transfer processes in self-assembled monolayers at metal surfaces using a density matrix approach.

PubMed

Prucker, V; Bockstedte, M; Thoss, M; Coto, P B

2018-03-28

A single-particle density matrix approach is introduced to simulate the dynamics of heterogeneous electron transfer (ET) processes at interfaces. The characterization of the systems is based on a model Hamiltonian parametrized by electronic structure calculations and a partitioning method. The method is applied to investigate ET in a series of nitrile-substituted (poly)(p-phenylene)thiolate self-assembled monolayers adsorbed at the Au(111) surface. The results show a significant dependence of the ET on the orbital symmetry of the donor state and on the molecular and electronic structure of the spacer.

Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of manganese (II) complex of picolinate: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Tamer, Ömer; Avcı, Davut; Atalay, Yusuf; Çoşut, Bünyemin; Zorlu, Yunus; Erkovan, Mustafa; Yerli, Yusuf

2016-02-01

A novel manganese (II) complex with picolinic acid (pyridine 2-carboxylic acid, Hpic), namely, [Mn(pic)2(H2O)2] was prepared and its crystal structure was fully characterized by using single crystal X-ray diffraction. Picolinate (pic) ligands were coordinated to the central manganese(II) ion as bidentate N,O-donors through the nitrogen atoms of pyridine rings and the oxygen atoms of carboxylate groups forming five-membered chelate rings. The spectroscopic characterization of Mn(II) complex was performed by the applications of FT-IR, Raman, UV-vis and EPR techniques. In order to support these studies, density functional theory (DFT) calculations were carried out by using B3LYP level. IR and Raman spectra were simulated at B3LYP level, and obtained results indicated that DFT calculations generally give compatible results to the experimental ones. The electronic structure of the Mn(II) complex was predicted using time dependent DFT (TD-DFT) method with polarizable continuum model (PCM). Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength were investigated by applying natural bond orbital (NBO) analysis. Nonlinear optical properties of Mn(II) complex were investigated by the determining of molecular polarizability (α) and hyperpolarizability (β) parameters.

Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

PubMed

Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

2012-03-05

Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

NATO Advanced Research Workshop: Optics of Biological Particles. Held in Novosibirsk, Russia on 3-6 Oct 2005

DTIC Science & Technology

2005-01-01

acterization of health relevant bacteria should be critically discussed, and experimentally further evidenced. References [1] D. Naumann, « Infrared spectroscopy ...application of conventional meth- ods for characterizing protein conformational transformations. Raman spectroscopy has been proven to be an efficient...appli- cation of deep ultraviolet res- onance Raman spectroscopy for structural characteriza- tion of a protein at all stages of fibrillation process

A novel integrated framework and improved methodology of computer-aided drug design.

PubMed

Chen, Calvin Yu-Chian

2013-01-01

Computer-aided drug design (CADD) is a critical initiating step of drug development, but a single model capable of covering all designing aspects remains to be elucidated. Hence, we developed a drug design modeling framework that integrates multiple approaches, including machine learning based quantitative structure-activity relationship (QSAR) analysis, 3D-QSAR, Bayesian network, pharmacophore modeling, and structure-based docking algorithm. Restrictions for each model were defined for improved individual and overall accuracy. An integration method was applied to join the results from each model to minimize bias and errors. In addition, the integrated model adopts both static and dynamic analysis to validate the intermolecular stabilities of the receptor-ligand conformation. The proposed protocol was applied to identifying HER2 inhibitors from traditional Chinese medicine (TCM) as an example for validating our new protocol. Eight potent leads were identified from six TCM sources. A joint validation system comprised of comparative molecular field analysis, comparative molecular similarity indices analysis, and molecular dynamics simulation further characterized the candidates into three potential binding conformations and validated the binding stability of each protein-ligand complex. The ligand pathway was also performed to predict the ligand "in" and "exit" from the binding site. In summary, we propose a novel systematic CADD methodology for the identification, analysis, and characterization of drug-like candidates.

Unitized Stiffened Composite Textile Panels: Manufacturing, Characterization, Experiments, and Analysis

NASA Astrophysics Data System (ADS)

Kosztowny, Cyrus Joseph Robert

Use of carbon fiber textiles in complex manufacturing methods creates new implementations of structural components by increasing performance, lowering manufacturing costs, and making composites overall more attractive across industry. Advantages of textile composites include high area output, ease of handling during the manufacturing process, lower production costs per material used resulting from automation, and provide post-manufacturing assembly mainstreaming because significantly more complex geometries such as stiffened shell structures can be manufactured with fewer pieces. One significant challenge with using stiffened composite structures is stiffener separation under compression. Axial compression loading conditions have frequently observed catastrophic structural failure due to stiffeners separating from the shell skin. Characterizing stiffener separation behavior is often costly computationally and experimentally. The objectives of this research are to demonstrate unitized stiffened textile composite panels can be manufactured to produce quality test specimens, that existing characterization techniques applied to state-of-the-art high-performance composites provide valuable information in modeling such structures, that the unitized structure concept successfully removes stiffener separation as a primary structural failure mode, and that modeling textile material failure modes are sufficient to accurately capture postbuckling and final failure responses of the stiffened structures. The stiffened panels in this study have taken the integrally stiffened concept to an extent such that the stiffeners and skin are manufactured at the same time, as one single piece, and from the same composite textile layers. Stiffener separation is shown to be removed as a primary structural failure mode for unitized stiffened composite textile panels loaded under axial compression well into the postbuckling regime. Instead of stiffener separation, a material damaging and failure model effectively captures local post-peak material response via incorporating a mesoscale model using a multiscaling framework with a smeared crack element-based failure model in the macroscale stiffened panel. Material damage behavior is characterized by simple experimental tests and incorporated into the post-peak stiffness degradation law in the smeared crack implementation. Computational modeling results are in overall excellent agreement compared to the experimental responses.

Electron Microscopy and Analytical X-ray Characterization of Compositional and Nanoscale Structural Changes in Fossil Bone

NASA Astrophysics Data System (ADS)

Boatman, Elizabeth Marie

The nanoscale structure of compact bone contains several features that are direct indicators of bulk tissue mechanical properties. Fossil bone tissues represent unique opportunities to understand the compact bone structure/property relationships from a deep time perspective, offering a possible array of new insights into bone diseases, biomimicry of composite materials, and basic knowledge of bioapatite composition and nanoscale bone structure. To date, most work with fossil bone has employed microscale techniques and has counter-indicated the survival of bioapatite and other nanoscale structural features. The obvious disconnect between the use of microscale techniques and the discernment of nanoscale structure has prompted this work. The goal of this study was to characterize the nanoscale constituents of fossil compact bone by applying a suite of diffraction, microscopy, and spectrometry techniques, representing the highest levels of spatial and energy resolution available today, and capable of complementary structural and compositional characterization from the micro- to the nanoscale. Fossil dinosaur and crocodile long bone specimens, as well as modern ratite and crocodile femurs, were acquired from the UC Museum of Paleontology. Preserved physiological features of significance were documented with scanning electron microscopy back-scattered imaging. Electron microprobe wavelength-dispersive X-ray spectroscopy (WDS) revealed fossil bone compositions enriched in fluorine with a complementary loss of oxygen. X-ray diffraction analyses demonstrated that all specimens were composed of apatite. Transmission electron microscopy (TEM) imaging revealed preserved nanocrystallinity in the fossil bones and electron diffraction studies further identified these nanocrystallites as apatite. Tomographic analyses of nanoscale elements imaged by TEM and small angle X-ray scattering were performed, with the results of each analysis further indicating that nanoscale structure is highly conserved in these four fossil specimens. Finally, the results of this study indicate that bioapatite can be preserved in even the most ancient vertebrate specimens, further supporting the idea that fossilization is a preservational process. This work also underlines the importance of using appropriately selected characterization and analytical techniques for the study of fossil bone, especially from the perspective of spatial resolution and the scale of the bone structural features in question.

Slits, plates, and Poisson-Boltzmann theory in a local formulation of nonlocal electrostatics

NASA Astrophysics Data System (ADS)

Paillusson, Fabien; Blossey, Ralf

2010-11-01

Polar liquids like water carry a characteristic nanometric length scale, the correlation length of orientation polarizations. Continuum theories that can capture this feature commonly run under the name of “nonlocal” electrostatics since their dielectric response is characterized by a scale-dependent dielectric function ɛ(q) , where q is the wave vector; the Poisson(-Boltzmann) equation then turns into an integro-differential equation. Recently, “local” formulations have been put forward for these theories and applied to water, solvated ions, and proteins. We review the local formalism and show how it can be applied to a structured liquid in slit and plate geometries, and solve the Poisson-Boltzmann theory for a charged plate in a structured solvent with counterions. Our results establish a coherent picture of the local version of nonlocal electrostatics and show its ease of use when compared to the original formulation.

A critical approach to the definition of Darwinian units of selection.

PubMed

Rinkevich, B

2000-12-01

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.

A preliminary characterization of applied-field MPD thruster plumes

NASA Technical Reports Server (NTRS)

Myers, Roger M.; Wehrle, David; Vernyi, Mark; Biaglow, James; Reese, Shawn

1991-01-01

Electric probes, quantitative imaging, and emission spectroscopy were used to study the plume characteristics of applied field magnetohydrodynamic thrusters. The measurements showed that the applied magnetic field plays the dominant role in establishing the plume structure, followed in importance by the cathode geometry and propellant. The anode radius had no measurable impact on the plume characteristics. For all cases studied the plume was highly ionized, though spectral lines of neutral species were always present. Centerline electron densities and temperatures ranged from 2 times 10 (exp 18) to 8 times 10 (exp 18) m(exp -3) and from 7500 to 20,000 K, respectively. The plume was strongly confined by the magnetic field, with radial density gradients increasing monotonically with applied field strength. Plasma potential measurements show a strong effect of the magnetic field on the electrical conductivity and indicate the presence of radial current conduction in the plume.

New approach for extraction of cellulose from tucumã's endocarp and its structural characterization

NASA Astrophysics Data System (ADS)

Manzato, L.; Rabelo, L. C. A.; de Souza, S. M.; da Silva, C. G.; Sanches, E. A.; Rabelo, D.; Mariuba, L. A. M.; Simonsen, J.

2017-09-01

The recycling of plant wasted materials into useful products represents a green alternative to prevent environmental problems. Tucumã palm fruit (Astrocaryum aculeatum Meyer) is widely used in Amazon region for food and crafts. Due to the large amount of wasted Tucumã's endocarp, this work proposes a new approach for extraction of cellulose and its structural characterization. X-ray Diffraction (XRD), Rietveld Refinement, Scanning Electron Microscopy (SEM), Infrared-transform Fourier Spectroscopy (FTIR) and Thermal Analysis (TG/DSC) have been used for characterization of the extracted cellulose. XRD patterns of the in natura tucumã's endocarp has showed a natural crystalline content embedded in a non-crystalline matrix. Nanocrystals of cellulose have been observed in the XRD pattern of the extracted cellulose, showing a good agreement with type II. Rietveld refinement allowed the cell parameters obtainment (a = 8.43(1) Å, b = 9.50(1) Å, c = 9.39(3) Å and γ = 118.43(4)°). Apparent average crystallite size and microstrain were, respectively, 20.0 Å and 0.1%. Two different methods were applied for estimative of crystallinity percentage. In the first method the height ratio between the intensity of the crystalline peak and the total intensity after the subtraction of the non-crystalline content was applied, leading to 48.5%. The second approach was performed using the amorphous area and the total area of the (1 1 0) peak from the experimental diffractogram, leading to 31.5%. The difference in crystallinity percentage concerning these two used approaches may be explained due to the first method does not consider the broad peaks resulted from nanocrystals diffraction. FTIR spectroscopy has evidenced a cellulose type II structure. SEM images showed micrometric sized fibers with ranged thicknesses. However, a new morphology of spherical nanostructures was observed on the type II matrix fibers. Thermal analysis suggests that the extracted cellulose have low thermal stability, which resulted from poor ordered, packed chains. A large exothermic band was found in DSC curve and associated to the release of energy from the amorphous phase degradation. Thus, this work successfully extracted cellulose from tucumã's endocarp and allowed its structural, morphological and thermal characterization.

Use of Large-Scale Multi-Configuration EMI Measurements to Characterize Subsurface Structures of the Vadose Zone.

NASA Astrophysics Data System (ADS)

Huisman, J. A.; Brogi, C.; Pätzold, S.; Weihermueller, L.; von Hebel, C.; Van Der Kruk, J.; Vereecken, H.

2017-12-01

Subsurface structures of the vadose zone can play a key role in crop yield potential, especially during water stress periods. Geophysical techniques like electromagnetic induction EMI can provide information about dominant shallow subsurface features. However, previous studies with EMI have typically not reached beyond the field scale. We used high-resolution large-scale multi-configuration EMI measurements to characterize patterns of soil structural organization (layering and texture) and their impact on crop productivity at the km2 scale. We collected EMI data on an agricultural area of 1 km2 (102 ha) near Selhausen (NRW, Germany). The area consists of 51 agricultural fields cropped in rotation. Therefore, measurements were collected between April and December 2016, preferably within few days after the harvest. EMI data were automatically filtered, temperature corrected, and interpolated onto a common grid of 1 m resolution. Inspecting the ECa maps, we identified three main sub-areas with different subsurface heterogeneity. We also identified small-scale geomorphological structures as well as anthropogenic activities such as soil management and buried drainage networks. To identify areas with similar subsurface structures, we applied image classification techniques. We fused ECa maps obtained with different coil distances in a multiband image and applied supervised and unsupervised classification methodologies. Both showed good results in reconstructing observed patterns in plant productivity and the subsurface structures associated with them. However, the supervised methodology proved more efficient in classifying the whole study area. In a second step, we selected hundred locations within the study area and obtained a soil profile description with type, depth, and thickness of the soil horizons. Using this ground truth data it was possible to assign a typical soil profile to each of the main classes obtained from the classification. The proposed methodology was effective in producing a high resolution subsurface model in a large and complex study area that extends well beyond the field scale.

Effect of Processing Parameters on Pore Structure and Thickness of Anodic Aluminum Oxide (AAO) Tubular Membranes.

PubMed

Belwalkar, A; Grasing, E; Van Geertruyden, W; Huang, Z; Misiolek, W Z

2008-07-01

Nanoporous anodic aluminum oxide (AAO) tubular membranes were fabricated from aluminum alloy tubes in sulfuric and oxalic acid electrolytes using a two-step anodization process. The membranes were investigated for characteristics such as pore size, interpore distance and thickness by varying applied voltage and electrolyte concentration. Morphology of the membranes was examined using light optical and scanning electron microscopy and characterized using ImageJ software. Results showed that membranes having narrow pore size and uniform pore distribution with parallel channel arrays were obtained. The pore sizes were ranging from 14 to 24 nm and the wall thicknesses as high as 76 microm. It was found that the pore size increased in direct proportion with the applied voltage and inversely with the electrolyte concentration while the interpore distance increased linearly with the applied voltage. It was also observed that increase in acid concentration increased tubular membrane wall thickness that improved mechanical handling. By using anodic alumina technology, robust ceramic tubes with uniformly distributed pore-structure and parallel nano-channels of lengths and sizes practical for industrial applications were reliably produced in quantity.

Effect of Processing Parameters on Pore Structure and Thickness of Anodic Aluminum Oxide (AAO) Tubular Membranes

PubMed Central

Belwalkar, A.; Grasing, E.; Huang, Z.; Misiolek, W.Z.

2008-01-01

Nanoporous anodic aluminum oxide (AAO) tubular membranes were fabricated from aluminum alloy tubes in sulfuric and oxalic acid electrolytes using a two-step anodization process. The membranes were investigated for characteristics such as pore size, interpore distance and thickness by varying applied voltage and electrolyte concentration. Morphology of the membranes was examined using light optical and scanning electron microscopy and characterized using ImageJ software. Results showed that membranes having narrow pore size and uniform pore distribution with parallel channel arrays were obtained. The pore sizes were ranging from 14 to 24 nm and the wall thicknesses as high as 76 µm. It was found that the pore size increased in direct proportion with the applied voltage and inversely with the electrolyte concentration while the interpore distance increased linearly with the applied voltage. It was also observed that increase in acid concentration increased tubular membrane wall thickness that improved mechanical handling. By using anodic alumina technology, robust ceramic tubes with uniformly distributed pore-structure and parallel nano-channels of lengths and sizes practical for industrial applications were reliably produced in quantity. PMID:19578471

Online social activity reflects economic status

NASA Astrophysics Data System (ADS)

Liu, Jin-Hu; Wang, Jun; Shao, Junming; Zhou, Tao

2016-09-01

To characterize economic development and diagnose the economic health condition, several popular indices such as gross domestic product (GDP), industrial structure and income growth are widely applied. However, computing these indices based on traditional economic census is usually costly and resources consuming, and more importantly, following a long time delay. In this paper, we analyzed nearly 200 million users' activities for four consecutive years in the largest social network (Sina Microblog) in China, aiming at exploring latent relationships between the online social activities and local economic status. Results indicate that online social activity has a strong correlation with local economic development and industrial structure, and more interestingly, allows revealing the macro-economic structure instantaneously with nearly no cost. Beyond, this work also provides a new venue to identify risky signal in local economic structure.

Bioelectrical Impedance Methods for Noninvasive Health Monitoring: A Review

PubMed Central

Bera, Tushar Kanti

2014-01-01

Under the alternating electrical excitation, biological tissues produce a complex electrical impedance which depends on tissue composition, structures, health status, and applied signal frequency, and hence the bioelectrical impedance methods can be utilized for noninvasive tissue characterization. As the impedance responses of these tissue parameters vary with frequencies of the applied signal, the impedance analysis conducted over a wide frequency band provides more information about the tissue interiors which help us to better understand the biological tissues anatomy, physiology, and pathology. Over past few decades, a number of impedance based noninvasive tissue characterization techniques such as bioelectrical impedance analysis (BIA), electrical impedance spectroscopy (EIS), electrical impedance plethysmography (IPG), impedance cardiography (ICG), and electrical impedance tomography (EIT) have been proposed and a lot of research works have been conducted on these methods for noninvasive tissue characterization and disease diagnosis. In this paper BIA, EIS, IPG, ICG, and EIT techniques and their applications in different fields have been reviewed and technical perspective of these impedance methods has been presented. The working principles, applications, merits, and demerits of these methods has been discussed in detail along with their other technical issues followed by present status and future trends. PMID:27006932

Thermal characterization of gallium nitride p-i-n diodes

NASA Astrophysics Data System (ADS)

Dallas, J.; Pavlidis, G.; Chatterjee, B.; Lundh, J. S.; Ji, M.; Kim, J.; Kao, T.; Detchprohm, T.; Dupuis, R. D.; Shen, S.; Graham, S.; Choi, S.

2018-02-01

In this study, various thermal characterization techniques and multi-physics modeling were applied to understand the thermal characteristics of GaN vertical and quasi-vertical power diodes. Optical thermography techniques typically used for lateral GaN device temperature assessment including infrared thermography, thermoreflectance thermal imaging, and Raman thermometry were applied to GaN p-i-n diodes to determine if each technique is capable of providing insight into the thermal characteristics of vertical devices. Of these techniques, thermoreflectance thermal imaging and nanoparticle assisted Raman thermometry proved to yield accurate results and are the preferred methods of thermal characterization of vertical GaN diodes. Along with this, steady state and transient thermoreflectance measurements were performed on vertical and quasi-vertical GaN p-i-n diodes employing GaN and Sapphire substrates, respectively. Electro-thermal modeling was performed to validate measurement results and to demonstrate the effect of current crowding on the thermal response of quasi-vertical diodes. In terms of mitigating the self-heating effect, both the steady state and transient measurements demonstrated the superiority of the tested GaN-on-GaN vertical diode compared to the tested GaN-on-Sapphire quasi-vertical structure.

Structural analysis of an innate immunostimulant from broccoli, Brassica oleracea var. italica.

PubMed

Urai, Makoto; Kataoka, Keiko; Nishida, Satoshi; Sekimizu, Kazuhisa

2017-11-22

Vegetables are eaten as part of a healthy diet throughout the world, and some are also applied topically as a traditional medicine. We evaluated the innate immunostimulating activities of hot water extracts of various vegetables using the silkworm muscle contraction assay system, and found that broccoli, Brassica oleracea var. italica, contains a strong innate immunostimulant. We purified the innate immunostimulant from broccoli, and characterized the chemical structure by chemical analyses and NMR spectroscopy. The innate immunostimulant comprised galacturonic acid, galactose, glucose, arabinose, and rhamnose, and had a pectic-like polysaccharide structure. To determine the structural motif involved in the innate immunostimulating activity, we modified the structure by chemical and enzymatic treatment, and found that the activity was attenuated by pectinase digestion. These findings suggest that a pectic-like polysaccharide purified from broccoli has innate immune-stimulating activity, for which the polygalacturonic acid structure is necessary.

Probing dynamic behavior of electric fields and band diagrams in complex semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Turkulets, Yury; Shalish, Ilan

2018-01-01

Modern bandgap engineered electronic devices are typically made of multi-semiconductor multi-layer heterostructures that pose a major challenge to silicon-era characterization methods. As a result, contemporary bandgap engineering relies mostly on simulated band structures that are hardly ever verified experimentally. Here, we present a method that experimentally evaluates bandgap, band offsets, and electric fields, in complex multi-semiconductor layered structures, and it does so simultaneously in all the layers. The method uses a modest optical photocurrent spectroscopy setup at ambient conditions. The results are analyzed using a simple model for electro-absorption. As an example, we apply the method to a typical GaN high electron mobility transistor structure. Measurements under various external electric fields allow us to experimentally construct band diagrams, not only at equilibrium but also under any other working conditions of the device. The electric fields are then used to obtain the charge carrier density and mobility in the quantum well as a function of the gate voltage over the entire range of operating conditions of the device. The principles exemplified here may serve as guidelines for the development of methods for simultaneous characterization of all the layers in complex, multi-semiconductor structures.

Characterization and classification of vegetation canopy structure and distribution within the Great Smoky Mountains National Park using LiDAR

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

Kumar, Jitendra; HargroveJr., William Walter; Norman, Steven P

Vegetation canopy structure is a critically important habit characteristic for many threatened and endangered birds and other animal species, and it is key information needed by forest and wildlife managers for monitoring and managing forest resources, conservation planning and fostering biodiversity. Advances in Light Detection and Ranging (LiDAR) technologies have enabled remote sensing-based studies of vegetation canopies by capturing three-dimensional structures, yielding information not available in two-dimensional images of the landscape pro- vided by traditional multi-spectral remote sensing platforms. However, the large volume data sets produced by airborne LiDAR instruments pose a significant computational challenge, requiring algorithms to identify andmore » analyze patterns of interest buried within LiDAR point clouds in a computationally efficient manner, utilizing state-of-art computing infrastructure. We developed and applied a computationally efficient approach to analyze a large volume of LiDAR data and to characterize and map the vegetation canopy structures for 139,859 hectares (540 sq. miles) in the Great Smoky Mountains National Park. This study helps improve our understanding of the distribution of vegetation and animal habitats in this extremely diverse ecosystem.« less

Cohesive Laws for Analyzing Through-Crack Propagation in Cross Ply Laminates

NASA Technical Reports Server (NTRS)

Bergan, Andrew C.; Davila, Carlos G.

2015-01-01

The laminate cohesive approach (LCA) is a methodology for the experimental characterization of cohesive through-the-thickness damage propagation in fiber-reinforced polymer matrix composites. LCA has several advantages over other existing approaches for cohesive law characterization, including: visual measurements of crack length are not required, structural effects are accounted for, and LCA can be applied when the specimen is too small to achieve steady-state fracture. In this work, the applicability of this method is investigated for two material systems: IM7/8552, a conventional prepreg, and AS4/VRM34, a non-crimp fabric cured using an out-of-autoclave process. The compact tension specimen configuration is used to propagate stable Mode I damage. Trilinear cohesive laws are characterized using the fracture toughness and the notch tip opening displacement. Test results are compared for the IM7/8552 specimens with notches machined by waterjet and by wire slurry saw. It is shown that the test results are nearly identical for both notch tip preparations methods, indicating that significant specimen preparation time and cost savings can be realized by using the waterjet to notch the specimen instead of the wire slurry saw. The accuracy of the cohesive laws characterized herein are assessed by reproducing the structural response of the test specimens using computational methods. The applicability of the characterization procedure for inferring lamina fracture toughness is also discussed.

Structural damage identification using damping: a compendium of uses and features

NASA Astrophysics Data System (ADS)

Cao, M. S.; Sha, G. G.; Gao, Y. F.; Ostachowicz, W.

2017-04-01

The vibration responses of structures under controlled or ambient excitation can be used to detect structural damage by correlating changes in structural dynamic properties extracted from responses with damage. Typical dynamic properties refer to modal parameters: natural frequencies, mode shapes, and damping. Among these parameters, natural frequencies and mode shapes have been investigated extensively for their use in damage characterization by associating damage with reduction in local stiffness of structures. In contrast, the use of damping as a dynamic property to represent structural damage has not been comprehensively elucidated, primarily due to the complexities of damping measurement and analysis. With advances in measurement technologies and analysis tools, the use of damping to identify damage is becoming a focus of increasing attention in the damage detection community. Recently, a number of studies have demonstrated that damping has greater sensitivity for characterizing damage than natural frequencies and mode shapes in various applications, but damping-based damage identification is still a research direction ‘in progress’ and is not yet well resolved. This situation calls for an overall survey of the state-of-the-art and the state-of-the-practice of using damping to detect structural damage. To this end, this study aims to provide a comprehensive survey of uses and features of applying damping in structural damage detection. First, we present various methods for damping estimation in different domains including the time domain, the frequency domain, and the time-frequency domain. Second, we investigate the features and applications of damping-based damage detection methods on the basis of two predominant infrastructure elements, reinforced concrete structures and fiber-reinforced composites. Third, we clarify the influential factors that can impair the capability of damping to characterize damage. Finally, we recommend future research directions for advancing damping-based damage detection. This work holds the promise of (a) helping researchers identify crucial components in damping-based damage detection theories, methods, and technologies, and (b) leading practitioners to better implement damping-based structural damage identification.

Preparation and characterization of kefiran electrospun nanofibers.

PubMed

Esnaashari, Seyedeh Sara; Rezaei, Sasan; Mirzaei, Esmaeil; Afshari, Hamed; Rezayat, Seyed Mahdi; Faridi-Majidi, Reza

2014-09-01

In this study, we report the first successful production of kefiran nanofibers through electrospinning process using distilled water as solvent. For this purpose, kefiran was extracted from cultured kefir grains, and homogenous kefiran solutions with different concentrations were prepared and then electrospun to obtain uniform nanofibers. The effect of main process parameters, including applied voltage, tip-to-collector distance, and feeding rate, on diameter and morphology of produced nanofibers, was studied. Scanning electron microscopy (SEM) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy were used to characterize electrospun mats. Rheological behavior of the kefiran solution was evaluated via a cone and plate rheometer too. The results exhibited that diameter of kefiran nanofibers increased with increasing polymer concentration, applied voltage, and polymer feeding rate, while tip-to-collector distance did not have significant effect on nanofiber diameter. ATR-FTIR spectra showed that kefiran has maintained its molecular structure during electrospinning process. Flow curves also demonstrated shear thinning behavior for kefiran solutions. Copyright © 2014 Elsevier B.V. All rights reserved.

Direct observation of conductive filament formation in Alq3 based organic resistive memories

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

Busby, Y., E-mail: yan.busby@unamur.be; Pireaux, J.-J.; Nau, S.

2015-08-21

This work explores resistive switching mechanisms in non-volatile organic memory devices based on tris(8-hydroxyquinolie)aluminum (Alq{sub 3}). Advanced characterization tools are applied to investigate metal diffusion in ITO/Alq{sub 3}/Ag memory device stacks leading to conductive filament formation. The morphology of Alq{sub 3}/Ag layers as a function of the metal evaporation conditions is studied by X-ray reflectivity, while depth profile analysis with X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry is applied to characterize operational memory elements displaying reliable bistable current-voltage characteristics. 3D images of the distribution of silver inside the organic layer clearly point towards the existence of conductive filamentsmore » and allow for the identification of the initial filament formation and inactivation mechanisms during switching of the device. Initial filament formation is suggested to be driven by field assisted diffusion of silver from abundant structures formed during the top electrode evaporation, whereas thermochemical effects lead to local filament inactivation.« less

A Mechanistic Pharmacokinetic Model for Liver Transporter Substrates Under Liver Cirrhosis Conditions

PubMed Central

Li, R; Barton, HA; Maurer, TS

2015-01-01

Liver cirrhosis is a disease characterized by the loss of functional liver mass. Physiologically based pharmacokinetic (PBPK) modeling was applied to interpret and predict how the interplay among physiological changes in cirrhosis affects pharmacokinetics. However, previous PBPK models under cirrhotic conditions were developed for permeable cytochrome P450 substrates and do not directly apply to substrates of liver transporters. This study characterizes a PBPK model for liver transporter substrates in relation to the severity of liver cirrhosis. A published PBPK model structure for liver transporter substrates under healthy conditions and the physiological changes for cirrhosis are combined to simulate pharmacokinetics of liver transporter substrates in patients with mild and moderate cirrhosis. The simulated pharmacokinetics under liver cirrhosis reasonably approximate observations. This analysis includes meta-analysis to obtain system-dependent parameters in cirrhosis patients and a top-down approach to improve understanding of the effect of cirrhosis on transporter-mediated drug disposition under cirrhotic conditions. PMID:26225262

The application of decision analysis to life support research and technology development

NASA Technical Reports Server (NTRS)

Ballin, Mark G.

1994-01-01

Applied research and technology development is often characterized by uncertainty, risk, and significant delays before tangible returns are obtained. Decision making regarding which technologies to advance and what resources to devote to them is a challenging but essential task. In the application of life support technology to future manned space flight, new technology concepts typically are characterized by nonexistent data and rough approximations of technology performance, uncertain future flight program needs, and a complex, time-intensive process to develop technology to a flight-ready status. Decision analysis is a quantitative, logic-based discipline that imposes formalism and structure to complex problems. It also accounts for the limits of knowledge that may be available at the time a decision is needed. The utility of decision analysis to life support technology R & D was evaluated by applying it to two case studies. The methodology was found to provide insight that is not possible from more traditional analysis approaches.

Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion

NASA Astrophysics Data System (ADS)

Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

2014-05-01

The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

Local Guided Wavefield Analysis for Characterization of Delaminations in Composites

NASA Technical Reports Server (NTRS)

Rogge, Matthew D.; Campbell Leckey, Cara A.

2012-01-01

Delaminations in composite laminates resulting from impact events may be accompanied by minimal indication of damage at the surface. As such, inspection techniques are required to ensure defects are within allowable limits. Conventional ultrasonic scanning techniques have been shown to effectively characterize the size and depth of delaminations but require physical contact with the structure. Alternatively, a noncontact scanning laser vibrometer may be used to measure guided wave propagation in the laminate structure. A local Fourier domain analysis method is presented for processing guided wavefield data to estimate spatially-dependent wavenumber values, which can be used to determine delamination depth. The technique is applied to simulated wavefields and results are analyzed to determine limitations of the technique with regards to determining defect size and depth. Finally, experimental wavefield data obtained in quasi-isotropic carbon fiber reinforced polymer (CFRP) laminates with impact damage is analyzed and wavenumber is measured to an accuracy of 8.5% in the region of shallow delaminations. Keywords: Ultrasonic wavefield imaging, Windowed Fourier transforms, Guided waves, Structural health monitoring, Nondestructive evaluation

Synthesis and characterization of hexaarylbenzenes with five or six different substituents enabled by programmed synthesis

NASA Astrophysics Data System (ADS)

Suzuki, Shin; Segawa, Yasutomo; Itami, Kenichiro; Yamaguchi, Junichiro

2015-03-01

Since its discovery in 1825, benzene has served as one of the most used and indispensable building blocks of chemical compounds, ranging from pharmaceuticals and agrochemicals to plastics and those used in organic electronic devices. Benzene has six hydrogen atoms that can each be replaced by different substituents, which means that the structural diversity of benzene derivatives is intrinsically extraordinary. The number of possible substituted benzenes from n different substituents is (2n + 2n2 + 4n3 + 3n4 + n6)/12. However, owing to a lack of general synthetic methods for making multisubstituted benzenes, this potentially huge structural diversity has not been fully exploited. Here, we describe a programmed synthesis of hexaarylbenzenes using C-H activation, cross-coupling and [4+2] cycloaddition reactions. The present method allows for the isolation and structure-property characterization of hexaarylbenzenes with distinctive aryl substituents at all positions for the first time. Moreover, the established protocol can be applied to the synthesis of tetraarylnaphthalenes and pentaarylpyridines.

Synthesis and structural characterization of CdS nanoparticles

NASA Astrophysics Data System (ADS)

Kotkata, M. F.; Masoud, A. E.; Mohamed, M. B.; Mahmoud, E. A.

2009-08-01

Amorphous CdS nanoparticles capped with cetyltrimethyl ammonium bromide (CTAB) were synthesised under various conditions using a coprecipitation method. A blue shift in the band gap was observed in the UV-visible absorption spectra indicating the formation of nanoparticles of an approximate size of 8 nm. The recorded transmission electron micrographs confirmed this result. The phase-nature, phase transformation as well as the structure of the synthesised CdS nanoparticles have been extensively characterized using X-ray diffraction (XRD), radial distribution function (RDF), differential scanning calorimetry (DSC), Fourier transform infrared (FT-IR), Raman scattering (RS) and/or heat stage X-ray diffraction (HSXRD). Analysis of the obtained results revealed that the synthesised amorphous CdS nanoparticles could be transformed into CdS nanocrystals having a zinc blende or a wurtzite structure, relying on the applied heat treatment scheme. The rate of nanocrystal growth depends on the aging period, prior filtering the reacted materials, and its relation to the quality of the capping process. Five days aging period tends to enhance the stability of the grown phase with a remarkable surface stability.

Velocimetry modalities for secondary flows in a curved artery test section

NASA Astrophysics Data System (ADS)

Bulusu, Kartik V.; Elkins, Christopher J.; Banko, Andrew J.; Plesniak, Michael W.; Eaton, John K.

2014-11-01

Secondary flow structures arise due to curvature-related centrifugal forces and pressure imbalances. These flow structures influence wall shear stress and alter blood particle residence times. Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) techniques were implemented independently, under the same physiological inflow conditions (Womersley number = 4.2). A 180-degree curved artery test section with curvature ratio (1/7) was used as an idealized geometry for curved arteries. Newtonian blood analog fluids were used for both MRV and PIV experiments. The MRV-technique offers the advantage of three-dimensional velocity field acquisition without requiring optical access or flow markers. Phase-averaged, two-dimensional, PIV-data at certain cross-sectional planes and inflow phases were compared to phase-averaged MRV-data to facilitate the characterization of large-scale, Dean-type vortices. Coherent structures detection methods that included a novel wavelet decomposition-based approach to characterize these flow structures was applied to both PIV- and MRV-data. The overarching goal of this study is the detection of motific, three-dimensional shapes of secondary flow structures using MRV techniques with guidance obtained from high fidelity, 2D-PIV measurements. This material is based in part upon work supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

Estimation of fatigue life using electromechanical impedance technique

NASA Astrophysics Data System (ADS)

Lim, Yee Yan; Soh, Chee Kiong

2010-04-01

Fatigue induced damage is often progressive and gradual in nature. Structures subjected to large number of fatigue load cycles will encounter the process of progressive crack initiation, propagation and finally fracture. Monitoring of structural health, especially for the critical components, is therefore essential for early detection of potential harmful crack. Recent advent of smart materials such as piezo-impedance transducer adopting the electromechanical impedance (EMI) technique and wave propagation technique are well proven to be effective in incipient damage detection and characterization. Exceptional advantages such as autonomous, real-time and online, remote monitoring may provide a cost-effective alternative to the conventional structural health monitoring (SHM) techniques. In this study, the main focus is to investigate the feasibility of characterizing a propagating fatigue crack in a structure using the EMI technique as well as estimating its remaining fatigue life using the linear elastic fracture mechanics (LEFM) approach. Uniaxial cyclic tensile load is applied on a lab-sized aluminum beam up to failure. Progressive shift in admittance signatures measured by the piezo-impedance transducer (PZT patch) corresponding to increase of loading cycles reflects effectiveness of the EMI technique in tracing the process of fatigue damage progression. With the use of LEFM, prediction of the remaining life of the structure at different cycles of loading is possible.

Structures and properties of fluorinated amorphous carbon films

NASA Astrophysics Data System (ADS)

Huang, K. P.; Lin, P.; Shih, H. C.

2004-07-01

Fluorinated amorphous carbon (a-C:F) films were deposited by radio frequency bias assisted microwave plasma electron cyclotron resonance chemical vapor deposition with tetrafluoromethane (CF4) and acetylene (C2H2) as precursors. The deposition process was performed at two flow ratios R=0.90 and R=0.97, where R=CF4/(CF4+C2H2). The samples were annealed at 300 °C for 30 min. in a N2 atmosphere. Both Fourier transform infrared and electron spectroscopy for chemical analyzer were used to characterize the a-C:F film chemical bond and fluorine concentration, respectively. A high resolution electron energy loss spectrometer was applied to detect the electronic structure. The higher CF4 flow ratio (R=0.97) produced more sp3 linear structure, and it made the a-C:F film smoother and softer. A lifetime of around 0.34 μs and an energy gap of ˜2.75 eV were observed in both the as-deposited and after annealing conditions. The short carriers lifetime in the a-C:F film made the photoluminescence peak blueshift. The annealing changed both the structure and composition of the a-C:F film. The type of fluorocarbon bond and electronic structure characterized the mechanical and physical properties of a-C:F film.

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours

PubMed Central

Wickham, Shelley; Large, Maryanne C.J; Poladian, Leon; Jermiin, Lars S

2005-01-01

Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused. PMID:16849221

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

PubMed

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Mg2+-induced DNA compaction, condensation, and phase separation in gene delivery vehicles based on zwitterionic phospholipids: a dynamic light scattering and surface-enhanced Raman spectroscopic study.

PubMed

Süleymanoğlu, Erhan

2017-12-01

Despite the significant efforts towards applying improved non-destructive and label-free measurements of biomolecular structures of lipid-based gene delivery vectors, little is achieved in terms of their structural relevance in gene transfections. Better understanding of structure-activity relationships of lipid-DNA complexes and their gene expression efficiencies thus becomes an essential issue. Raman scattering offers a complimentary measurement technique for following the structural transitions of both DNA and lipid vesicles employed for their transfer. This work describes the use of SERS coupled with light scattering approaches for deciphering the bioelectrochemical phase formations between nucleic acids and lipid vesicles within lipoplexes and their surface parameters that could influence both the uptake of non-viral gene carriers and the endocytic routes of interacting cells. As promising non-viral alternatives of currently employed risky viral systems or highly cytotoxic cationic liposomes, complexations of both nucleic acids and zwitterionic lipids in the presence of Mg 2+ were studied applying colloidal Ag nanoparticles. It is shown that the results could be employed in further conformational characterizations of similar polyelectrolyte gene delivery systems.

β-sheet-like formation during the mechanical unfolding of prion protein

NASA Astrophysics Data System (ADS)

Tao, Weiwei; Yoon, Gwonchan; Cao, Penghui; Eom, Kilho; Park, Harold S.

2015-09-01

Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrPC, whose misfolded form PrPSc can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

Electric-field-induced local and mesoscale structural changes in polycrystalline dielectrics and ferroelectrics

DOE PAGES

Usher, Tedi -Marie; Levin, Igor; Daniels, John E.; ...

2015-10-01

In this study, the atomic-scale response of dielectrics/ferroelectrics to electric fields is central to their functionality. Here we introduce an in situ characterization method that reveals changes in the local atomic structure in polycrystalline materials under fields. The method employs atomic pair distribution functions (PDFs), determined from X-ray total scattering that depends on orientation relative to the applied field, to probe structural changes over length scales from sub-Ångstrom to several nanometres. The PDF is sensitive to local ionic displacements and their short-range order, a key uniqueness relative to other techniques. The method is applied to representative ferroelectrics, BaTiO 3 andmore » Na ½Bi ½TiO 3, and dielectric SrTiO 3. For Na ½Bi ½TiO 3, the results reveal an abrupt field-induced monoclinic to rhombohedral phase transition, accompanied by ordering of the local Bi displacements and reorientation of the nanoscale ferroelectric domains. For BaTiO 3 and SrTiO 3, the local/nanoscale structural changes observed in the PDFs are dominated by piezoelectric lattice strain and ionic polarizability, respectively.« less

β-sheet-like formation during the mechanical unfolding of prion protein

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

Tao, Weiwei; Cao, Penghui; Park, Harold S., E-mail: parkhs@bu.edu

2015-09-28

Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP{sup C}, whose misfolded form PrP{sup Sc} can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundredsmore » of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.« less

Composite laminate failure parameter optimization through four-point flexure experimentation and analysis

DOE PAGES

Nelson, Stacy; English, Shawn; Briggs, Timothy

2016-05-06

Fiber-reinforced composite materials offer light-weight solutions to many structural challenges. In the development of high-performance composite structures, a thorough understanding is required of the composite materials themselves as well as methods for the analysis and failure prediction of the relevant composite structures. However, the mechanical properties required for the complete constitutive definition of a composite material can be difficult to determine through experimentation. Therefore, efficient methods are necessary that can be used to determine which properties are relevant to the analysis of a specific structure and to establish a structure's response to a material parameter that can only be definedmore » through estimation. The objectives of this paper deal with demonstrating the potential value of sensitivity and uncertainty quantification techniques during the failure analysis of loaded composite structures; and the proposed methods are applied to the simulation of the four-point flexural characterization of a carbon fiber composite material. Utilizing a recently implemented, phenomenological orthotropic material model that is capable of predicting progressive composite damage and failure, a sensitivity analysis is completed to establish which material parameters are truly relevant to a simulation's outcome. Then, a parameter study is completed to determine the effect of the relevant material properties' expected variations on the simulated four-point flexural behavior as well as to determine the value of an unknown material property. This process demonstrates the ability to formulate accurate predictions in the absence of a rigorous material characterization effort. Finally, the presented results indicate that a sensitivity analysis and parameter study can be used to streamline the material definition process as the described flexural characterization was used for model validation.« less

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.

Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations.

PubMed

Barradas-Bautista, Didier; Fernández-Recio, Juan

2017-01-01

Next-generation sequencing (NGS) technologies are providing genomic information for an increasing number of healthy individuals and patient populations. In the context of the large amount of generated genomic data that is being generated, understanding the effect of disease-related mutations at molecular level can contribute to close the gap between genotype and phenotype and thus improve prevention, diagnosis or treatment of a pathological condition. In order to fully characterize the effect of a pathological mutation and have useful information for prediction purposes, it is important first to identify whether the mutation is located at a protein-binding interface, and second to understand the effect on the binding affinity of the affected interaction/s. Computational methods, such as protein docking are currently used to complement experimental efforts and could help to build the human structural interactome. Here we have extended the original pyDockNIP method to predict the location of disease-associated nsSNPs at protein-protein interfaces, when there is no available structure for the protein-protein complex. We have applied this approach to the pathological interaction networks of six diseases with low structural data on PPIs. This approach can almost double the number of nsSNPs that can be characterized and identify edgetic effects in many nsSNPs that were previously unknown. This can help to annotate and interpret genomic data from large-scale population studies, and to achieve a better understanding of disease at molecular level.

Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations

PubMed Central

2017-01-01

Next-generation sequencing (NGS) technologies are providing genomic information for an increasing number of healthy individuals and patient populations. In the context of the large amount of generated genomic data that is being generated, understanding the effect of disease-related mutations at molecular level can contribute to close the gap between genotype and phenotype and thus improve prevention, diagnosis or treatment of a pathological condition. In order to fully characterize the effect of a pathological mutation and have useful information for prediction purposes, it is important first to identify whether the mutation is located at a protein-binding interface, and second to understand the effect on the binding affinity of the affected interaction/s. Computational methods, such as protein docking are currently used to complement experimental efforts and could help to build the human structural interactome. Here we have extended the original pyDockNIP method to predict the location of disease-associated nsSNPs at protein-protein interfaces, when there is no available structure for the protein-protein complex. We have applied this approach to the pathological interaction networks of six diseases with low structural data on PPIs. This approach can almost double the number of nsSNPs that can be characterized and identify edgetic effects in many nsSNPs that were previously unknown. This can help to annotate and interpret genomic data from large-scale population studies, and to achieve a better understanding of disease at molecular level. PMID:28841721

The chemical modification and characterization of polypropylene membrane with environment response by in-situ chlorinating graft copolymerization

NASA Astrophysics Data System (ADS)

Zhang, Yue; Liu, Jiankai; Hu, Wenjie; Feng, Ying; Zhao, Jiruo

2017-08-01

In this study, a novel chemical surface modification method of polyolefin membranes is applied following the in-situ chlorinating graft copolymerization (ISCGC). Polypropylene (PP)/methyl methacrylate (MMA) system was used as an example. A unique structure was formed by the modification process on the original membrane surface and the product exhibited an environmental response. Chlorine free radicals were generated using ultraviolet and heat and were used to capture the hydrogen in the polymer chains on the substrate surface. The formed macromolecular radicals could react with MMA over 2 h to achieve a high coverage ratio polymer on the PP membrane surface. The graft copolymers were characterized using FTIR, 1H-NMR, DSC, and XPS, which all proved the feasibility of chemically modifying the PP membrane surface by ISCGC. The surface morphology of the grafted PP membrane was characterized using SEM and AFM. The results showed that the grafted product presents a uniform, neat, and dense mastoid structure with an average thickness of 4.44 μm, which was expected to be similar to the brush-like surface structure. The contact angle and AFM tests indicated that the product surface is responsive to solvent and pH. The experimental results showed that the PP membrane surface structure can be reconstructed using ISCGC, a method that can be used for environment-responsive polymer materials. Moreover, the product has the characteristics of polymer interfacial brush.

Crystal Structure of StaL, A Glycopeptide Antibiotic Sulfotransferase from Streptomyces Toyocaensis

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

Shi,R.; Lamb, S.; Bhat, S.

2007-01-01

Over the past decade, antimicrobial resistance has emerged as a major public health crisis. Glycopeptide antibiotics such as vanco-mycin and teicoplanin are clinically important for the treatment of Gram-positive bacterial infections. StaL is a 3'-phosphoadenosine 5'-phosphosulfate-dependent sulfotransferase capable of sulfating the cross-linked heptapeptide substrate both in vivo and in vitro, yielding the product A47934 [GenBank], unique teicoplanin-class glycopeptide antibiotic. The sulfonation reaction catalyzed by StaL constitutes the final step in A47934 [GenBank] biosynthesis. Here we report the crystal structure of StaL and its complex with the cofactor product 3'-phosphoadenosine 5'-phosphate. This is only the second prokaryotic sulfotransferase to be structurallymore » characterized. StaL belongs to the large sulfotransferase family and shows higher similarity to cytosolic sulfotransferases (ST) than to the bacterial ST (Stf0). StaL has a novel dimerization motif, different from any other STs that have been structurally characterized. We have also applied molecular modeling to investigate the binding mode of the unique substrate, desulfo-A47934. Based on the structural analysis and modeling results, a series of residues was mutated and kinetically characterized. In addition to the conserved residues (Lys{sup 12}, His{sup 67}, and Ser{sup 98}), molecular modeling, fluorescence quenching experiments, and mutagenesis studies identified several other residues essential for substrate binding and/or activity, including Trp{sup 34}, His{sup 43}, Phe{sup 77}, Trp{sup 132}, and Glu{sup 205}.« less

Photonic crystal microprisms obtained by carving artificial opals

NASA Astrophysics Data System (ADS)

Fenollosa, R.; Ibisate, M.; Rubio, S.; López, C.; Meseguer, F.; Sánchez-Dehesa, J.

2003-01-01

A method for fabrication of photonic crystal prisms is demonstrated. The procedure is based on micromanipulation techniques, here applied to artificial opals. By means of a microgrinder an opal prism comprising a single crystal (several tens of microns in size) has been carved with three different faces: (111), (110), and (100). The faces were morphologically characterized by scanning electron microscopy and their optical reflectance spectra measured and compared with the theoretical band structure.

Surface relief model for photopolymers without cover plating.

PubMed

Gallego, S; Márquez, A; Ortuño, M; Francés, J; Marini, S; Beléndez, A; Pascual, I

2011-05-23

Relief surface changes provide interesting possibilities for storing diffractive optical elements on photopolymers and are an important source of information to characterize and understand the material behaviour. In this paper we present a 3-dimensional model based on direct measurements of parameters to predict the relief structures generated on the material. This model is successfully applied to different photopolymers with different values of monomer diffusion. The importance of monomer diffusion in depth is also discussed.

Dispersed metal cluster catalysts by design. Synthesis, characterization, structure, and performance

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

Arslan, Ilke; Dixon, David A.; Gates, Bruce C.

2015-09-30

To understand the class of metal cluster catalysts better and to lay a foundation for the prediction of properties leading to improved catalysts, we have synthesized metal catalysts with well-defined structures and varied the cluster structures and compositions systematically—including the ligands bonded to the metals. These ligands include supports and bulky organics that are being tuned to control both the electron transfer to or from the metal and the accessibility of reactants to influence catalytic properties. We have developed novel syntheses to prepare these well-defined catalysts with atomic-scale control the environment by choice and placement of ligands and applied state-of-themore » art spectroscopic, microscopic, and computational methods to determine their structures, reactivities, and catalytic properties. The ligands range from nearly flat MgO surfaces to enveloping zeolites to bulky calixarenes to provide controlled coverages of the metal clusters, while also enforcing unprecedented degrees of coordinative unsaturation at the metal site—thereby facilitating bonding and catalysis events at exposed metal atoms. With this wide range of ligand properties and our arsenal of characterization tools, we worked to achieve a deep, fundamental understanding of how to synthesize robust supported and ligand-modified metal clusters with controlled catalytic properties, thereby bridging the gap between active site structure and function in unsupported and supported metal catalysts. We used methods of organometallic and inorganic chemistry combined with surface chemistry for the precise synthesis of metal clusters and nanoparticles, characterizing them at various stages of preparation and under various conditions (including catalytic reaction conditions) and determining their structures and reactivities and how their catalytic properties depend on their compositions and structures. Key characterization methods included IR, NMR, and EXAFS spectroscopies to identify ligands on the metals and their reactions; EXAFS spectroscopy and high-resolution STEM to determine cluster framework structures and changes resulting from reactant treatment and locations of metal atoms on support surfaces; X-ray diffraction crystallography to determine full structures of cluster-ligand combinations in the absence of a support, and TEM with tomographic methods to observe individual metal atoms and determine three-dimensional structures of catalysts. Electronic structure calculations were used to verify and interpret spectra and extend the understanding of reactivity beyond what is measurable experimentally.« less

Poissonian renormalizations, exponentials, and power laws.

PubMed

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive "renormalization study" of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to "white noise" and to "1/f noise." Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

Magneto-optical mode conversion in a hybrid glass waveguide made by sol-gel and ion-exchange techniques

NASA Astrophysics Data System (ADS)

Royer, François; Amata, Hadi; Parsy, François; Jamon, Damien; Ghibaudo, Elise; Broquin, Jean-Emmanuel; Neveu, Sophie

2012-01-01

The integration of magneto-optical materials with classical technologies being still a difficult problem, this study explores the possibility to realize a mode converter based on a hybrid structure. A composite magneto-optical layer made of a silica/zirconia matrix doped by magnetic nanoparticles is coated on the top face of ion-exchanged glass waveguides. Optical characterizations that have been carried out demonstrated the efficiency of these hybrid structures in terms of lateral confinement. Furthermore, TE to TM mode conversion has been observed when a longitudinal magnetic field is applied to the device. The amount of this conversion is analysed taking into account the magneto-optical confinement and the modal birefringence of the structure.

Characterization of Nanocomposites by Thermal Analysis

PubMed Central

Corcione, Carola Esposito; Frigione, Mariaenrica

2012-01-01

In materials research, the development of polymer nanocomposites (PN) is rapidly emerging as a multidisciplinary research field with results that could broaden the applications of polymers to many different industries. PN are polymer matrices (thermoplastics, thermosets or elastomers) that have been reinforced with small quantities of nano-sized particles, preferably characterized by high aspect ratios, such as layered silicates and carbon nanotubes. Thermal analysis (TA) is a useful tool to investigate a wide variety of properties of polymers and it can be also applied to PN in order to gain further insight into their structure. This review illustrates the versatile applications of TA methods in the emerging field of polymer nanomaterial research, presenting some examples of applications of differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), dynamic mechanical thermal analysis (DMTA) and thermal mechanical analysis (TMA) for the characterization of nanocomposite materials.

Photometric Application of the Gram Stain Method To Characterize Natural Bacterial Populations in Aquatic Environments

PubMed Central

Saida, H.; Ytow, N.; Seki, H.

1998-01-01

The Gram stain method was applied to the photometric characterization of aquatic bacterial populations with a charge-coupled device camera and an image analyzer. Escherichia coli and Bacillus subtilis were used as standards of typical gram-negative and gram-positive bacteria, respectively. A mounting agent to obtain clear images of Gram-stained bacteria on Nuclepore membrane filters was developed. The bacterial stainability by the Gram stain was indicated by the Gram stain index (GSI), which was applicable not only to the dichotomous classification of bacteria but also to the characterization of cell wall structure. The GSI spectra of natural bacterial populations in water with various levels of eutrophication showed a distinct profile, suggesting possible staining specificity that indicates the presence of a particular bacterial population in the aquatic environment. PMID:9464416

Seeking instructional specificity: An example from analogical instruction

NASA Astrophysics Data System (ADS)

Kuo, Eric; Wieman, Carl E.

2015-12-01

Broad instructional methods like "interactive engagement" have been shown to be effective, but such general characterization provides little guidance on the details of how to structure instructional materials. In this study, we seek instructional specificity by comparing two ways of using an analogy to learn a target physical principle: (i) applying the analogy to the target physical domain on a case-by-case basis and (ii) using the analogy to create a general rule in the target physical domain. In the discussion sections of a large, introductory physics course (N =2 3 1 ), students who sought a general rule were better able to discover and apply a correct physics principle than students who analyzed the examples case by case. The difference persisted at a reduced level after subsequent direct instruction. We argue that students who performed case-by-case analyses were more likely to focus on idiosyncratic problem-specific features rather than the deep structural features. This study provides an example of investigations into how the specific structure of instructional materials can be consequential for what is learned.

ComDim for explorative multi-block data analysis of Cantal-type cheeses: Effects of salts, gentle heating and ripening.

PubMed

Loudiyi, M; Rutledge, D N; Aït-Kaddour, A

2018-10-30

Common Dimension (ComDim) chemometrics method for multi-block data analysis was employed to evaluate the impact of different added salts and ripening times on physicochemical, color, dynamic low amplitude oscillatory rheology, texture profile, and molecular structure (fluorescence and MIR spectroscopies) of five Cantal-type cheeses. Firstly, Independent Components Analysis (ICA) was applied separately on fluorescence and MIR spectra in order to extract the relevant signal source and the associated proportions related to molecular structure characteristics. ComDim was then applied on the 31 data tables corresponding to the proportion of ICA signals obtained for spectral methods and the global analysis of cheeses by the other techniques. The ComDim results indicated that generally cheeses made with 50% NaCl or with 75:25% NaCl/KCl exhibit the equivalent characteristics in structural, textural, meltability and color properties. The proposed methodology demonstrates the applicability of ComDim for the characterization of samples when different techniques describe the same samples. Copyright © 2018 Elsevier Ltd. All rights reserved.

Thermographic inspection of marine composite structures

NASA Astrophysics Data System (ADS)

Jones, Thomas S.; Lindgren, Eric A.

1994-03-01

The marine industry is now facing the problems that were faced by the aircraft industry 20 to 25 years ago: glass-fiber-composite structures do not lend themselves to traditional methods of interrogation. Both the material response and the failure modes of composites are different from traditional materials. Infrared thermographic techniques were investigated for application to composite hull structures and found to be very effective in locating and identifying damage to both solid laminate and sandwich panel construction. The thermographic techniques have been applied to cruising as well as racing yachts with good results. Indicated damage has matched well with the damage discovered during repair operations. More recently, the thermographic techniques have been applied to much thicker solid laminate hull construction used in a new U.S. Navy mine hunter, the MHC-51, U.S.S. Osprey. Thermographic investigations were performed on large test panels used to evaluate different material systems for this vessel and on the vessel itself to provide a baseline thermal characterization. Later this year, shock trials will be performed on the U.S.S. Osprey. Additional thermographic studies are planned following the shock trials.

The effect of BaM/PANI composition with epoxy paint matrix on single and double layers coating with spray coating method for radar absorbing materials applications

NASA Astrophysics Data System (ADS)

Widyastuti, Fajarin, Rindang; Pratiwi, Vania Mitha; Kholid, Rifki Rachman; Habib, Abdulloh

2018-04-01

In this study, RAM composite has been succesfully synthesized by mixing BaM as magnetic materials and PANI as conductive materials. BaM and PANI materials were prepared separately by solid state method and polymerization method, respectively. To investigated the presence of BaM phase and magnetic property of the as prepared BaM, XRD pert PAN analytical and VSM 250 Dexing Magnet were employed. Inductance Capacitance Resistance technique was carried out to measure electrical conductivity of the synthesized PANI materials. In order to further characterized the structural features of BaM and PANI, SEM-EDX FEI 850 and FTIR characterizations were conducted. RAM composite was prepared by mixing BaM and PANI powders with ultrasonic cleaner. Afterwards, VNA (Vector Network Analyzer) characterization was carried out to determine reflection loss value of RAM by applying mixed RAM composite and epoxy paint on aluminum plate using spray gun. Microscopic characterization was employed to investigated the distribution of RAM particles on the substrate. It was found that reflection loss value as low as -27.153 dB was achieved when applied 15 wt% BaM/PANi composite at 100.6 µm thickness. In addition, the absorption of electromagnetic waves value increase as the addition of RAM composite composition increases.

The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

PubMed

Del Galdo, Sara; Amadei, Andrea

2016-10-12

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.

Preparation and Characterization of an Amphipathic Magnetic Nanosphere

PubMed Central

Ji, Yongsheng; Lv, Ruihong; Xu, Zhigang; Zhao, Chuande; Zhang, Haixia

2014-01-01

The amphipathic magnetic nanospheres were synthesized using C8 and polyethylene glycol as ligands. Their morphology, structure, and composition were characterized by transmission electron microscope, Fourier transform infrared, and elementary analysis. The prepared materials presented uniform sphere with size distribution about 200 nm. The magnetic characteristics of magnetic nanomaterials were measured by vibrating sample magnetometer. The target products had a saturation magnetization value of 50 emu g−1 and superparamagnetism. The adsorption capability was also studied by static tests, and the material was applied to enrich benzenesulfonamide from calf serum. The results exhibited that the C8-PEG phase owned better adsorption capability, biocompatible property, and dispersivity in aqueous samples. PMID:24729917

Crystallographic Characterization of Extraterrestrial Materials by Energy-Scanning X-ray Diffraction

NASA Technical Reports Server (NTRS)

Hagiya, Kenji; Mikouchi, Takashi; Ohsumi, Kazumasa; Terada, Yasuko; Yagi, Naoto; Komatsu, Mutsumi; Yamaguchi, Shoki; Hirata, Arashi; Kurokawa, Ayaka; Zolensky, Michael E. (Principal Investigator)

2016-01-01

We have continued our long-term project using X-ray diffraction to characterize a wide range of extraterrestrial samples. The stationary sample method with polychromatic X-rays is advantageous because the irradiated area of the sample is always same and fixed, meaning that all diffraction spots occur from the same area of the sample, however, unit cell parameters cannot be directly obtained by this method though they are very important for identification of mineral and for determination of crystal structures. In order to obtain the cell parameters even in the case of the sample stationary method, we apply energy scanning of a micro-beam of monochromatic SR at SPring-8.

Characterization and Discrimination of Gram-Positive Bacteria Using Raman Spectroscopy with the Aid of Principal Component Analysis.

PubMed

Colniță, Alia; Dina, Nicoleta Elena; Leopold, Nicolae; Vodnar, Dan Cristian; Bogdan, Diana; Porav, Sebastian Alin; David, Leontin

2017-09-01

Raman scattering and its particular effect, surface-enhanced Raman scattering (SERS), are whole-organism fingerprinting spectroscopic techniques that gain more and more popularity in bacterial detection. In this work, two relevant Gram-positive bacteria species, Lactobacillus casei ( L. casei ) and Listeria monocytogenes ( L. monocytogenes ) were characterized based on their Raman and SERS spectral fingerprints. The SERS spectra were used to identify the biochemical structures of the bacterial cell wall. Two synthesis methods of the SERS-active nanomaterials were used and the recorded spectra were analyzed. L. casei and L. monocytogenes were successfully discriminated by applying Principal Component Analysis (PCA) to their specific spectral data.

Characterization and Discrimination of Gram-Positive Bacteria Using Raman Spectroscopy with the Aid of Principal Component Analysis

PubMed Central

Leopold, Nicolae; Vodnar, Dan Cristian; Bogdan, Diana; Porav, Sebastian Alin; David, Leontin

2017-01-01

Raman scattering and its particular effect, surface-enhanced Raman scattering (SERS), are whole-organism fingerprinting spectroscopic techniques that gain more and more popularity in bacterial detection. In this work, two relevant Gram-positive bacteria species, Lactobacillus casei (L. casei) and Listeria monocytogenes (L. monocytogenes) were characterized based on their Raman and SERS spectral fingerprints. The SERS spectra were used to identify the biochemical structures of the bacterial cell wall. Two synthesis methods of the SERS-active nanomaterials were used and the recorded spectra were analyzed. L. casei and L. monocytogenes were successfully discriminated by applying Principal Component Analysis (PCA) to their specific spectral data. PMID:28862655

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex*

PubMed Central

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

2014-01-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. PMID:25161197

A planar lens based on the electrowetting of two immiscible liquids

NASA Astrophysics Data System (ADS)

Liu, Chao-Xuan; Park, Jihwan; Choi, Jin-Woo

2008-03-01

This paper reports the development and characterization of a planar liquid lens based on electrowetting. The working concept of electrowetting two immiscible liquids is demonstrated with measurement and characterization of contact angles with regard to externally applied electric voltages. Consequently, a planar liquid lens is designed and implemented based on this competitive electrowetting. A droplet of silicone oil confined in an aqueous solution (1% KCl) works as a liquid lens. Electrowetting then controls the shape of the confined silicone oil and the focal length of the liquid lens varies depending upon an applied dc voltage. A unique feature of this lens design is the double-ring planar electrodes beneath the hydrophobic substrate. While an outer ring electrode provides an initial boundary for the silicone oil droplet, an inner ring works as the actuation electrode for the lens. Further, the planar electrodes, instead of vertical or out-of-plane wall electrodes, facilitate the integration of liquid lenses into microfluidic systems. With the voltage applied in the range of 50-250 V, the confined silicone oil droplet changed its shape and the optical magnification of a 3 mm-diameter liquid lens was clearly demonstrated. Moreover, focal lengths of liquid lenses with diameters of 2 mm, 3 mm and 4 mm were characterized, respectively. The obtained results suggest that a larger lens diameter yields a longer focal length and a wider range of focal length change in response to voltage. The demonstrated liquid lens has a simple structure and is easy to fabricate.

Structural characterization and inhibition on α-d-glucosidase activity of non-starch polysaccharides from Fagopyrum tartaricum.

PubMed

Wang, Xiao-Ting; Zhu, Zhen-Yuan; Zhao, Liang; Sun, Hui-Qing; Meng, Meng; Zhang, Jin-Yu; Zhang, Yong-Min

2016-11-20

In the present study, the crude polysaccharide was extracted from Fagopyrum tartaricum and purified by Sephadex G-25 and G-75 column to produce a polysaccharide fraction termed TBP-II. Its average molecular weight was 26kDa. The structural characterization of TBP-II was investigated by gas chromatography, periodate oxidation-Smith degradation, Methylation and NMR. Congo red was applied to explore its advanced structures. The results revealed that chemical composition and structural characteristic of TBP-II was mainly consisted of galactose, arabinose, xylose and glucose with a molar ratio of 0.7:1:6.3:74.2. The backbone of TBP-II was composed of (1→4)-linked α-d-glucopyranosyl (Glcp), while the branches comprised of (1→3)-linked α-d-glucopyranosyl (Glcp), (1→6)-linked α-d-galactopyranosyl (Galp) and (1→2,4)-linked α-d-rhamnopyranosyl (Rhap). The structure of TBP-II was 1,3 and 1,6-branched-galactorhamnoglucan that had a linear backbone of (1→4)-linked α-d-glucopyranose (Glcp). Using Congo red assay showed that it was absent of triple helix structure. The α-d-glucosidase inhibitory activity of TBP-II was determined using acarbose as positive control. The result showed that the inhibition rate depended on the concentration of polysaccharides. Copyright © 2016 Elsevier Ltd. All rights reserved.

Constellation of phase singularities in a speckle-like pattern for optical vortex metrology applied to biological kinematic analysis.

PubMed

Wang, Wei; Qiao, Yu; Ishijima, Reika; Yokozeki, Tomoaki; Honda, Daigo; Matsuda, Akihiro; Hanson, Steen G; Takeda, Mitsuo

2008-09-01

A novel technique for biological kinematic analysis is proposed that makes use of the pseudophase singularities in a complex signal generated from a speckle-like pattern. In addition to the information about the locations and the anisotropic core structures of the pseudophase singularities, we also detect the spatial structures of a cluster of phase singularities, which serves as a unique constellation characterizing the mutual position relation between the individual pseudophase singularities. Experimental results of in vivo measurements for a swimming fish along with its kinematic analysis are presented, which demonstrate the validity of the proposed technique.

Mirrorless lasing from light emitters in percolating clusters

NASA Astrophysics Data System (ADS)

Burlak, Gennadiy; Rubo, Y. G.

2015-07-01

We describe the lasing effect in the three-dimensional percolation system, where the percolating cluster is filled by active media composed by light emitters excited noncoherently. We show that, due to the presence of a topologically nontrivial photonic structure, the stimulated emission is modified with respect to both conventional and random lasers. The time dynamics and spectra of the lasing output are studied numerically with finite-difference time-domain approach. The Fermat principle and Monte Carlo approach are applied to characterize the optimal optical path and interconnection between the radiating emitters. The spatial structure of the laser mode is found by a long-time FDTD simulation.

Stress corrosion cracking properties of 15-5PH steel

NASA Technical Reports Server (NTRS)

Rosa, Ferdinand

1993-01-01

Unexpected occurrence of failures, due to stress corrosion cracking (SCC) of structural components, indicate a need for improved characterization of materials and more advanced analytical procedures for reliably predicting structures performance. Accordingly, the purpose of this study was to determine the stress corrosion susceptibility of 15-5PH steel over a wide range of applied strain rates in a highly corrosive environment. The selected environment for this investigation was a highly acidified sodium chloride (NaCl) aqueous solution. The selected alloy for the study was a 15-5PH steel in the H900 condition. The slow strain rate technique was selected to test the metals specimens.

Mechanical behavior of precipitation hardenable steels exposed to highly corrosive environment

NASA Technical Reports Server (NTRS)

Rosa, Ferdinand

1994-01-01

Unexpected occurrences of failures, due to stress corrosion cracking (SCC) of structural components, indicate a need for improved characterization of materials and more advanced analytical procedures for reliably predicting structures performance. Accordingly, the purpose of this study was to determine the stress corrosion susceptibility of 15 - 5 PH steel over a wide range of applied strain rates in a highly corrosive environment. The selected environment for this investigation was a 3.5 percent NaCl aqueous solution. The material selected for the study was 15 - 5 PH steel in the H 900 condition. The Slow Strain Rate technique was used to test the metallic specimens.

Process parameter and surface morphology of pineapple leaf electrospun nanofibers (PALF)

NASA Astrophysics Data System (ADS)

Surip, S. N.; Aziz, F. M. A.; Bonnia, N. N.; Sekak, K. A.; Zakaria, M. N.

2017-09-01

In recent times, nanofibers have attracted the attention of researchers due to their pronounced micro and nano structural characteristics that enable the development of advanced materials that have sophisticated applications. The production of nanofibers by the electrospinning process is influenced both by the electrostatic forces and the viscoelastic behavior of the polymer. Process parameters, like solution feed rate, applied voltage, nozzle-collector distance, and spinning environment, and material properties, like solution concentration, viscosity, surface tension, conductivity, and solvent vapor pressure, influence the structure and properties of electrospun nanofibers. Significant work has been done to characterize the properties of PALF nanofibers as a function of process and material parameters.

A comparison of heuristic and model-based clustering methods for dietary pattern analysis.

PubMed

Greve, Benjamin; Pigeot, Iris; Huybrechts, Inge; Pala, Valeria; Börnhorst, Claudia

2016-02-01

Cluster analysis is widely applied to identify dietary patterns. A new method based on Gaussian mixture models (GMM) seems to be more flexible compared with the commonly applied k-means and Ward's method. In the present paper, these clustering approaches are compared to find the most appropriate one for clustering dietary data. The clustering methods were applied to simulated data sets with different cluster structures to compare their performance knowing the true cluster membership of observations. Furthermore, the three methods were applied to FFQ data assessed in 1791 children participating in the IDEFICS (Identification and Prevention of Dietary- and Lifestyle-Induced Health Effects in Children and Infants) Study to explore their performance in practice. The GMM outperformed the other methods in the simulation study in 72 % up to 100 % of cases, depending on the simulated cluster structure. Comparing the computationally less complex k-means and Ward's methods, the performance of k-means was better in 64-100 % of cases. Applied to real data, all methods identified three similar dietary patterns which may be roughly characterized as a 'non-processed' cluster with a high consumption of fruits, vegetables and wholemeal bread, a 'balanced' cluster with only slight preferences of single foods and a 'junk food' cluster. The simulation study suggests that clustering via GMM should be preferred due to its higher flexibility regarding cluster volume, shape and orientation. The k-means seems to be a good alternative, being easier to use while giving similar results when applied to real data.

A first-principles study on second-order ferroelectric phase transition in two-dimensional puckered group V materials

NASA Astrophysics Data System (ADS)

Lee, Sang-Hoon; Jhi, Seung-Hoon

We study two-dimensional group V materials (P, As, Sb, and Bi) in puckered honeycomb structure using first-principles calculations. Two factors, the degree of puckering and buckling characterize not only the atomic structure but also the electronic structure and its topological phase. By analyzing the lone-pair character of constituent elements and the softening of the phonon mode, we clarify the origin of the buckling. We show that the phonon softening leads the second-order type structural phase transition from a flat to a buckled configuration. The inversion symmetry breaking associated with the structural transition induces the spontaneous polarization in these homogenous materials. Our calculations suggest that external strains or n-type doping are effective methods to control the degree of buckling. We find that the ferroelectric and non-trivial topological phase can coexist in puckered Bi when tensile strains are applied.

Free-decay time-domain modal identification for large space structures

NASA Technical Reports Server (NTRS)

Kim, Hyoung M.; Vanhorn, David A.; Doiron, Harold H.

1992-01-01

Concept definition studies for the Modal Identification Experiment (MIE), a proposed space flight experiment for the Space Station Freedom (SSF), have demonstrated advantages and compatibility of free-decay time-domain modal identification techniques with the on-orbit operational constraints of large space structures. Since practical experience with modal identification using actual free-decay responses of large space structures is very limited, several numerical and test data reduction studies were conducted. Major issues and solutions were addressed, including closely-spaced modes, wide frequency range of interest, data acquisition errors, sampling delay, excitation limitations, nonlinearities, and unknown disturbances during free-decay data acquisition. The data processing strategies developed in these studies were applied to numerical simulations of the MIE, test data from a deployable truss, and launch vehicle flight data. Results of these studies indicate free-decay time-domain modal identification methods can provide accurate modal parameters necessary to characterize the structural dynamics of large space structures.

Perspective: Structural fluctuation of protein and Anfinsen's thermodynamic hypothesis

NASA Astrophysics Data System (ADS)

Hirata, Fumio; Sugita, Masatake; Yoshida, Masasuke; Akasaka, Kazuyuki

2018-01-01

The thermodynamics hypothesis, casually referred to as "Anfinsen's dogma," is described theoretically in terms of a concept of the structural fluctuation of protein or the first moment (average structure) and the second moment (variance and covariance) of the structural distribution. The new theoretical concept views the unfolding and refolding processes of protein as a shift of the structural distribution induced by a thermodynamic perturbation, with the variance-covariance matrix varying. Based on the theoretical concept, a method to characterize the mechanism of folding (or unfolding) is proposed. The transition state, if any, between two stable states is interpreted as a gap in the distribution, which is created due to an extensive reorganization of hydrogen bonds among back-bone atoms of protein and with water molecules in the course of conformational change. Further perspective to applying the theory to the computer-aided drug design, and to the material science, is briefly discussed.

Study of nanoscale structural biology using advanced particle beam microscopy

NASA Astrophysics Data System (ADS)

Boseman, Adam J.

This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

The (2 × 2) tunnels structured manganese dioxide nanorods with α phase for lithium air batteries

NASA Astrophysics Data System (ADS)

Ghouri, Zafar Khan; Zahoor, Awan; Barakat, Nasser A. M.; Alsoufi, Mohammad S.; Bawazeer, Tahani M.; Mohamed, Ahmed F.; Kim, Hak Yong

2016-02-01

The (2 × 2) tunnels structured manganese dioxide nanorods with α phase (α-MnO2) are synthesized via simplistic hydrothermal method at low temperature. The obtained tunnels structured α-MnO2 nanorods are characterized by, Transmission electron microscopy, Scanning electron microscopy, and X-ray diffraction techniques. The oxygen reduction reaction (ORR) activity was studied by cyclic voltammetry and rotating ring-disc electrode voltammetry techniques in alkaline media. Moreover; the highly electrocatalytic tunnels structured α-MnO2 nanorods were then also applied as cathode in rechargeable Li-O2 cells. The Li-O2 cells exhibited initial discharge capacity as high as ∼4000 mAh/g with the tunnels structured α-MnO2 nanorods which was double the original capacity of the cells without any catalyst. Also we obtained 100% round trip efficiency upon cycling with limited capacity for more than 50 cycles.

Rapid thermal process by RF heating of nano-graphene layer/silicon substrate structure: Heat explosion theory approach

NASA Astrophysics Data System (ADS)

Sinder, M.; Pelleg, J.; Meerovich, V.; Sokolovsky, V.

2018-03-01

RF heating kinetics of a nano-graphene layer/silicon substrate structure is analyzed theoretically as a function of the thickness and sheet resistance of the graphene layer, the dimensions and thermal parameters of the structure, as well as of cooling conditions and of the amplitude and frequency of the applied RF magnetic field. It is shown that two regimes of the heating can be realized. The first one is characterized by heating of the structure up to a finite temperature determined by equilibrium between the dissipated loss power caused by induced eddy-currents and the heat transfer to environment. The second regime corresponds to a fast unlimited temperature increase (heat explosion). The criterions of realization of these regimes are presented in the analytical form. Using the criterions and literature data, it is shown the possibility of the heat explosion regime for a graphene layer/silicon substrate structure at RF heating.

Molecular-dynamics simulations of self-assembled monolayers (SAM) on parallel computers

NASA Astrophysics Data System (ADS)

Vemparala, Satyavani

The purpose of this dissertation is to investigate the properties of self-assembled monolayers, particularly alkanethiols and Poly (ethylene glycol) terminated alkanethiols. These simulations are based on realistic interatomic potentials and require scalable and portable multiresolution algorithms implemented on parallel computers. Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing and molecular chain-length. Results show that the alkanethiol chains tilt from the surface normal by a collective angle of 25° along next-nearest neighbor direction at 300K. At 350K the system transforms to a disordered phase characterized by small tilt angle, flexible tilt direction, and random distribution of backbone planes. With increasing lattice spacing, a, the tilt angle increases rapidly from a nearly zero value at a = 4.7A to as high as 34° at a = 5.3A at 300K. We also studied the effect of end groups on the tilt structure of SAM films. We characterized the system with respect to temperature, the alkane chain length, lattice spacing, and the length of the end group. We found that the gauche defects were predominant only in the tails, and the gauche defects increased with the temperature and number of EG units. Effect of electric field on the structure of poly (ethylene glycol) (PEG) terminated alkanethiol self assembled monolayer (SAM) on gold has been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied anti-parallel to the surface normal causes a reversible transition to an ordered state in which the oxygen atoms are exposed. On the other hand, an electric field applied in a direction parallel to the surface normal introduces considerable disorder in the system and the oxygen atoms are buried inside.

Topological study of nanomaterials using surface-enhanced ellipsometric contrast microscopy (SEEC)

NASA Astrophysics Data System (ADS)

Muckenhirn, Sylvain

2016-03-01

Innovations in nanotechnology are empowering scientists to deepen their understanding of physical, chemical and biological mechanisms. Powerful and precise characterization systems are essential to meet researchers' requirements. SEEC (Surface Enhanced Ellipsometric Contrast) microscopy is an innovative advanced optical technique based on ellipsometric and interference fringes of Fizeau principles. This technique offers live and label-free topographic imaging of organic, inorganic and biological samples with high Z resolution (down to 0.1nm thickness), and enhanced X-Y detection limit (down to 1.5nm width). This technique has been successfully applied to the study of nanometric films and structures, biological layers, and nano-objects. We applied SEEC technology to different applications explored below.

[Laser Raman Spectroscopy and Its Application in Gas Hydrate Studies].

PubMed

Fu, Juan; Wu, Neng-you; Lu, Hai-long; Wu, Dai-dai; Su, Qiu-cheng

2015-11-01

Gas hydrates are important potential energy resources. Microstructural characterization of gas hydrate can provide information to study the mechanism of gas hydrate formation and to support the exploitation and application of gas hydrate technology. This article systemly introduces the basic principle of laser Raman spectroscopy and summarizes its application in gas hydrate studies. Based on Raman results, not only can the information about gas composition and structural type be deduced, but also the occupancies of large and small cages and even hydration number can be calculated from the relative intensities of Raman peaks. By using the in-situ analytical technology, laser Raman specstropy can be applied to characterize the formation and decomposition processes of gas hydrate at microscale, for example the enclathration and leaving of gas molecules into/from its cages, to monitor the changes in gas concentration and gas solubility during hydrate formation and decomposition, and to identify phase changes in the study system. Laser Raman in-situ analytical technology has also been used in determination of hydrate structure and understanding its changing process under the conditions of ultra high pressure. Deep-sea in-situ Raman spectrometer can be employed for the in-situ analysis of the structures of natural gas hydrate and their formation environment. Raman imaging technology can be applied to specify the characteristics of crystallization and gas distribution over hydrate surface. With the development of laser Raman technology and its combination with other instruments, it will become more powerful and play a more significant role in the microscopic study of gas hydrate.

Analysis of the status of pre-release cracks in prestressed concrete structures using long-gauge sensors

NASA Astrophysics Data System (ADS)

Abdel-Jaber, H.; Glisic, B.

2015-02-01

Prestressed structures experience limited tensile stresses in concrete, which limits or completely eliminates the occurrence of cracks. However, in some cases, large tensile stresses can develop during the early age of the concrete due to thermal gradients and shrinkage effects. Such stresses can cause early-age cracks, termed ‘pre-release cracks’, which occur prior to the transfer of the prestressing force. When the prestressing force is applied to the cross-section, it is assumed that partial or full closure of the cracks occurs by virtue of the force transfer through the cracked cross-section. Verification of the closure of the cracks after the application of the prestressing force is important as it can either confirm continued structural integrity or indicate and approximate reduced structural capacity. Structural health monitoring (SHM) can be used for this purpose. This paper researches an SHM method that can be applied to prestressed beam structures to assess the condition of pre-release cracks. The sensor network used in this method consists of parallel long-gauge fiber optic strain sensors embedded in the concrete cross-sections at various locations. The same network is used for damage detection, i.e. detection and characterization of the pre-release cracks, and for monitoring the prestress force transfer. The method is validated on a real structure, a curved continuous girder. Results from the analysis confirm the safety and integrity of the structure. The method and its application are presented in this paper.

Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure.

PubMed

Arbogast, Luke W; Delaglio, Frank; Schiel, John E; Marino, John P

2017-11-07

Two-dimensional (2D) 1 H- 13 C methyl NMR provides a powerful tool to probe the higher order structure (HOS) of monoclonal antibodies (mAbs), since spectra can readily be acquired on intact mAbs at natural isotopic abundance, and small changes in chemical environment and structure give rise to observable changes in corresponding spectra, which can be interpreted at atomic resolution. This makes it possible to apply 2D NMR spectral fingerprinting approaches directly to drug products in order to systematically characterize structure and excipient effects. Systematic collections of NMR spectra are often analyzed in terms of the changes in specifically identified peak positions, as well as changes in peak height and line widths. A complementary approach is to apply principal component analysis (PCA) directly to the matrix of spectral data, correlating spectra according to similarities and differences in their overall shapes, rather than according to parameters of individually identified peaks. This is particularly well-suited for spectra of mAbs, where some of the individual peaks might not be well resolved. Here we demonstrate the performance of the PCA method for discriminating structural variation among systematic sets of 2D NMR fingerprint spectra using the NISTmAb and illustrate how spectral variability identified by PCA may be correlated to structure.

Mechanisms of action of particles used for fouling mitigation in membrane bioreactors.

PubMed

Loulergue, P; Weckert, M; Reboul, B; Cabassud, C; Uhl, W; Guigui, C

2014-12-01

Adding chemicals to the biofluid is an option to mitigate membrane fouling in membrane bioreactors. In particular, previous studies have shown that the addition of particles could enhance activated sludge filterability. Nevertheless, the mechanisms responsible for the improved filtration performance when particles are added are still unclear. Two main mechanisms might occur: soluble organic matter adsorption onto the particles and/or cake structure modification. To date, no studies have clearly dissociated the impact of these two phenomena as a method was needed for the in-line characterization of the cake structure during filtration. The objective of this study was thus to apply, for the first time, an optical method for in-situ, non-invasive, characterization of cake structure during filtration of a real biofluid in presence of particles. This method was firstly used to study local cake compressibility during the biofluid filtration. It was found that the first layers of the cake were incompressible whereas the cake appeared to be compressible at global scale. This questions the global scale analysis generally used to study cake compressibility and highlights the interest of coupling local characterization with overall process performance analysis. Secondly, the impact of adding submicronic melamine particles into the biofluid was studied. It appears that particles added into the biofluid strongly influence the cake properties, making it thicker and more permeable. Furthermore, by using liquid chromatography with an organic carbon detector to determine the detailed characteristics of the feed and permeate, it was shown that the modification of cake structure also affected the retention of soluble organic compounds by the membrane and thus the cake composition. Simultaneous use of a method for in-situ characterization of the cake structure with a detailed analysis of the fluid composition and monitoring of the global performance is thus a powerful method for evaluating cake structure and composition and their impact on global process performance. The use of this methodology should allow "cake engineering" to be developed so that cake properties (structure, composition) can be controlled and process performance optimized. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ligand-Assisted Protein Structure (LAPS): An Experimental Paradigm for Characterizing Cannabinoid-Receptor Ligand-Binding Domains.

PubMed

Janero, David R; Korde, Anisha; Makriyannis, Alexandros

2017-01-01

Detailed characterization of the ligand-binding motifs and structure-function correlates of the principal GPCRs of the endocannabinoid-signaling system, the cannabinoid 1 (CB1R) and cannabinoid 2 (CB2R) receptors, is essential to inform the rational design of drugs that modulate CB1R- and CB2R-dependent biosignaling for therapeutic gain. We discuss herein an experimental paradigm termed "ligand-assisted protein structure" (LAPS) that affords a means of characterizing, at the amino acid level, CB1R and CB2R structural features key to ligand engagement and receptor-dependent information transmission. For this purpose, LAPS integrates three key disciplines and methodologies: (a) medicinal chemistry: design and synthesis of high-affinity, pharmacologically active probes as reporters capable of reacting irreversibly with particular amino acids at (or in the immediate vicinity of) the ligand-binding domain of the functionally active receptor; (b) molecular and cellular biology: introduction of discrete, conservative point mutations into the target GPCR and determination of their effect on probe binding and pharmacological activity; (c) analytical chemistry: identification of the site(s) of probe-GPCR interaction through focused, bottom-up, amino acid-level proteomic identification of the probe-receptor complex using liquid chromatography tandem mass spectrometry. Subsequent in silico methods including ligand docking and computational modeling provide supplementary data on the probe-receptor interaction as defined by LAPS. Examples of LAPS as applied to human CB2R orthosteric binding site characterization for a biarylpyrazole antagonist/inverse agonist and a classical cannabinoid agonist belonging to distinct chemical classes of cannabinergic compounds are given as paradigms for further application of this methodology to other therapeutic protein targets. LAPS is well positioned to complement other experimental and in silico methods in contemporary structural biology such as X-ray crystallography. © 2017 Elsevier Inc. All rights reserved.

Old document image segmentation using the autocorrelation function and multiresolution analysis

NASA Astrophysics Data System (ADS)

Mehri, Maroua; Gomez-Krämer, Petra; Héroux, Pierre; Mullot, Rémy

2013-01-01

Recent progress in the digitization of heterogeneous collections of ancient documents has rekindled new challenges in information retrieval in digital libraries and document layout analysis. Therefore, in order to control the quality of historical document image digitization and to meet the need of a characterization of their content using intermediate level metadata (between image and document structure), we propose a fast automatic layout segmentation of old document images based on five descriptors. Those descriptors, based on the autocorrelation function, are obtained by multiresolution analysis and used afterwards in a specific clustering method. The method proposed in this article has the advantage that it is performed without any hypothesis on the document structure, either about the document model (physical structure), or the typographical parameters (logical structure). It is also parameter-free since it automatically adapts to the image content. In this paper, firstly, we detail our proposal to characterize the content of old documents by extracting the autocorrelation features in the different areas of a page and at several resolutions. Then, we show that is possible to automatically find the homogeneous regions defined by similar indices of autocorrelation without knowledge about the number of clusters using adapted hierarchical ascendant classification and consensus clustering approaches. To assess our method, we apply our algorithm on 316 old document images, which encompass six centuries (1200-1900) of French history, in order to demonstrate the performance of our proposal in terms of segmentation and characterization of heterogeneous corpus content. Moreover, we define a new evaluation metric, the homogeneity measure, which aims at evaluating the segmentation and characterization accuracy of our methodology. We find a 85% of mean homogeneity accuracy. Those results help to represent a document by a hierarchy of layout structure and content, and to define one or more signatures for each page, on the basis of a hierarchical representation of homogeneous blocks and their topology.

Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae

PubMed Central

Udatha, D. B. R. K. Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth

2012-01-01

Background Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. Methodology/Principal Findings The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Conclusions/Significance Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods. PMID:22745763

Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae.

PubMed

Udatha, D B R K Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth

2012-01-01

Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods.

Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

PubMed Central

Warfield, Becka M.

2017-01-01

RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are present the population of binding-competent aptamer states increases more than twofold. This population change, rather than direct interactions between Mg2+ and theophylline, accounts for altered theophylline binding kinetics. PMID:28437473

Novel Integral Equation Methods Applied to the Analysis of New Guiding and Radiating Structures and Optically-Inspired Phenomena at Microwaves

NASA Astrophysics Data System (ADS)

Gomez-Diaz, Juan Sebastian

This PhD. dissertation presents a multidisciplinary work, which involves the development of different novel formulations applied to the accurate and efficient analysis of a wide variety of new structures, devices, and phenomena at themicrowave frequency region. The objectives of the present work can be divided into three main research lines: (1) The first research line is devoted to the Green's function analysis of multilayered enclosures with convex arbitrarily-shaped cross section. For this purpose, three accurate spatial-domain formulations are developed at the Green's functions level. These techniques are then efficiently incorporated into a mixed-potential integral equation framework, which allows the fast and accurate analysis of multilayered printed circuits in shielded enclosures. The study of multilayered shielded circuits has lead to the development of the novel hybridwaveguide-microstrip filter technology, which is light, compact, low-loss and presents important advantages for the space industry. (2) The second research line is related to the impulse-regime study ofmetamaterial-based composite right/left-handed (CRLH) structures and the subsequent theoretical and practical demonstration of several novel optically-inspired phenomena and applications at microwaves, in both, the guided and the radiative region. This study allows the development of new devices for ultra wide band and high data-rate communications systems. Besides, this research line also deals with the simple and accurate characterization of CRLH leaky-wave antennas using transmission line theory. (3) The third and last research line presents a novel CRLH parallel-plate waveguide leaky-wave antenna structure, and a rigorous iterative modal-based technique for its fast and complete characterization, including a systematic calculation of the antenna physical dimensions. It is important to point out that all the theoretical developments and novel structures presented in thiswork have been numerically confirmed, by the use of both, home-made software and commercial full-wave simulations, and experimentally verified, by the use of measurements from fabricated prototypes.

In Situ Mechanical Testing of Nanostructured Bijel Fibers.

PubMed

Haase, Martin F; Sharifi-Mood, Nima; Lee, Daeyeon; Stebe, Kathleen J

2016-06-28

Bijels are a class of soft materials with potential for application in diverse areas including healthcare, food, energy, and reaction engineering due to their unique structural, mechanical, and transport properties. To realize their potential, means to fabricate, characterize, and manipulate bijel mechanics are needed. We recently developed a method based on solvent transfer-induced phase separation (STRIPS) that enables continuous fabrication of hierarchically structured bijel fibers from a broad array of constituent fluids and nanoparticles using a microfluidic platform. Here, we introduce an in situ technique to characterize bijel fiber mechanics at initial and final stages of the formation process within a microfluidics device. By manipulation of the hydrodynamic stresses applied to the fiber, the fiber is placed under tension until it breaks into segments. Analysis of the stress field allows fracture strength to be inferred; fracture strengths can be as high as several thousand Pa, depending on nanoparticle content. These findings broaden the potential for the use of STRIPS bijels in applications with different mechanical demands. Moreover, our in situ mechanical characterization method could potentially enable determination of properties of other soft fibrous materials made of hydrogels, capillary suspensions, colloidal gels, or high internal phase emulsions.

Statistical and sampling issues when using multiple particle tracking

NASA Astrophysics Data System (ADS)

Savin, Thierry; Doyle, Patrick S.

2007-08-01

Video microscopy can be used to simultaneously track several microparticles embedded in a complex material. The trajectories are used to extract a sample of displacements at random locations in the material. From this sample, averaged quantities characterizing the dynamics of the probes are calculated to evaluate structural and/or mechanical properties of the assessed material. However, the sampling of measured displacements in heterogeneous systems is singular because the volume of observation with video microscopy is finite. By carefully characterizing the sampling design in the experimental output of the multiple particle tracking technique, we derive estimators for the mean and variance of the probes’ dynamics that are independent of the peculiar statistical characteristics. We expose stringent tests of these estimators using simulated and experimental complex systems with a known heterogeneous structure. Up to a certain fundamental limitation, which we characterize through a material degree of sampling by the embedded probe tracking, these estimators can be applied to quantify the heterogeneity of a material, providing an original and intelligible kind of information on complex fluid properties. More generally, we show that the precise assessment of the statistics in the multiple particle tracking output sample of observations is essential in order to provide accurate unbiased measurements.

Computational methods for 2D materials: discovery, property characterization, and application design.

PubMed

Paul, J T; Singh, A K; Dong, Z; Zhuang, H; Revard, B C; Rijal, B; Ashton, M; Linscheid, A; Blonsky, M; Gluhovic, D; Guo, J; Hennig, R G

2017-11-29

The discovery of two-dimensional (2D) materials comes at a time when computational methods are mature and can predict novel 2D materials, characterize their properties, and guide the design of 2D materials for applications. This article reviews the recent progress in computational approaches for 2D materials research. We discuss the computational techniques and provide an overview of the ongoing research in the field. We begin with an overview of known 2D materials, common computational methods, and available cyber infrastructures. We then move onto the discovery of novel 2D materials, discussing the stability criteria for 2D materials, computational methods for structure prediction, and interactions of monolayers with electrochemical and gaseous environments. Next, we describe the computational characterization of the 2D materials' electronic, optical, magnetic, and superconducting properties and the response of the properties under applied mechanical strain and electrical fields. From there, we move on to discuss the structure and properties of defects in 2D materials, and describe methods for 2D materials device simulations. We conclude by providing an outlook on the needs and challenges for future developments in the field of computational research for 2D materials.

Computational methods for 2D materials: discovery, property characterization, and application design

NASA Astrophysics Data System (ADS)

Paul, J. T.; Singh, A. K.; Dong, Z.; Zhuang, H.; Revard, B. C.; Rijal, B.; Ashton, M.; Linscheid, A.; Blonsky, M.; Gluhovic, D.; Guo, J.; Hennig, R. G.

2017-11-01

The discovery of two-dimensional (2D) materials comes at a time when computational methods are mature and can predict novel 2D materials, characterize their properties, and guide the design of 2D materials for applications. This article reviews the recent progress in computational approaches for 2D materials research. We discuss the computational techniques and provide an overview of the ongoing research in the field. We begin with an overview of known 2D materials, common computational methods, and available cyber infrastructures. We then move onto the discovery of novel 2D materials, discussing the stability criteria for 2D materials, computational methods for structure prediction, and interactions of monolayers with electrochemical and gaseous environments. Next, we describe the computational characterization of the 2D materials’ electronic, optical, magnetic, and superconducting properties and the response of the properties under applied mechanical strain and electrical fields. From there, we move on to discuss the structure and properties of defects in 2D materials, and describe methods for 2D materials device simulations. We conclude by providing an outlook on the needs and challenges for future developments in the field of computational research for 2D materials.

Quantitative image analysis for evaluating the coating thickness and pore distribution in coated small particles.

PubMed

Laksmana, F L; Van Vliet, L J; Hartman Kok, P J A; Vromans, H; Frijlink, H W; Van der Voort Maarschalk, K

2009-04-01

This study aims to develop a characterization method for coating structure based on image analysis, which is particularly promising for the rational design of coated particles in the pharmaceutical industry. The method applies the MATLAB image processing toolbox to images of coated particles taken with Confocal Laser Scanning Microscopy (CSLM). The coating thicknesses have been determined along the particle perimeter, from which a statistical analysis could be performed to obtain relevant thickness properties, e.g. the minimum coating thickness and the span of the thickness distribution. The characterization of the pore structure involved a proper segmentation of pores from the coating and a granulometry operation. The presented method facilitates the quantification of porosity, thickness and pore size distribution of a coating. These parameters are considered the important coating properties, which are critical to coating functionality. Additionally, the effect of the coating process variations on coating quality can straight-forwardly be assessed. Enabling a good characterization of the coating qualities, the presented method can be used as a fast and effective tool to predict coating functionality. This approach also enables the influence of different process conditions on coating properties to be effectively monitored, which latterly leads to process tailoring.

Electrical characterization of anodic alumina substrate with via-in-pad structure

NASA Astrophysics Data System (ADS)

Kim, Moonjung

2013-10-01

An anodic alumina substrate has been developed as a package substrate for dynamic random access memory devices. Unlike the conventional package substrates commonly made by laminating an epoxy-based core and cladding with copper, this substrate is fabricated using aluminum anodization technology. The anodization process produces a thick aluminum oxide layer on the aluminum substrate to be used as a dielectric layer. Placing copper patterns on the anodic aluminum oxide layer forms a new substrate structure that consists of a layered structure of aluminum, anodic aluminum oxide, and copper. Using selective anodization in the fabrication process, a via structure connecting the top copper layer and bottom aluminum layer is demonstrated. Additionally, by putting vias directly in the bond and ball pads in the substrate design, the via-in-pad structure is applied in this work. These two-layer metal structures and via-in-pad arrangements make routing easier and thus provide more design flexibility. Additionally, this new package substrate has improved the power distribution network impedance given the characteristics of these structures.

Electric Potential and Electric Field Imaging with Dynamic Applications: 2017 Research Award Innovation

NASA Technical Reports Server (NTRS)

Generazio, Ed

2017-01-01

The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field may be used for illuminating volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e- Sensor enhancements (ephemeral e-Sensor) are discussed. Critical design elements of current linear and real-time two-dimensional (2D) measurement systems are highlighted, and the development of a three dimensional (3D) EFI system is presented. Demonstrations for structural, electronic, human, and memory applications are shown. Recent work demonstrates that phonons may be used to create and annihilate electric dipoles within structures. Phonon induced dipoles are ephemeral and their polarization, strength, and location may be quantitatively characterized by EFI providing a new subsurface Phonon-EFI imaging technology. Initial results from real-time imaging of combustion and ion flow, and their measurement complications, will be discussed. These new EFI capabilities are demonstrated to characterize electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, crime scene forensics, design and materials selection for advanced sensors, combustion science, on-orbit space potential, container inspection, remote characterization of electronic circuits and level of activation, dielectric morphology of structures, tether integrity, organic molecular memory, atmospheric science, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

Characterization and Application of Four-Layer Semiconductor Structures in Pulse Mode Operation

DTIC Science & Technology

2006-09-01

the cutting edge adaptive AI of the Marathon videogame [14] and can be directly applied to Information Operations in Military Operations Other Than...walk behavior is lost because the DC motor does not develop sufficient power to turn the wheels. This was overcome by converting the spikes into...motivation for creating a micro-robotic swarm is to demonstrate the capability of a simple logic circuit in developing a distributed processing system. The

Factors influencing preparation of polyaniline doped with hydrochloric acid

NASA Astrophysics Data System (ADS)

Chuanyu, Sun; Yu, Wang

2014-12-01

Factors influencing the reaction of chemical polymerization during aniline doping with hydrochloric acid (HCl) have been studied in this work. The optimal parameters for the preparation of polyaniline were determined as follows: aniline concentration - 4 mass %, molar ratios of oxidant (NH4)2S2O8:aniline - 1.2:1 and 1.3:1, the concentration of dopant - 1 mol/L. Fourier transform infrared spectroscopy (FT-IR) was applied to characterize the structure of polyaniline.

Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model

PubMed Central

Voss-Böhme, Anja

2012-01-01

Cellular Potts models (CPMs) are used as a modeling framework to elucidate mechanisms of biological development. They allow a spatial resolution below the cellular scale and are applied particularly when problems are studied where multiple spatial and temporal scales are involved. Despite the increasing usage of CPMs in theoretical biology, this model class has received little attention from mathematical theory. To narrow this gap, the CPMs are subjected to a theoretical study here. It is asked to which extent the updating rules establish an appropriate dynamical model of intercellular interactions and what the principal behavior at different time scales characterizes. It is shown that the longtime behavior of a CPM is degenerate in the sense that the cells consecutively die out, independent of the specific interdependence structure that characterizes the model. While CPMs are naturally defined on finite, spatially bounded lattices, possible extensions to spatially unbounded systems are explored to assess to which extent spatio-temporal limit procedures can be applied to describe the emergent behavior at the tissue scale. To elucidate the mechanistic structure of CPMs, the model class is integrated into a general multiscale framework. It is shown that the central role of the surface fluctuations, which subsume several cellular and intercellular factors, entails substantial limitations for a CPM's exploitation both as a mechanistic and as a phenomenological model. PMID:22984409

Multi-Scale and Object-Oriented Analysis for Mountain Terrain Segmentation and Geomorphological Assessment

NASA Astrophysics Data System (ADS)

Marston, B. K.; Bishop, M. P.; Shroder, J. F.

2009-12-01

Digital terrain analysis of mountain topography is widely utilized for mapping landforms, assessing the role of surface processes in landscape evolution, and estimating the spatial variation of erosion. Numerous geomorphometry techniques exist to characterize terrain surface parameters, although their utility to characterize the spatial hierarchical structure of the topography and permit an assessment of the erosion/tectonic impact on the landscape is very limited due to scale and data integration issues. To address this problem, we apply scale-dependent geomorphometric and object-oriented analyses to characterize the hierarchical spatial structure of mountain topography. Specifically, we utilized a high resolution digital elevation model to characterize complex topography in the Shimshal Valley in the Western Himalaya of Pakistan. To accomplish this, we generate terrain objects (geomorphological features and landform) including valley floors and walls, drainage basins, drainage network, ridge network, slope facets, and elemental forms based upon curvature. Object-oriented analysis was used to characterize object properties accounting for object size, shape, and morphometry. The spatial overlay and integration of terrain objects at various scales defines the nature of the hierarchical organization. Our results indicate that variations in the spatial complexity of the terrain hierarchical organization is related to the spatio-temporal influence of surface processes and landscape evolution dynamics. Terrain segmentation and the integration of multi-scale terrain information permits further assessment of process domains and erosion, tectonic impact potential, and natural hazard potential. We demonstrate this with landform mapping and geomorphological assessment examples.

Electric Potential and Electric Field Imaging with Applications

NASA Technical Reports Server (NTRS)

Generazio, Ed

2016-01-01

The technology and techniques for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field may be used for (illuminating) volumes to be inspected with EFI. The baseline sensor technology, electric field sensor (e-sensor), and its construction, optional electric field generation (quasistatic generator), and current e-sensor enhancements (ephemeral e-sensor) are discussed. Demonstrations for structural, electronic, human, and memory applications are shown. This new EFI capability is demonstrated to reveal characterization of electric charge distribution, creating a new field of study that embraces areas of interest including electrostatic discharge mitigation, crime scene forensics, design and materials selection for advanced sensors, dielectric morphology of structures, inspection of containers, inspection for hidden objects, tether integrity, organic molecular memory, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

Effective Perron-Frobenius eigenvalue for a correlated random map

NASA Astrophysics Data System (ADS)

Pool, Roman R.; Cáceres, Manuel O.

2010-09-01

We investigate the evolution of random positive linear maps with various type of disorder by analytic perturbation and direct simulation. Our theoretical result indicates that the statistics of a random linear map can be successfully described for long time by the mean-value vector state. The growth rate can be characterized by an effective Perron-Frobenius eigenvalue that strongly depends on the type of correlation between the elements of the projection matrix. We apply this approach to an age-structured population dynamics model. We show that the asymptotic mean-value vector state characterizes the population growth rate when the age-structured model has random vital parameters. In this case our approach reveals the nontrivial dependence of the effective growth rate with cross correlations. The problem was reduced to the calculation of the smallest positive root of a secular polynomial, which can be obtained by perturbations in terms of Green’s function diagrammatic technique built with noncommutative cumulants for arbitrary n -point correlations.

Impurity profiling of liothyronine sodium by means of reversed phase HPLC, high resolution mass spectrometry, on-line H/D exchange and UV/Vis absorption.

PubMed

Ruggenthaler, M; Grass, J; Schuh, W; Huber, C G; Reischl, R J

2017-09-05

For the first time, a comprehensive investigation of the impurity profile of the synthetic thyroid API (active pharmaceutical ingredient) liothyronine sodium (LT 3 Na) was performed by using reversed phase HPLC and advanced structural elucidation techniques including high resolution tandem mass spectrometry (HRMS/MS) and on-line hydrogen-deuterium (H/D) exchange. Overall, 39 compounds were characterized and 25 of these related substances were previously unknown to literature. The impurity classification system recently developed for the closely related API levothyroxine sodium (LT 4 Na) could be applied to the newly characterized liothyronine sodium impurities resulting in a wholistic thyroid API impurity classification system. Furthermore, the mass-spectrometric CID-fragmentation of specific related substances was discussed and rationalized by detailed fragmentation pathways. Moreover, the UV/Vis absorption characteristics of the API and selected impurities were investigated to corroborate chemical structure assignments derived from MS data. Copyright © 2017 Elsevier B.V. All rights reserved.

Automated selection of stabilizing mutations in designed and natural proteins.

PubMed

Borgo, Benjamin; Havranek, James J

2012-01-31

The ability to engineer novel protein folds, conformations, and enzymatic activities offers enormous potential for the development of new protein therapeutics and biocatalysts. However, many de novo and redesigned proteins exhibit poor hydrophobic packing in their predicted structures, leading to instability or insolubility. The general utility of rational, structure-based design would greatly benefit from an improved ability to generate well-packed conformations. Here we present an automated protocol within the RosettaDesign framework that can identify and improve poorly packed protein cores by selecting a series of stabilizing point mutations. We apply our method to previously characterized designed proteins that exhibited a decrease in stability after a full computational redesign. We further demonstrate the ability of our method to improve the thermostability of a well-behaved native protein. In each instance, biophysical characterization reveals that we were able to stabilize the original proteins against chemical and thermal denaturation. We believe our method will be a valuable tool for both improving upon designed proteins and conferring increased stability upon native proteins.

Automated selection of stabilizing mutations in designed and natural proteins

PubMed Central

Borgo, Benjamin; Havranek, James J.

2012-01-01

The ability to engineer novel protein folds, conformations, and enzymatic activities offers enormous potential for the development of new protein therapeutics and biocatalysts. However, many de novo and redesigned proteins exhibit poor hydrophobic packing in their predicted structures, leading to instability or insolubility. The general utility of rational, structure-based design would greatly benefit from an improved ability to generate well-packed conformations. Here we present an automated protocol within the RosettaDesign framework that can identify and improve poorly packed protein cores by selecting a series of stabilizing point mutations. We apply our method to previously characterized designed proteins that exhibited a decrease in stability after a full computational redesign. We further demonstrate the ability of our method to improve the thermostability of a well-behaved native protein. In each instance, biophysical characterization reveals that we were able to stabilize the original proteins against chemical and thermal denaturation. We believe our method will be a valuable tool for both improving upon designed proteins and conferring increased stability upon native proteins. PMID:22307603

A mathematical characterization of vegetation effect on microwave remote sensing from the Earth

NASA Technical Reports Server (NTRS)

Choe, Y.; Tsang, L.

1983-01-01

In passive microwave remote sensing of the earth, a theoretical model that utilizes the radiative transfer equations was developed to account for the volume scattering effects of the vegetation canopy. Vegetation canopies such as alfalfa, sorghum, and corn are simulated by a layer of ellipsoidal scatterers and cylindrical structures. The ellipsoidal scatterers represent the leaves of vegetation and are randomly positioned and oriented. The orientation of ellipsoids is characterized by a probability density function of Eulerian angles of rotation. The cylindrical structures represent the stalks of vegetation and their radii are assumed to be much smaller than their lengths. The underlying soil is represented by a half-space medium with a homogeneous permittivity and uniform temperature profile. The radiative transfer quations are solved by a numerical method using a Gaussian quadrature formula to compute both the vertical and horizontal polarized brightness temperature as a function of observation angle. The theory was applied to the interpretation of experimental data obtained from sorghum covered fields near College Station, Texas.

Mining of the Pyrrolamide Antibiotics Analogs in Streptomyces netropsis Reveals the Amidohydrolase-Dependent “Iterative Strategy” Underlying the Pyrrole Polymerization

PubMed Central

Deng, Zixin; Zhao, Changming; Yu, Yi

2014-01-01

In biosynthesis of natural products, potential intermediates or analogs of a particular compound in the crude extracts are commonly overlooked in routine assays due to their low concentration, limited structural information, or because of their insignificant bio-activities. This may lead into an incomplete and even an incorrect biosynthetic pathway for the target molecule. Here we applied multiple compound mining approaches, including genome scanning and precursor ion scan-directed mass spectrometry, to identify potential pyrrolamide compounds in the fermentation culture of Streptomyces netropsis. Several novel congocidine and distamycin analogs were thus detected and characterized. A more reasonable route for the biosynthesis of pyrrolamides was proposed based on the structures of these newly discovered compounds, as well as the functional characterization of several key biosynthetic genes of pyrrolamides. Collectively, our results implied an unusual “iterative strategy” underlying the pyrrole polymerization in the biosynthesis of pyrrolamide antibiotics. PMID:24901640

Elastic plastic fracture mechanics methodology for surface cracks

NASA Astrophysics Data System (ADS)

Ernst, Hugo A.; Boatwright, D. W.; Curtin, W. J.; Lambert, D. M.

1993-08-01

The Elastic Plastic Fracture Mechanics (EPFM) Methodology has evolved significantly in the last several years. Nevertheless, some of these concepts need to be extended further before the whole methodology can be safely applied to structural parts. Specifically, there is a need to include the effect of constraint in the characterization of material resistance to crack growth and also to extend these methods to the case of 3D defects. As a consequence, this project was started as a 36 month research program with the general objective of developing an EPFM methodology to assess the structural reliability of pressure vessels and other parts of interest to NASA containing defects. This report covers a computer modelling algorithm used to simulate the growth of a semi-elliptical surface crack; the presentation of a finite element investigation that compared the theoretical (HRR) stress field to that produced by elastic and elastic-plastic models; and experimental efforts to characterize three dimensional aspects of fracture present in 'two dimensional', or planar configuration specimens.

Fast contactless vibrating structure characterization using real time field programmable gate array-based digital signal processing: demonstrations with a passive wireless acoustic delay line probe and vision.

PubMed

Goavec-Mérou, G; Chrétien, N; Friedt, J-M; Sandoz, P; Martin, G; Lenczner, M; Ballandras, S

2014-01-01

Vibrating mechanical structure characterization is demonstrated using contactless techniques best suited for mobile and rotating equipments. Fast measurement rates are achieved using Field Programmable Gate Array (FPGA) devices as real-time digital signal processors. Two kinds of algorithms are implemented on FPGA and experimentally validated in the case of the vibrating tuning fork. A first application concerns in-plane displacement detection by vision with sampling rates above 10 kHz, thus reaching frequency ranges above the audio range. A second demonstration concerns pulsed-RADAR cooperative target phase detection and is applied to radiofrequency acoustic transducers used as passive wireless strain gauges. In this case, the 250 ksamples/s refresh rate achieved is only limited by the acoustic sensor design but not by the detection bandwidth. These realizations illustrate the efficiency, interest, and potentialities of FPGA-based real-time digital signal processing for the contactless interrogation of passive embedded probes with high refresh rates.

Characterization and calibration of a viscoelastic simplified potential energy clock model for inorganic glasses

DOE PAGES

Chambers, Robert S.; Tandon, Rajan; Stavig, Mark E.

2015-07-07

In this study, to analyze the stresses and strains generated during the solidification of glass-forming materials, stress and volume relaxation must be predicted accurately. Although the modeling attributes required to depict physical aging in organic glassy thermosets strongly resemble the structural relaxation in inorganic glasses, the historical modeling approaches have been distinctly different. To determine whether a common constitutive framework can be applied to both classes of materials, the nonlinear viscoelastic simplified potential energy clock (SPEC) model, developed originally for glassy thermosets, was calibrated for the Schott 8061 inorganic glass and used to analyze a number of tests. A practicalmore » methodology for material characterization and model calibration is discussed, and the structural relaxation mechanism is interpreted in the context of SPEC model constitutive equations. SPEC predictions compared to inorganic glass data collected from thermal strain measurements and creep tests demonstrate the ability to achieve engineering accuracy and make the SPEC model feasible for engineering applications involving a much broader class of glassy materials.« less

Elastic plastic fracture mechanics methodology for surface cracks

NASA Technical Reports Server (NTRS)

Ernst, Hugo A.; Boatwright, D. W.; Curtin, W. J.; Lambert, D. M.

1993-01-01

The Elastic Plastic Fracture Mechanics (EPFM) Methodology has evolved significantly in the last several years. Nevertheless, some of these concepts need to be extended further before the whole methodology can be safely applied to structural parts. Specifically, there is a need to include the effect of constraint in the characterization of material resistance to crack growth and also to extend these methods to the case of 3D defects. As a consequence, this project was started as a 36 month research program with the general objective of developing an EPFM methodology to assess the structural reliability of pressure vessels and other parts of interest to NASA containing defects. This report covers a computer modelling algorithm used to simulate the growth of a semi-elliptical surface crack; the presentation of a finite element investigation that compared the theoretical (HRR) stress field to that produced by elastic and elastic-plastic models; and experimental efforts to characterize three dimensional aspects of fracture present in 'two dimensional', or planar configuration specimens.

Application-Oriented Chemical Optimization of a Metakaolin Based Geopolymer.

PubMed

Ferone, Claudio; Colangelo, Francesco; Roviello, Giuseppina; Asprone, Domenico; Menna, Costantino; Balsamo, Alberto; Prota, Andrea; Cioffi, Raffaele; Manfredi, Gaetano

2013-05-10

In this study the development of a metakaolin based geopolymeric mortar to be used as bonding matrix for external strengthening of reinforced concrete beams is reported. Four geopolymer formulations have been obtained by varying the composition of the activating solution in terms of SiO₂/Na₂O ratio. The obtained samples have been characterized from a structural, microstructural and mechanical point of view. The differences in structure and microstructure have been correlated to the mechanical properties. A major issue of drying shrinkage has been encountered in the high Si/Al ratio samples. In the light of the characterization results, the optimal geopolymer composition was then applied to fasten steel fibers to reinforced concrete beams. The mechanical behavior of the strengthened reinforced beams was evaluated by four-points bending tests, which were performed also on reinforced concrete beams as they are for comparison. The preliminary results of the bending tests point out an excellent behavior of the geopolymeric mixture tested, with the failure load of the reinforced beams roughly twice that of the control beam.

Integrated Surface and Mechanical Characterization of Freestanding Biological and Other Nano-Structures Using Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Wang, Xin

This dissertation is focused on surface and mechanical characterization of freestanding biological and other nano-structures using atomic force microscopy including two parts: cell mechanics and nano-structure mechanics. The main purpose of this work is to investigate how the nano- / micro-scale mechanical properties affect macro-scale function. In cancer cells, efficacy of drug delivery is oftentimes declined due to the thick dendritic network of oligosaccharide mucin chains on the cell surface. AFM is used to measure the force needed to pierce the mucin layer to reach the cell surface. A pool of ovarian, pancreatic, lung, colorectal and breast cancer cells are characterized. The studies offer additional support for the development of clinical and pharmaceutical approaches to combat mucin over-expression in tumors during cancer chemotherapy. Macroscopic adhesion-aggregation and subsequent transportation of microorganisms in porous medium are closely related to the microscopic deformation and adhesion mechanical properties. The classical Tabor's parameter is modified. Multiple bacterial strains are characterized in terms of aggregates size, aggregation index and transportation kinetics. AFM is employed to obtain the microscopic coupled adhesion-deformation properties. The strong correlation between Tabor's parameter and aggregation-deposition-transportation suggests the AFM characterization is capable of making reliable predication of macroscopic behavior. A novel "nano-cheese-cutter" is fabricated on tipless AFM cantilever to measure elastic modulus and interfacial adhesion of a 1-D freestanding nano-structure. A single electrospun fiber is attached to the free end of AFM cantilever, while another fiber is similarly prepared on a mica substrate in an orthogonal direction. An external load is applied to deform the two fibers into complementary V-shapes. This work is extended to investigate the interfacial adhesion energy between dissimilar materials. SWCNT thin film promises a broad range of potential applications in electronic devices due to unique electrical and mechanical properties. SWCNT thin film is transferred onto micro-patterned SU-8 strips using wet contact print method, forming a freestanding nano-structure. AFM with tipless cantilever is used to deform the suspended thin film under mixed bending and stretching for mechanical and electromechanical characterization. The experiment helps to construct the base for next generation flexible electronic devices with fundamental understanding in morphology-property relation.

Micropolar continuum modelling of bi-dimensional tetrachiral lattices

PubMed Central

Chen, Y.; Liu, X. N.; Hu, G. K.; Sun, Q. P.; Zheng, Q. S.

2014-01-01

The in-plane behaviour of tetrachiral lattices should be characterized by bi-dimensional orthotropic material owing to the existence of two orthogonal axes of rotational symmetry. Moreover, the constitutive model must also represent the chirality inherent in the lattices. To this end, a bi-dimensional orthotropic chiral micropolar model is developed based on the theory of irreducible orthogonal tensor decomposition. The obtained constitutive tensors display a hierarchy structure depending on the symmetry of the underlying microstructure. Eight additional material constants, in addition to five for the hemitropic case, are introduced to characterize the anisotropy under Z2 invariance. The developed continuum model is then applied to a tetrachiral lattice, and the material constants of the continuum model are analytically derived by a homogenization process. By comparing with numerical simulations for the discrete lattice, it is found that the proposed continuum model can correctly characterize the static and wave properties of the tetrachiral lattice. PMID:24808754

Characterizing the boundary lateral to the shear direction of deformation twins in magnesium

DOE PAGES

Liu, Y.; Li, N.; Shao, S.; ...

2016-06-01

The three-dimensional nature of twins, especially the atomic structures and motion mechanisms of the boundary lateral to the shear direction of the twin, has never been characterized at the atomic level, because such boundary is, in principle, crystallographically unobservable. We thus refer to it here as the dark side of the twin. Here, using high-resolution transmission electron microscopy and atomistic simulations, we characterize the dark side of {101 ⁻2} deformation twins in magnesium. It is found that the dark side is serrated and comprised of {101 ⁻2} coherent twin boundaries and semi-coherent twist prismatic–prismatic {211 ⁻0} boundaries that control twinmore » growth. The conclusions we find in this work apply to the same twin mode in other hexagonal close-packed materials, and the conceptual ideas discussed here should hold for all twin modes in crystalline materials.« less

Eddy Current Pulsed Thermography with Different Excitation Configurations for Metallic Material and Defect Characterization.

PubMed

Tian, Gui Yun; Gao, Yunlai; Li, Kongjing; Wang, Yizhe; Gao, Bin; He, Yunze

2016-06-08

This paper reviews recent developments of eddy current pulsed thermography (ECPT) for material characterization and nondestructive evaluation (NDE). Due to the fact that line-coil-based ECPT, with the limitation of non-uniform heating and a restricted view, is not suitable for complex geometry structures evaluation, Helmholtz coils and ferrite-yoke-based excitation configurations of ECPT are proposed and compared. Simulations and experiments of new ECPT configurations considering the multi-physical-phenomenon of hysteresis losses, stray losses, and eddy current heating in conjunction with uniform induction magnetic field have been conducted and implemented for ferromagnetic and non-ferromagnetic materials. These configurations of ECPT for metallic material and defect characterization are discussed and compared with conventional line-coil configuration. The results indicate that the proposed ECPT excitation configurations can be applied for different shapes of samples such as turbine blade edges and rail tracks.

Anisotropic physical properties of single-crystal U2Rh2Sn in high magnetic fields

NASA Astrophysics Data System (ADS)

Prokeš, K.; Gorbunov, D. I.; Reehuis, M.; Klemke, B.; Gukasov, A.; Uhlířová, K.; Fabrèges, X.; Skourski, Y.; Yokaichiya, F.; Hartwig, S.; Andreev, A. V.

2017-05-01

We report on the crystal and magnetic structures, magnetic, transport, and thermal properties of U2Rh2Sn single crystals studied in part in high magnetic fields up to 58 T. The material adopts a U3Si2 -related tetragonal crystal structure and orders antiferromagnetically below TN=25 K. The antiferromagnetic structure is characterized by a propagation vector k =(00 1/2 ) . The magnetism in U2Rh2Sn is found to be associated mainly with 5 f states. However, both unpolarized and polarized neutron experiments reveal at low temperatures in zero field non-negligible magnetic moments also on Rh sites. U moments of 0.50(2) μB are directed along the tetragonal axis while Rh moments of 0.06(4) μB form a noncollinear arrangement confined to the basal plane. The response to applied magnetic field is highly anisotropic. Above ˜15 K the easy magnetization direction is along the tetragonal axis. At lower temperatures, however, a stronger response is found perpendicular to the c axis. While for the a axis no magnetic phase transition is observed up to 58 T, for the field applied at 1.8 K along the tetragonal axis we observe above 22.5 T a field-polarized state. A magnetic phase diagram for the field applied along the c axis is presented.

[Non-invasive analysis of proteins in living cells using NMR spectroscopy].

PubMed

Tochio, Hidehito; Murayama, Shuhei; Inomata, Kohsuke; Morimoto, Daichi; Ohno, Ayako; Shirakawa, Masahiro

2015-01-01

NMR spectroscopy enables structural analyses of proteins and has been widely used in the structural biology field in recent decades. NMR spectroscopy can be applied to proteins inside living cells, allowing characterization of their structures and dynamics in intracellular environments. The simplest "in-cell NMR" approach employs bacterial cells; in this approach, live Escherichia coli cells overexpressing a specific protein are subjected to NMR. The cells are grown in an NMR active isotope-enriched medium to ensure that the overexpressed proteins are labeled with the stable isotopes. Thus the obtained NMR spectra, which are derived from labeled proteins, contain atomic-level information about the structure and dynamics of the proteins. Recent progress enables us to work with higher eukaryotic cells such as HeLa and HEK293 cells, for which a number of techniques have been developed to achieve isotope labeling of the specific target protein. In this review, we describe successful use of electroporation for in-cell NMR. In addition, (19)F-NMR to characterize protein-ligand interactions in cells is presented. Because (19)F nuclei rarely exist in natural cells, when (19)F-labeled proteins are delivered into cells and (19)F-NMR signals are observed, one can safely ascertain that these signals originate from the delivered proteins and not other molecules.

An NMR Study of Biomimetic Fluorapatite – Gelatine Mesocrystals

PubMed Central

Vyalikh, Anastasia; Simon, Paul; Rosseeva, Elena; Buder, Jana; Scheler, Ulrich; Kniep, Rüdiger

2015-01-01

The mesocrystal system fluoroapatite—gelatine grown by double-diffusion is characterized by hierarchical composite structure on a mesoscale. In the present work we apply solid state NMR to characterize its structure on the molecular level and provide a link between the structural organisation on the mesoscale and atomistic computer simulations. Thus, we find that the individual nanocrystals are composed of crystalline fluorapatite domains covered by a thin boundary apatite-like layer. The latter is in contact with an amorphous layer, which fills the interparticle space. The amorphous layer is comprised of the organic matrix impregnated by isolated phosphate groups, Ca3F motifs and water molecules. Our NMR data provide clear evidence for the existence of precursor complexes in the gelatine phase, which were not involved in the formation of apatite crystals, proving hence theoretical predictions on the structural pre-treatment of gelatine by ion impregnation. The interfacial interactions, which may be described as the glue holding the composite materials together, comprise hydrogen bond interactions with the apatite PO43− groups. The reported results are in a good agreement with molecular dynamics simulations, which address the mechanisms of a growth control by collagen fibers, and with experimental observations of an amorphous cover layer in biominerals. PMID:26515127

Brain structure and function correlates of cognitive subtypes in schizophrenia.

PubMed

Geisler, Daniel; Walton, Esther; Naylor, Melissa; Roessner, Veit; Lim, Kelvin O; Charles Schulz, S; Gollub, Randy L; Calhoun, Vince D; Sponheim, Scott R; Ehrlich, Stefan

2015-10-30

Stable neuropsychological deficits may provide a reliable basis for identifying etiological subtypes of schizophrenia. The aim of this study was to identify clusters of individuals with schizophrenia based on dimensions of neuropsychological performance, and to characterize their neural correlates. We acquired neuropsychological data as well as structural and functional magnetic resonance imaging from 129 patients with schizophrenia and 165 healthy controls. We derived eight cognitive dimensions and subsequently applied a cluster analysis to identify possible schizophrenia subtypes. Analyses suggested the following four cognitive clusters of schizophrenia: (1) Diminished Verbal Fluency, (2) Diminished Verbal Memory and Poor Motor Control, (3) Diminished Face Memory and Slowed Processing, and (4) Diminished Intellectual Function. The clusters were characterized by a specific pattern of structural brain changes in areas such as Wernicke's area, lingual gyrus and occipital face area, and hippocampus as well as differences in working memory-elicited neural activity in several fronto-parietal brain regions. Separable measures of cognitive function appear to provide a method for deriving cognitive subtypes meaningfully related to brain structure and function. Because the present study identified brain-based neural correlates of the cognitive clusters, the proposed groups of individuals with schizophrenia have some external validity. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Poissonian renormalizations, exponentials, and power laws

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive “renormalization study” of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to “white noise” and to “1/f noise.” Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

Nanoscale measurements of unoccupied band dispersion in few-layer graphene.

PubMed

Jobst, Johannes; Kautz, Jaap; Geelen, Daniël; Tromp, Rudolf M; van der Molen, Sense Jan

2015-11-26

The properties of any material are fundamentally determined by its electronic band structure. Each band represents a series of allowed states inside a material, relating electron energy and momentum. The occupied bands, that is, the filled electron states below the Fermi level, can be routinely measured. However, it is remarkably difficult to characterize the empty part of the band structure experimentally. Here, we present direct measurements of unoccupied bands of monolayer, bilayer and trilayer graphene. To obtain these, we introduce a technique based on low-energy electron microscopy. It relies on the dependence of the electron reflectivity on incidence angle and energy and has a spatial resolution ∼10 nm. The method can be easily applied to other nanomaterials such as van der Waals structures that are available in small crystals only.

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

2011-01-01

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535

Experimental and theoretical studies on the structural, spectroscopic and hydrogen bonding on 4-nitro-n-(2,4-dinitrophenyl) benzenamine

NASA Astrophysics Data System (ADS)

Subhapriya, G.; Kalyanaraman, S.; Jeyachandran, M.; Ragavendran, V.; Krishnakumar, V.

2018-04-01

Synthesized 4-nitro-N-(2,4-dinitrophenyl) benzenamine (NDPBA) molecule was confirmed applying the tool of NMR. Theoretical prediction addressed the NMR chemical shifts and correlated well with the experimental data. The molecule subjected to theoretical DFT at 6-311++G** level unraveled the spectroscopic and structural properties of the NDPBA molecule. Moreover the structural features proved the occurrence of intramolecular Nsbnd H· · O hydrogen bonding in the molecule which was further confirmed with the help of Frontier molecular orbital analysis. Vibrational spectroscopic characterization through FT-IR and Raman experimentally and theoretically gave an account for the vibrational properties. An illustration of the topology of the molecule theoretically helped also in finding the hydrogen bonding energy.

Calculations vs. measurements of remnant dose rates for SNS spent structures

NASA Astrophysics Data System (ADS)

Popova, I. I.; Gallmeier, F. X.; Trotter, S.; Dayton, M.

2018-06-01

Residual dose rate measurements were conducted on target vessel #13 and proton beam window #5 after extraction from their service locations. These measurements were used to verify calculation methods of radionuclide inventory assessment that are typically performed for nuclear waste characterization and transportation of these structures. Neutronics analyses for predicting residual dose rates were carried out using the transport code MCNPX and the transmutation code CINDER90. For transport analyses complex and rigorous geometry model of the structures and their surrounding are applied. The neutronics analyses were carried out using Bertini and CEM high energy physics models for simulating particles interaction. Obtained preliminary calculational results were analysed and compared to the measured dose rates and overall are showing good agreement with in 40% in average.

Syntheses, structural, computational, and thermal analysis of acid-base complexes of picric acid with N-heterocyclic bases.

PubMed

Goel, Nidhi; Singh, Udai P

2013-10-10

Four new acid-base complexes using picric acid [(OH)(NO2)3C6H2] (PA) and N-heterocyclic bases (1,10-phenanthroline (phen)/2,2';6',2"-terpyridine (terpy)/hexamethylenetetramine (hmta)/2,4,6-tri(2-pyridyl)-1,3,5-triazine (tptz)) were prepared and characterized by elemental analysis, IR, NMR and X-ray crystallography. Crystal structures provide detailed information of the noncovalent interactions present in different complexes. The optimized structures of the complexes were calculated in terms of the density functional theory. The thermolysis of these complexes was investigated by TG-DSC and ignition delay measurements. The model-free isoconversional and model-fitting kinetic approaches have been applied to isothermal TG data for kinetics investigation of thermal decomposition of these complexes.

Calculations vs. measurements of remnant dose rates for SNS spent structures

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

Popova, Irina I.; Gallmeier, Franz X.; Trotter, Steven M.

Residual dose rate measurements were conducted on target vessel #13 and proton beam window #5 after extraction from their service locations. These measurements were used to verify calculation methods of radionuclide inventory assessment that are typically performed for nuclear waste characterization and transportation of these structures. Neutronics analyses for predicting residual dose rates were carried out using the transport code MCNPX and the transmutation code CINDER90. For transport analyses complex and rigorous geometry model of the structures and their surrounding are applied. The neutronics analyses were carried out using Bertini and CEM high energy physics models for simulating particles interaction.more » Obtained preliminary calculational results were analysed and compared to the measured dose rates and overall are showing good agreement with in 40% in average.« less

New Electrical Resistivity Tomography approach for karst cave characterization: Castello di Lepre karst cave (Marsico Nuovo, Southern Italy).

NASA Astrophysics Data System (ADS)

Guerriero, Merilisa; Capozzoli, Luigi; De Martino, Gregory; Perciante, Felice; Gueguen, Erwan; Rizzo, Enzo

2017-04-01

Geophysical methods are commonly applied to characterize karst cave. Several geophysical method are used such as electrical resistivity tomography (ERT), gravimetric prospecting (G), ground penetrating radar (GPR) and seismic methods (S), in order to provide information on cave geometry and subsurface geological structure. In detail, in some complex karst systems, each geophysical method can only give partial information if used in normal way due to a low resolution for deep target. In order to reduce uncertainty and avoid misinterpretations based on a normal use of the electrical resistivity tomography method, a new ERT approach has been applied in karst cave Castello di Lepre (Marsico Nuovo, Basilicata region, Italy) located in the Mezo-Cenozoic carbonate substratum of the Monti della Maddalena ridge (Southern Appenines). In detail, a cross-ERT acquisition system was applied in order to improve the resolution on the electrical resistivity distribution on the surrounding geological structure of a karst cave. The cross-ERT system provides a more uniform model resolution vertically, increasing the resolution of the surface resistivity imaging. The usual cross-ERT is made by electrode setting in two or more borehole in order to acquire the resistivity data distribution. In this work the cross-ERT was made between the electrodes located on surface and along a karst cave, in order to obtain an high resolution of the electrical resistivity distributed between the cave and the surface topography. Finally, the acquired cross-ERT is potentially well-suited for imaging fracture zones since electrical current flow in fractured rock is primarily electrolytic via the secondary porosity associated with the fractures.

Calculating Nozzle Side Loads using Acceleration Measurements of Test-Based Models

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; Ruf, Joe

2007-01-01

As part of a NASA/MSFC research program to evaluate the effect of different nozzle contours on the well-known but poorly characterized "side load" phenomena, we attempt to back out the net force on a sub-scale nozzle during cold-flow testing using acceleration measurements. Because modeling the test facility dynamics is problematic, new techniques for creating a "pseudo-model" of the facility and nozzle directly from modal test results are applied. Extensive verification procedures were undertaken, resulting in a loading scale factor necessary for agreement between test and model based frequency response functions. Side loads are then obtained by applying a wide-band random load onto the system model, obtaining nozzle response PSD's, and iterating both the amplitude and frequency of the input until a good comparison of the response with the measured response PSD for a specific time point is obtained. The final calculated loading can be used to compare different nozzle profiles for assessment during rocket engine nozzle development and as a basis for accurate design of the nozzle and engine structure to withstand these loads. The techniques applied within this procedure have extensive applicability to timely and accurate characterization of all test fixtures used for modal test.A viewgraph presentation on a model-test based pseudo-model used to calculate side loads on rocket engine nozzles is included. The topics include: 1) Side Loads in Rocket Nozzles; 2) Present Side Loads Research at NASA/MSFC; 3) Structural Dynamic Model Generation; 4) Pseudo-Model Generation; 5) Implementation; 6) Calibration of Pseudo-Model Response; 7) Pseudo-Model Response Verification; 8) Inverse Force Determination; 9) Results; and 10) Recent Work.

O' Connell bridge inspection by means of Ground Penetrating Radar

NASA Astrophysics Data System (ADS)

Santos Assuncao, Sonia, ,, Dr

2016-04-01

Ground Penetrating Radar (GPR) is a well-known technique successfully applied in different areas. In structural inspection the methodology may expose information about structural arrangement and pathologies. GPR emits high frequency electromagnetic impulses allowing to detect changes on the electromagnetic properties: electrical conductivity, dielectric constant and magnetic permeability. The central frequency of the each antenna is characterized by a specific resolution and penetration depth. Therefore, different scales of structures can be analysed. High frequency antennas output high resolution images/signals about the shallowest elements such as rebar and the thickness of the first layer. On the other hand, intermediate or lower frequency antennas locate deeper structures, such as the thickness of the arch. The compilation of distinct frequencies gives a better understanding and a more accurate detection of elements in the inner structure. O'Connell Bridge (1877) is one of 24 bridges along River Liffey and one the most famous historical structures in Dublin. It is composed by sandstones and granite and covered by asphalt which represents a suitable structure to evaluate by means of GPR. The lack of inner structural information, especially the thickness of the layer, presence of reinforcement or other metallic elements of support required, at least, a dual frequency analysis of the bridge. In this case, it was applied the (200 MHz and 600 MHz) Multi-Channel Stream EM combined with 1.6 GHz GSSI high frequency antenna. The inspection of bridges by means of GPR may provide not exclusively interesting structural data but historical information and the state of conservation.

The pseudotachylites from the Vredefort structure and the Witwatersrand basin

NASA Technical Reports Server (NTRS)

Reimold, W. U.; Colliston, W. P.

1992-01-01

Pseudotachylite (PT) from both the Sudbury structure in Ontario and the Vredefort Dome in South Africa have been widely cited as the result of shock (impact)-induced brecciation. In the scientific and popular literature PT has been described as shock melt or even as impact melt rock. In contrast, others have for years requested that a clarification of the definitions for PT and impact melt rock be pursued. We have suggested that, until that time when well-defined criteria for genetically different melt rock types (e.g., generated by impact or tectonic processes) will have been established, the term PT should only be used as a descriptive one and that, wherever genetic implications are discussed, other terms, such as impact melt (rock) or friction melt, should be applied. It is obvious that these suggestions are not only of value for the discussion of terrestrial melt rocks of controversial origin, but also apply to the characterization of melt veins in extraterrestrial materials. Important observations on Vredefort and Witwatersrand pseudotachylite are summarized.

Pressure cell for investigations of solid-liquid interfaces by neutron reflectivity.

PubMed

Kreuzer, Martin; Kaltofen, Thomas; Steitz, Roland; Zehnder, Beat H; Dahint, Reiner

2011-02-01

We describe an apparatus for measuring scattering length density and structure of molecular layers at planar solid-liquid interfaces under high hydrostatic pressure conditions. The device is designed for in situ characterizations utilizing neutron reflectometry in the pressure range 0.1-100 MPa at temperatures between 5 and 60 °C. The pressure cell is constructed such that stratified molecular layers on crystalline substrates of silicon, quartz, or sapphire with a surface area of 28 cm(2) can be investigated against noncorrosive liquid phases. The large substrate surface area enables reflectivity to be measured down to 10(-5) (without background correction) and thus facilitates determination of the scattering length density profile across the interface as a function of applied load. Our current interest is on the stability of oligolamellar lipid coatings on silicon surfaces against aqueous phases as a function of applied hydrostatic pressure and temperature but the device can also be employed to probe the structure of any other solid-liquid interface.

Kinetic control of block copolymer self-assembly into multicompartment and novel geometry nanoparticles

NASA Astrophysics Data System (ADS)

Chen, Yingchao; Wang, Xiaojun; Zhang, Ke; Wooley, Karen; Mays, Jimmy; Percec, Virgil; Pochan, Darrin

2012-02-01

Micelles with the segregation of hydrophobic blocks trapped in the same nanoparticle core have been produced through co-self-assembly of two block copolymers in THF/water dilute solution. The dissolution of two block copolymer sharing the same polyacrylic acid PAA blocks in THF undergoes consequent aggregation and phase separation through either slow water titration or quick water addition that triggers the micellar formation. The combination and comparison of the two water addition kinetic pathways are the keys of forming multicompartment structures at high water content. Importantly, the addition of organic diamine provides for acid-base complexation with the PAA side chains which, in turn, plays the key role of trapping unlike hydrophobic blocks from different block copolymers into one nanoparticle core. The kinetic control of solution assembly can be applied to other molecular systems such as dendrimers as well as other block copolymer molecules. Transmission electron microscopy, cryogenic transmission electron microscopy, light scattering have been applied to characterize the micelle structures.

A study on thermal properties of biodegradable polymers using photothermal methods

NASA Astrophysics Data System (ADS)

Siqueira, A. P. L.; Poley, L. H.; Sanchez, R.; da Silva, M. G.; Vargas, H.

2005-06-01

In this work is reported the use of photothermal techniques applied to the thermal characterization of biodegradable polymers of Polyhydroxyalkanoates (PHAs) family. This is a family of polymer produced by bacteria using renewable resources. It exhibits thermoplastic properties and therefore it can be an alternative product for engineering plastics, being also applied as packages for food industry and fruits. Thermal diffusivities were determined using the open photoacoustic cell (OPC) configuration. Specific heat capacity measurements were performed monitoring temperature of the samples under white light illumination against time. Typical values obtained for the thermal properties are in good agreement with those found in the literature for other polymers. Due to the incorporation of hydroxyvalerate in the monomer structure, the thermal diffusivity and thermal conductivity increase reaching a saturation value, otherwise the specific thermal capacity decreases as the concentration of the hydroxyvalerate (HV) increases. These results can be explained by polymers internal structure and are allowing new applications of these materials.

Remote geologic structural analysis of Yucca Flat

NASA Astrophysics Data System (ADS)

Foley, M. G.; Heasler, P. G.; Hoover, K. A.; Rynes, N. J.; Thiessen, R. L.; Alfaro, J. L.

1991-12-01

The Remote Geologic Analysis (RGA) system was developed by Pacific Northwest Laboratory (PNL) to identify crustal structures that may affect seismic wave propagation from nuclear tests. Using automated methods, the RGA system identifies all valleys in a digital elevation model (DEM), fits three-dimensional vectors to valley bottoms, and catalogs all potential fracture or fault planes defined by coplanar pairs of valley vectors. The system generates a cluster hierarchy of planar features having greater-than-random density that may represent areas of anomalous topography manifesting structural control of erosional drainage development. Because RGA uses computer methods to identify zones of hypothesized control of topography, ground truth using a well-characterized test site was critical in our evaluation of RGA's characterization of inaccessible test sites for seismic verification studies. Therefore, we applied RGA to a study area centered on Yucca Flat at the Nevada Test Site (NTS) and compared our results with both mapped geology and geologic structures and with seismic yield-magnitude models. This is the final report of PNL's RGA development project for peer review within the U.S. Department of Energy Office of Arms Control (OAC) seismic-verification community. In this report, we discuss the Yucca Flat study area, the analytical basis of the RGA system and its application to Yucca Flat, the results of the analysis, and the relation of the analytical results to known topography, geology, and geologic structures.

Application of far-infrared spectroscopy to the structural identification of protein materials.

PubMed

Han, Yanchen; Ling, Shengjie; Qi, Zeming; Shao, Zhengzhong; Chen, Xin

2018-05-03

Although far-infrared (IR) spectroscopy has been shown to be a powerful tool to determine peptide structure and to detect structural transitions in peptides, it has been overlooked in the characterization of proteins. Herein, we used far-IR spectroscopy to monitor the structure of four abundant non-bioactive proteins, namely, soybean protein isolate (SPI), pea protein isolate (PPI) and two types of silk fibroins (SFs), domestic Bombyx mori and wild Antheraea pernyi. The two globular proteins SPI and PPI result in broad and weak far-IR bands (between 50 and 700 cm-1), in agreement with those of some other bioactive globular proteins previously studied (lysozyme, myoglobin, hemoglobin, etc.) that generally only have random amino acid sequences. Interestingly, the two SFs, which are characterized by a structure composed of highly repetitive motifs, show several sharp far-IR characteristic absorption peaks. Moreover, some of these characteristic peaks (such as the peaks at 260 and 428 cm-1 in B. mori, and the peaks at 245 and 448 cm-1 in A. pernyi) are sensitive to conformational changes; hence, they can be directly used to monitor conformational transitions in SFs. Furthermore, since SF absorption bands clearly differ from those of globular proteins and different SFs even show distinct adsorption bands, far-IR spectroscopy can be applied to distinguish and determine the specific SF component within protein blends.

Volumetric Stress-Strain Analysis of Optohydrodynamically Suspended Biological Cells

PubMed Central

Liang, Yu; Saha, Asit K.

2011-01-01

Ongoing investigations are exploring the biomechanical properties of isolated and suspended biological cells in pursuit of understanding single-cell mechanobiology. An optical tweezer with minimal applied laser power has positioned biologic cells at the geometric center of a microfluidic cross-junction, creating a novel optohydrodynamic trap. The resulting fluid flow environment facilitates unique multiaxial loading of single cells with site-specific normal and shear stresses resulting in a physical albeit extensional state. A recent two-dimensional analysis has explored the cytoskeletal strain response due to these fluid-induced stresses [Wilson and Kohles, 2010, “Two-Dimensional Modeling of Nanomechanical Stresses-Strains in Healthy and Diseased Single-Cells During Microfluidic Manipulation,” J Nanotechnol Eng Med, 1(2), p. 021005]. Results described a microfluidic environment having controlled nanometer and piconewton resolution. In this present study, computational fluid dynamics combined with multiphysics modeling has further characterized the applied fluid stress environment and the solid cellular strain response in three dimensions to accompany experimental cell stimulation. A volumetric stress-strain analysis was applied to representative living cell biomechanical data. The presented normal and shear stress surface maps will guide future microfluidic experiments as well as provide a framework for characterizing cytoskeletal structure influencing the stress to strain response. PMID:21186894

Comportement dynamique d'alliages a memoire de forme et application aux composites-AMF

NASA Astrophysics Data System (ADS)

de Santis, Silvio

Meeting current industrial, governmental and international standards regarding vibration and noise levels is a challenging task facing many engineers. These specifications are present in just about all fields of engineering, from aerospace to marine transportation, from automotive to railway transportation, from computer equipment to industrial working environments. An appropriate use of the remarkable properties of high damping metals (HIDAMETS) and shape memory alloy (SMA) reinforced composites emerges as a possible solution to these problems. Among many obstacles to overcome in developing such a technology, the implementation of reliable and adequate characterization techniques to determine dynamic properties of these materials appears to be of prime importance. The research efforts presented in this thesis are aimed at developing advanced techniques to characterize the dynamic behavior of HIDAMETS and SMA reinforced composites. These characterization results lead to the enhancement of numerical (finite element) and/or analytical methods for the simulation of dynamic responses of structures made of these materials. In particular, the research work has focused on three themes: the numerical and experimental validation of applying a characterization procedure developed for traditional composites to SMA reinforced composites; the development of a test bench for uniaxial hysteresis characterization of HIDAMETS in the medium frequency range; the hysteresis characterization and modeling of manganese copper (MnCu) and nickel titanium samples. The results obtained in the course of these efforts show that the characterization technique developed for traditional composites at the University of Brussels is sufficiently precise to successfully predict natural frequencies of complex SMA reinforced composite structures. Using the characterization to predict structural damping ratios, we observe a bias error in the prediction with respect to experimental results although the relative values between modes are consistent. Regarding the development of the test bench for uniaxial hysteresis characterization of HIDAMETS, results suggest that with the introduction of a few minor enhancements and with particular experimental precautions, the test bench can play an important role in characterizing HIDAMETS dynamic properties at various frequencies and strain amplitudes and in understanding micro mechanical mechanisms responsible for energy dissipation. Finally, uniaxial hysteresis loops and related parameters have been obtained with MnCu and NiTi samples. A material model based on dual kriging interpolation that expresses the tangent stiffness along these hysteresis loops as a function of strain and strain amplitude has also been developed.

Sensitive detection of strong acidic condition by a novel rhodamine-based fluorescent pH chemosensor.

PubMed

Tan, Jia-Lian; Yang, Ting-Ting; Liu, Yu; Zhang, Xue; Cheng, Shu-Jin; Zuo, Hua; He, Huawei

2016-05-01

A novel rhodamine-based fluorescent pH probe responding to extremely low pH values has been synthesized and characterized. This probe showed an excellent photophysical response to pH on the basis that the colorless spirocyclic structure under basic conditions opened to a colored and highly fluorescent form under extreme acidity. The quantitative relationship between fluorescence intensity and pH value (1.75-2.62) was consistent with the equilibrium equation pH = pKa + log[(Imax - I)/(I - Imin)]. This sensitive pH probe was also characterized with good reversibility and no interaction with interfering metal ions, and was successfully applied to image Escherichia coli under strong acidity. Copyright © 2015 John Wiley & Sons, Ltd.

Principle of two-dimensional characterization of copolymers.

PubMed

Weidner, Steffen; Falkenhagen, Jana; Krueger, Ralph-Peter; Just, Ulrich

2007-07-01

Two-dimensional polymer characterization is used for a simultaneous analysis of molar masses and chemical heterogeneities (e.g., end groups, copolymer composition, etc.). This principle is based on coupling of two different chromatographic modes. Liquid adsorption chromatography at critical conditions (LACCC) is applied for a separation according to the chemical heterogeneity, whereas in the second-dimension fractions are analyzed with regard to their molar mass distribution by means of size exclusion chromatography (SEC). Because appropriate standards for a calibration of the SEC are seldom available, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was used to substitute the SEC. The LACCC-MALDI MS coupling enables acquiring additional structural information on copolymer composition, which can considerably enhance the performance of this coupled method.

Assembly and microscopic characterization of DNA origami structures.

PubMed

Scheible, Max; Jungmann, Ralf; Simmel, Friedrich C

2012-01-01

DNA origami is a revolutionary method for the assembly of molecular nanostructures from DNA with precisely defined dimensions and with an unprecedented yield. This can be utilized to arrange nanoscale components such as proteins or nanoparticles into pre-defined patterns. For applications it will now be of interest to arrange such components into functional complexes and study their geometry-dependent interactions. While commonly DNA nanostructures are characterized by atomic force microscopy or electron microscopy, these techniques often lack the time-resolution to study dynamic processes. It is therefore of considerable interest to also apply fluorescence microscopic techniques to DNA nanostructures. Of particular importance here is the utilization of novel super-resolved microscopy methods that enable imaging beyond the classical diffraction limit.

Metal oxide nanostructures: preparation, characterization and functional applications as chemical sensors.

PubMed

Zappa, Dario; Bertuna, Angela; Comini, Elisabetta; Kaur, Navpreet; Poli, Nicola; Sberveglieri, Veronica; Sberveglieri, Giorgio

2017-01-01

Preparation and characterization of different metal oxide (NiO, WO 3 , ZnO, SnO 2 and Nb 2 O 5 ) nanostructures for chemical sensing are presented. p-Type (NiO) and n-type (WO 3 , SnO 2 , ZnO and Nb 2 O 5 ) metal oxide nanostructures were grown on alumina substrates using evaporation-condensation, thermal oxidation and hydrothermal techniques. Surface morphologies and crystal structures were investigated through scanning electron microscopy and Raman spectroscopy. Furthermore, different batches of sensors have been prepared, and their sensing performances towards carbon monoxide and nitrogen dioxide have been explored. Moreover, metal oxide nanowires have been integrated into an electronic nose and successfully applied to discriminate between drinking and contaminated water.

Radar polarimetry - Analysis tools and applications

NASA Technical Reports Server (NTRS)

Evans, Diane L.; Farr, Tom G.; Van Zyl, Jakob J.; Zebker, Howard A.

1988-01-01

The authors have developed several techniques to analyze polarimetric radar data from the NASA/JPL airborne SAR for earth science applications. The techniques determine the heterogeneity of scatterers with subregions, optimize the return power from these areas, and identify probable scattering mechanisms for each pixel in a radar image. These techniques are applied to the discrimination and characterization of geologic surfaces and vegetation cover, and it is found that their utility varies depending on the terrain type. It is concluded that there are several classes of problems amenable to single-frequency polarimetric data analysis, including characterization of surface roughness and vegetation structure, and estimation of vegetation density. Polarimetric radar remote sensing can thus be a useful tool for monitoring a set of earth science parameters.

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

PubMed Central

de Sanctis, Daniele

2017-01-01

Synchrotron radiation is the most versatile way to explore biological materials in different states: monocrystalline, polycrystalline, solution, colloids and multiscale architectures. Steady improvements in instrumentation have made synchrotrons the most flexible intense X-ray source. The wide range of applications of synchrotron radiation is commensurate with the structural diversity and complexity of the molecules and macromolecules that form the collection of substrates investigated by glycoscience. The present review illustrates how synchrotron-based experiments have contributed to our understanding in the field of structural glycobiology. Structural characterization of protein–carbohydrate interactions of the families of most glycan-interacting proteins (including glycosyl transferases and hydrolases, lectins, antibodies and GAG-binding proteins) are presented. Examples concerned with glycolipids and colloids are also covered as well as some dealing with the structures and multiscale architectures of polysaccharides. Insights into the kinetics of catalytic events observed in the crystalline state are also presented as well as some aspects of structure determination of protein in solution. PMID:28684994

Advanced composite structures. [metal matrix composites - structural design criteria for spacecraft construction materials

NASA Technical Reports Server (NTRS)

1974-01-01

A monograph is presented which establishes structural design criteria and recommends practices to ensure the design of sound composite structures, including composite-reinforced metal structures. (It does not discuss design criteria for fiber-glass composites and such advanced composite materials as beryllium wire or sapphire whiskers in a matrix material.) Although the criteria were developed for aircraft applications, they are general enough to be applicable to space vehicles and missiles as well. The monograph covers four broad areas: (1) materials, (2) design, (3) fracture control, and (4) design verification. The materials portion deals with such subjects as material system design, material design levels, and material characterization. The design portion includes panel, shell, and joint design, applied loads, internal loads, design factors, reliability, and maintainability. Fracture control includes such items as stress concentrations, service-life philosophy, and the management plan for control of fracture-related aspects of structural design using composite materials. Design verification discusses ways to prove flightworthiness.

A simplified method of evaluating the stress wave environment of internal equipment

NASA Technical Reports Server (NTRS)

Colton, J. D.; Desmond, T. P.

1979-01-01

A simplified method called the transfer function technique (TFT) was devised for evaluating the stress wave environment in a structure containing internal equipment. The TFT consists of following the initial in-plane stress wave that propagates through a structure subjected to a dynamic load and characterizing how the wave is altered as it is transmitted through intersections of structural members. As a basis for evaluating the TFT, impact experiments and detailed stress wave analyses were performed for structures with two or three, or more members. Transfer functions that relate the wave transmitted through an intersection to the incident wave were deduced from the predicted wave response. By sequentially applying these transfer functions to a structure with several intersections, it was found that the environment produced by the initial stress wave propagating through the structure can be approximated well. The TFT can be used as a design tool or as an analytical tool to determine whether a more detailed wave analysis is warranted.

A Data-Driven Diagnostic Framework for Wind Turbine Structures: A Holistic Approach

PubMed Central

Bogoevska, Simona; Spiridonakos, Minas; Chatzi, Eleni; Dumova-Jovanoska, Elena; Höffer, Rudiger

2017-01-01

The complex dynamics of operational wind turbine (WT) structures challenges the applicability of existing structural health monitoring (SHM) strategies for condition assessment. At the center of Europe’s renewable energy strategic planning, WT systems call for implementation of strategies that may describe the WT behavior in its complete operational spectrum. The framework proposed in this paper relies on the symbiotic treatment of acting environmental/operational variables and the monitored vibration response of the structure. The approach aims at accurate simulation of the temporal variability characterizing the WT dynamics, and subsequently at the tracking of the evolution of this variability in a longer-term horizon. The bi-component analysis tool is applied on long-term data, collected as part of continuous monitoring campaigns on two actual operating WT structures located in different sites in Germany. The obtained data-driven structural models verify the potential of the proposed strategy for development of an automated SHM diagnostic tool. PMID:28358346

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

PubMed

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P; Chait, Brian T

2014-11-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼ 600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

Structural, magnetic, and magnetocaloric properties of bilayer manganite La1.38Sr1.62Mn2O7

NASA Astrophysics Data System (ADS)

Yang, Yu-E.; Xie, Yunfei; Xu, Lisha; Hu, Dazhi; Ma, Chunlan; Ling, Langsheng; Tong, Wei; Pi, Li; Zhang, Yuheng; Fan, Jiyu

2018-04-01

In this study, we investigated the structural, magnetic phase transition, and magnetocaloric properties of bilayer perovskite manganite La1.38Sr1.62Mn2O7 based on X-ray diffraction, electron paramagnetic resonance, and temperature-/magnetic field-dependent magnetization measurements. The structural characterization results showed the prepared sample had a tetragonal structure with the space group I4/mmm. The Curie temperature was determined as 114 K in the magnetization studies and a second-order paramagnetic-ferromagnetic transition was confirmed by the Arrott plot, which showed that the slopes were positive for all the curves. According to the variation in the electron paramagnetic resonance spectrum, we detected obvious electronic phase separation across a broad temperature range from 220 to 80 K in this magnetic material, thereby indicating that the paramagnetic and ferromagnetic phases coexist above as well as below the Curie temperature. Based on a plot of the isothermal magnetization versus the magnetic applied field, we deduced the maximum magnetic entropy change, which only reached 1.89 J/kg.K under an applied magnetic field of 7.0 T. These theoretical investigations indicated that in addition to the magnetoelastic couplings and electron interaction, electronic phase separation and anisotropic exchange interactions also affect the magnetic entropy changes in this bilayer manganite.

Quantitative polarized light microscopy of unstained mammalian cochlear sections

NASA Astrophysics Data System (ADS)

Kalwani, Neil M.; Ong, Cheng Ai; Lysaght, Andrew C.; Haward, Simon J.; McKinley, Gareth H.; Stankovic, Konstantina M.

2013-02-01

Hearing loss is the most common sensory deficit in the world, and most frequently it originates in the inner ear. Yet, the inner ear has been difficult to access for diagnosis because of its small size, delicate nature, complex three-dimensional anatomy, and encasement in the densest bone in the body. Evolving optical methods are promising to afford cellular diagnosis of pathologic changes in the inner ear. To appropriately interpret results from these emerging technologies, it is important to characterize optical properties of cochlear tissues. Here, we focus on that characterization using quantitative polarized light microscopy (qPLM) applied to unstained cochlear sections of the mouse, a common animal model of human hearing loss. We find that the most birefringent cochlear materials are collagen fibrils and myelin. Retardance of the otic capsule, the spiral ligament, and the basilar membrane are substantially higher than that of other cochlear structures. Retardance of the spiral ligament and the basilar membrane decrease from the cochlear base to the apex, compared with the more uniform retardance of other structures. The intricate structural details revealed by qPLM of unstained cochlear sections ex vivo strongly motivate future application of polarization-sensitive optical coherence tomography to human cochlea in vivo.

Structural characterization of arginine-vasopressin and lysine-vasopressin by Fourier- transform ion cyclotron resonance mass spectrometry and infrared multiphoton dissociation.

PubMed

Bianco, Giuliana; Battista, Fabio; Buchicchio, Alessandro; Amarena, Concetta G; Schmitt-Kopplin, Philippe; Guerrieri, Antonio

2015-01-01

Arginine-vasopressin (AVP) and lysine-vasopressin (LVP) were analyzed by reversed-phase liquid chromatography/mass spectrometry (LC-MS) using Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) electrospray ionization (ESI) in the positive ion mode. LVP and AVP exhibited the protonated adduct [M+H](+) as the predominant ion at m/z 1056.43965 and at m/z 1084.44561, respectively. Infrared multiphoton dissociation (IRMPD), using a CO(2) laser source at a wavelength of 10.6 μm, was applied to protonated vasopressin molecules. The IRMPD mass spectra presented abundant mass fragments essential for a complete structural information. Several fragment ions, shared between two target molecules, are discussed in detail. Some previously unpublished fragments were identified unambiguously utilizing the high resolution and accurate mass information provided by the FT-ICR mass spectrometer. The opening of the disulfide loop and the cleavage of the peptide bonds within the ring were observed even under low-energy fragmentation conditions. Coupling the high-performance FT-ICR mass spectrometer with IRMPD as a contemporary fragmentation technique proved to be very promising for the structural characterization of vasopressin.

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

Krumeich, F., E-mail: krumeich@inorg.chem.ethz.ch; Mueller, E.; Wepf, R.A.

While HRTEM is the well-established method to characterize the structure of dodecagonal tantalum (vanadium) telluride quasicrystals and their periodic approximants, phase-contrast imaging performed on an aberration-corrected scanning transmission electron microscope (STEM) represents a favorable alternative. The (Ta,V){sub 151}Te{sub 74} clusters, the basic structural unit in all these phases, can be visualized with high resolution. A dependence of the image contrast on defocus and specimen thickness has been observed. In thin areas, the projected crystal potential is basically imaged with either dark or bright contrast at two defocus values close to Scherzer defocus as confirmed by image simulations utilizing the principlemore » of reciprocity. Models for square-triangle tilings describing the arrangement of the basic clusters can be derived from such images. - Graphical abstract: PC-STEM image of a (Ta,V){sub 151}Te{sub 74} cluster. Highlights: Black-Right-Pointing-Pointer C{sub s}-corrected STEM is applied for the characterization of dodecagonal quasicrystals. Black-Right-Pointing-Pointer The projected potential of the structure is mirrored in the images. Black-Right-Pointing-Pointer Phase-contrast STEM imaging depends on defocus and thickness. Black-Right-Pointing-Pointer For simulations of phase-contrast STEM images, the reciprocity theorem is applicable.« less

Quantitative polarized light microscopy of unstained mammalian cochlear sections

PubMed Central

Kalwani, Neil M.; Ong, Cheng Ai; Lysaght, Andrew C.; Haward, Simon J.; McKinley, Gareth H.

2013-01-01

Abstract. Hearing loss is the most common sensory deficit in the world, and most frequently it originates in the inner ear. Yet, the inner ear has been difficult to access for diagnosis because of its small size, delicate nature, complex three-dimensional anatomy, and encasement in the densest bone in the body. Evolving optical methods are promising to afford cellular diagnosis of pathologic changes in the inner ear. To appropriately interpret results from these emerging technologies, it is important to characterize optical properties of cochlear tissues. Here, we focus on that characterization using quantitative polarized light microscopy (qPLM) applied to unstained cochlear sections of the mouse, a common animal model of human hearing loss. We find that the most birefringent cochlear materials are collagen fibrils and myelin. Retardance of the otic capsule, the spiral ligament, and the basilar membrane are substantially higher than that of other cochlear structures. Retardance of the spiral ligament and the basilar membrane decrease from the cochlear base to the apex, compared with the more uniform retardance of other structures. The intricate structural details revealed by qPLM of unstained cochlear sections ex vivo strongly motivate future application of polarization-sensitive optical coherence tomography to human cochlea in vivo. PMID:23407909

Structure, vibrational spectra and DFT characterization of the intra- and inter-molecular interactions in 2-hydroxy-5-methylpyridine-3-carboxylic acid--normal modes of the eight-membered HB ring.

PubMed

Godlewska, P; Jańczak, J; Kucharska, E; Hanuza, J; Lorenc, J; Michalski, J; Dymińska, L; Węgliński, Z

2014-01-01

Fourier transform IR and Raman spectra, XRD studies and DFT quantum chemical calculations have been used to characterize the structural and vibrational properties of 2-hydroxy-5-methylpyridine-3-carboxylic acid. In the unit-cell of this compound two molecules related by the inversion center interact via OH⋯N hydrogen bonds. The double hydrogen bridge system is spaced parallel to the (102) crystallographic plane forming eight-membered arrangement characteristic for pyridine derivatives. The six-membered ring is the second characteristic unit formed via the intramolecular OH⋯O hydrogen bond. The geometry optimization of the monomer and dimer have been performed applying the Gaussian03 program package. All calculations were performed in the B3LYP/6-31G(d,p) basis set using the XRD data as input parameters. The relation between the molecular and crystal structures has been discussed in terms of the hydrogen bonds formed in the unit cell. The vibrations of the dimer have been discussed in terms of the resonance inside the system built of five rings coupled via hydrogen bonds. Copyright © 2013 Elsevier B.V. All rights reserved.

Environmental and Geotechnical Assessment of the Steel Slags as a Material for Road Structure.

PubMed

Sas, Wojciech; Głuchowski, Andrzej; Radziemska, Maja; Dzięcioł, Justyna; Szymański, Alojzy

2015-07-30

Slags are the final solid wastes from the steel industry. Their production from waste and associated materials is a proper implementation of the basic objectives and principles of the waste management. This study aims to investigate the chemical and selected significant geotechnical parameters of steel slag as the alternative materials used in road construction. These investigations are strongly desired for successful application in engineering. Young's modules E , and resilient modules M r showed that their values corresponding with requirements for subbase (principal or auxiliary) and riding surface as well. Tested mechanical properties were conducted in soaked and un-soaked (optimal moisture content) conditions. The designated high content of chromium and zinc are strongly associated with the internal crystal structure of steel slag. The results do not lead to threats when they are applied in roads' structures. Mechanical characterization was obtained by performing California bearing ratio (CBR) tests for steel slag in fixed compaction and moisture content conditions. Moreover, cyclic loading of steel slag was conducted with the application of cyclic California bearing ratio (cCBR) apparatus to characterization of this material as a controlled low-strength material. Finally, field studies that consist of static load plate VSS tests were presented.

A bifractal nature of reticular patterns induced by oxygen plasma on polymer films

NASA Astrophysics Data System (ADS)

Bae, Junwan; Lee, I. J.

2015-05-01

Plasma etching was demonstrated to be a promising tool for generating self-organized nano-patterns on various commercial films. Unfortunately, dynamic scaling approach toward fundamental understanding of the formation and growth of the plasma-induced nano-structure has not always been straightforward. The temporal evolution of self-aligned nano-patterns may often evolve with an additional scale-invariance, which leads to breakdown of the well-established dynamic scaling law. The concept of a bifractal interface is successfully applied to reticular patterns induced by oxygen plasma on the surface of polymer films. The reticular pattern, composed of nano-size self-aligned protuberances and underlying structure, develops two types of anomalous dynamic scaling characterized by super-roughening and intrinsic anomalous scaling, respectively. The diffusion and aggregation of short-cleaved chains under the plasma environment are responsible for the regular distribution of the nano-size protuberances. Remarkably, it is uncovered that the dynamic roughening of the underlying structure is governed by a relaxation mechanism described by the Edwards-Wilkinson universality class with a conservative noise. The evidence for the basic phase, characterized by the negative roughness and growth exponents, has been elusive since its first theoretical consideration more than two decades ago.

Evaluation of protein immobilization capacity on various carbon nanotube embedded hydrogel biomaterials.

PubMed

Derkus, Burak; Emregul, Kaan Cebesoy; Emregul, Emel

2015-11-01

This study investigates effective immobilization of proteins, an important procedure in many fields of bioengineering and medicine, using various biomaterials. Gelatin, alginate and chitosan were chosen as polymeric carriers, and applied in both their composites and nanocomposite forms in combination with carbon nanotubes (CNTs). The prepared nano/composite structures were characterized using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TG) and contact angle analysis (CA). Electrochemical impedance spectroscopy analysis revealed gelatin composites in general to exhibit better immobilization performance relative to the native gelatin which can be attributed to enhanced film morphologies of the composite structures. Moreover, superior immobilization efficiencies were obtained with the addition of carbon nanotubes, due to their conducting and surface enhancement features, especially in the gelatin-chitosan structures due to the presence of structural active groups. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthesis, structure, biochemical, and docking studies of a new dinitrosyl iron complex [Fe2(μ-SC4H3SCH2)2(NO)4

NASA Astrophysics Data System (ADS)

Davidovich, P. B.; Fischer, A. I.; Korchagin, D. V.; Panchuk, V. V.; Shchukarev, A. V.; Garabadzhiu, A. V.; Belyaev, A. N.

2015-07-01

A new dinitrosyl iron complex of binuclear structure [Fe2(μ-S-2-methylthiophene)2(NO)4] was first synthesized and structurally characterized by XRD and theoretical methods. Using caspase-3 as an example it was shown that [Fe2(μ-S-2-methylthiophene)2(NO)4] and its analog [Fe2(μ-S-2-methylfurane)2(NO)4] can inhibit the action of active site cysteine proteins; the difference in inhibitory activity was explained by molecular docking studies. Biochemical and in silico studies give grounds that the biological activity of dinitrosyl iron complexes is a μ-SR bridging ligand structure function. Thus the rational design strategy of [Fe2(μ-SR)2(NO)4] complexes can be applied to make NO prodrugs with high affinity to therapeutically significant targets involved in cancer and inflammation.

Superestructuras en el universo: caracterización e identificación en el catálgo SDSS-DR7

NASA Astrophysics Data System (ADS)

Luparello, H. E.; Lares, M.; García Lambas, D.; Padilla, N.

Superclusters are the largest gravitationally bound systems in the Universe. These structures are not presently virialized, so the application of theoreti- cal arguments in their identification is not straightforward. Luparello et al., (2011) present an identification method and establish the values of the pa- rameters in order to ensure that superstructures in the present Universe will evolve into virialized structures. In this work we define and characterize the largest structures in the Universe, in the framework of the cosmological model CDM. We briefly describe the Future Virialized Structures (FVS) identification method applied to the seventh data release of the Sloan Dig- ital Sky Survey (SDSS-DR7, Abazajian et al., 2009) in the redshift range 0.04 < z < 0.12 and present the main properties of the FVS catalogue. FULL TEXT IN SPANISH

Preparation of composite micro/nano structure on the silicon surface by reactive ion etching: Enhanced anti-reflective and hydrophobic properties

NASA Astrophysics Data System (ADS)

Zeng, Yu; Fan, Xiaoli; Chen, Jiajia; He, Siyu; Yi, Zao; Ye, Xin; Yi, Yougen

2018-05-01

A silicon substrate with micro-pyramid structure (black silicon) is prepared by wet chemical etching and then subjected to reactive ion etching (RIE) in the mixed gas condition of SF6, CHF3 and He. We systematically study the impacts of flow rates of SF6, CHF3 and He, the etching pressure and the etching time on the surface morphology and reflectivity through various characterizations. Meanwhile, we explore and obtain the optimal combination of parameters for the preparation of composite structure that match the RIE process based on the basis of micro-pyramid silicon substrate. The composite sample prepared under the optimum parameters exhibits excellent anti-reflective performance, hydrophobic, self-cleaning and anti-corrosive properties. Based on the above characteristics, the composite micro/nano structure can be applied to solar cells, photodetectors, LEDs, outdoor devices and other important fields.

Two-dimensional nuclear magnetic resonance structure determination module for introductory biochemistry: synthesis and structural characterization of lyso-glycerophospholipids.

PubMed

Garrett, Teresa A; Rose, Rebecca L; Bell, Sidney M

2013-01-01

In this laboratory module, introductory biochemistry students are exposed to two-dimensional (1) H-nuclear magnetic resonance of glycerophospholipids (GPLs). Working in groups of three, students enzymatically synthesized and purified a variety of 2-acyl lyso GPLs. The structure of the 2-acyl lyso GPL was verified using (1) H-correlation spectroscopy. Students scored significantly higher on an assessment of NMR knowledge after having participated in this lab module and in comparison to a similar cohort who did not participate. Inaddition, student confidence in their NMR knowledge and abilities increased 62% following the module and correlated with their ability to apply their NMR knowledge. Based on these results, the laboratory module was very effective at providing students with a more extensive understanding of the underlying concepts of NMR as a tool for structural determination. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Side-wall spacer passivated sub-μm Josephson junction fabrication process

NASA Astrophysics Data System (ADS)

Grönberg, Leif; Kiviranta, Mikko; Vesterinen, Visa; Lehtinen, Janne; Simbierowicz, Slawomir; Luomahaara, Juho; Prunnila, Mika; Hassel, Juha

2017-12-01

We present a structure and a fabrication method for superconducting tunnel junctions down to the dimensions of 200 nm using i-line UV lithography. The key element is a sidewall-passivating spacer structure (SWAPS) which is shaped for smooth crossline contacting and low parasitic capacitance. The SWAPS structure enables formation of junctions with dimensions at or below the lithography-limited linewidth. An additional benefit is avoiding the excessive use of amorphous dielectric materials which is favorable in sub-Kelvin microwave applications often plagued by nonlinear and lossy dielectrics. We apply the structure to niobium trilayer junctions, and provide characterization results yielding evidence on wafer-scale scalability, and critical current density tuning in the range of 0.1-3.0 kA cm-2. We discuss the applicability of the junction process in the context of different applications, such as SQUID magnetometers and Josephson parametric amplifiers.

Thermal modal analysis of novel non-pneumatic mechanical elastic wheel based on FEM and EMA

NASA Astrophysics Data System (ADS)

Zhao, Youqun; Zhu, Mingmin; Lin, Fen; Xiao, Zhen; Li, Haiqing; Deng, Yaoji

2018-01-01

A combination of Finite Element Method (FEM) and Experiment Modal Analysis (EMA) have been employed here to characterize the structural dynamic response of mechanical elastic wheel (ME-Wheel) operating under a specific thermal environment. The influence of high thermal condition on the structural dynamic response of ME-Wheel is investigated. The obtained results indicate that the EMA results are in accordance with those obtained using the proposed Finite Element (FE) model, indicting the high reliability of this FE model applied in analyzing the modal of ME-Wheel working under practical thermal environment. It demonstrates that the structural dynamic response of ME-Wheel operating under a specific thermal condition can be predicted and evaluated using the proposed analysis method, which is beneficial for the dynamic optimization design of the wheel structure to avoid tire temperature related vibration failure and improve safety of tire.

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.

PubMed

Abrouk, Michael; Balcárková, Barbora; Šimková, Hana; Komínkova, Eva; Martis, Mihaela M; Jakobson, Irena; Timofejeva, Ljudmilla; Rey, Elodie; Vrána, Jan; Kilian, Andrzej; Järve, Kadri; Doležel, Jaroslav; Valárik, Miroslav

2017-02-01

The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Preparation and characterization of multi-layer biodegradable nanofibers by coaxial electrospinning and their potential for tissue engineering

NASA Astrophysics Data System (ADS)

Liu, Wenwen

As an evolution of conventional electrospinning, coaxial electrospinning became popular soon after its debut as a novel way to develop nanofibers with special structures, such as core-shell and hollow interior. In recent years, there has been an increasing interest in a modified coaxial electrospinning, tri-layer coaxial electrospinning, to develop more complex structures, such as multi-layer and nanowire-in-microtube. Previous studies have primarily concentrated on the fabrication of tri-layered inorganic fibers while studies on tri-layered coaxial polymeric fibers has not been reported until very recently. Our research focuses on the fabrication of core-shell and tri-layer structured biodegradable polymeric nanofibers with coaxial electrospinning. Different characterization methods have been applied to observe the internal structure in single nanofibers and the potential application of tri-layer coaxial electrospinning has been discussed. The material system consists of biodegradable natural polymer gelatin, synthetic polymers poly (epsilon-caprolactone) (PCL) and poly (lactic-co-glycolic acid) (PLGA). A uniquely designed three-needle concentric spinneret is developed to perform tri-layer coaxial electrospinning. Different kinds of core-shell structured nanofibers, including gelatin/PCL, PCL/gelatin, gelatin/PLGA and PCL/PLGA, have been fabricated with a customized coaxial electrospinning apparatus. Two kinds of tri-layer coaxial nanofibers, two-component ABA structured gelatin/PCL/gelatin biodegradable nanofibers and tri-component ABC structured gelatin/PCL/PLGA biodegradable nanofibers, have been developed with the customized three needle coaxial electrospinning setup. The core-shell and tri-layered structures of electrospun nanofibers have been characterized by several commonly used techniques, such as laser scanning confocal microscopy (LSCM) and transmission electron microscopy (TEM). Besides the conventional methods, other newer techniques, including focused ion beam-scanning electron microscopy (FIB-SEM), super-resolution structured illumination microscopy (SR-SIM) and nanoscale-infrared spectroscopy (nano-IR), have been explored to investigate the internal structure in singles fibers. Additionally, the potential application of coaxial electrospinning in the fabrication of bioactive scaffolds for tissue engineering has been studied. Different kinds of coaxial nanofibers were fabricated and studied to determine the potential for BSA and growth factor release and some preliminary results were obtained.

Least Squares Best Fit Method for the Three Parameter Weibull Distribution: Analysis of Tensile and Bend Specimens with Volume or Surface Flaw Failure

NASA Technical Reports Server (NTRS)

Gross, Bernard

1996-01-01

Material characterization parameters obtained from naturally flawed specimens are necessary for reliability evaluation of non-deterministic advanced ceramic structural components. The least squares best fit method is applied to the three parameter uniaxial Weibull model to obtain the material parameters from experimental tests on volume or surface flawed specimens subjected to pure tension, pure bending, four point or three point loading. Several illustrative example problems are provided.

Processing and interpretation of experiments in the microwave interferometry of shock waves in a weakly ionized plasma

NASA Astrophysics Data System (ADS)

Ershov, A. P.; Klishin, S. V.; Kuzovnikov, S. V.; Ponomareva, S. E.; Pyt'ev, Iu. P.

1990-12-01

The reduction method is applied to the microwave interferometry of shock waves in a weakly ionized plasma, making it possible to improve the spatial resolution of the instrument. It is shown experimentally that the structure of the shock wave electron component in a high-frequency discharge plasma in atomic and molecular gases is characterized by the presence of a precursor in the form of a rarefaction wave. The origin of the precursor is examined.

Effect of Selective Co Addition on Magnetic Properties of Nd2(FeCo)14B/alpha-Fe Nanocomposite Magnets

DTIC Science & Technology

2012-12-13

pressure of ∼2.5 GPa. The final bulk magnets having dimensions Ø6 mm × 1.5 mm were characterized for morphology and the crystalline structure using scanning... Magnetic properties were measured with a superconducting quantum interference device (SQUID) magnetometer with a maximum applied field of 70 kOe. To...calculate the true energy product (BH)max of the bulk sample, we determined the demagnetization factor experimentally as described in [9]. Figure 1 shows

Digital processing of the Mariner 10 images of Venus and Mercury

NASA Technical Reports Server (NTRS)

Soha, J. M.; Lynn, D. J.; Mosher, J. A.; Elliot, D. A.

1977-01-01

An extensive effort was devoted to the digital processing of the Mariner 10 images of Venus and Mercury at the Image Processing Laboratory of the Jet Propulsion Laboratory. This effort was designed to optimize the display of the considerable quantity of information contained in the images. Several image restoration, enhancement, and transformation procedures were applied; examples of these techniques are included. A particular task was the construction of large mosaics which characterize the surface of Mercury and the atmospheric structure of Venus.

Graphene field-effect devices

NASA Astrophysics Data System (ADS)

Echtermeyer, T. J.; Lemme, M. C.; Bolten, J.; Baus, M.; Ramsteiner, M.; Kurz, H.

2007-09-01

In this article, graphene is investigated with respect to its electronic properties when introduced into field effect devices (FED). With the exception of manual graphene deposition, conventional top-down CMOS-compatible processes are applied. Few and monolayer graphene sheets are characterized by scanning electron microscopy, atomic force microscopy and Raman spectroscopy. The electrical properties of monolayer graphene sandwiched between two silicon dioxide films are studied. Carrier mobilities in graphene pseudo-MOS structures are compared to those obtained from double-gated Graphene-FEDs and silicon metal-oxide-semiconductor field-effect-transistors (MOSFETs).

Mass spectrometry in systems biology an introduction.

PubMed

Dunn, Warwick B

2011-01-01

The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of proteins and metabolites. Here, the role of mass spectrometry in systems biology will be assessed, the advantages and disadvantages discussed, and the instrument configurations available described. Finally, general applications will be briefly reviewed. Copyright © 2011 Elsevier Inc. All rights reserved.

Fabrication and Characterization of Three Dimensional Photonic Crystals Generated by Multibeam Interference Lithography

DTIC Science & Technology

2009-01-01

and J. A. Lewis, "Microperiodic structures - Direct writing of three-dimensional webs ," Nature, vol. 428, pp. 386-386, 2004. [9] M. Campbell, D. N...of Applied Physics Part 1-Regular Papers Brief Communications & Review Papers , vol. 44, pp. 6355-6367, 2005. [75] P. Cloetens, W. Ludwig, J... paper screen on the sample holder and marking the beam position. If the central beam is properly aligned, the spot on the screen remains at the

Microscopic Optical Characterization of Free Standing III-Nitride Substrates, ZnO Bulk Crystals, and III-V Structures for Non-Linear Optics

DTIC Science & Technology

2013-03-01

necessary. Therefore, a study of the main defects involved in these materials is essential to the understanding of their main properties and to...working with various strains, growth conditions, temperature variation, and impurities, and studies crystal growth parameters necessary to improve the...Sirtl applied with Light), and the stress distribution around the domain walls. This study shows how to improve the crystal quality of the OP GaAs

Relief diffracted elements recorded on absorbent photopolymers.

PubMed

Gallego, S; Márquez, A; Ortuño, M; Francés, J; Pascual, I; Beléndez, A

2012-05-07

Relief surface changes provide interesting possibilities for storing diffractive optical elements on photopolymers and are an important source of information for characterizing and understanding the material behavior. In this paper we use a 3-dimensional model, based on direct parameter measurements, for predicting the relief structures generated on without-coverplate photopolymers. We have analyzed different spatial frequency and recording intensity distributions such as binary and blazed periodic patterns. This model was successfully applied to different photopolymers with different values of monomer diffusion.

Rigorous Approach in Investigation of Seismic Structure and Source Characteristicsin Northeast Asia: Hierarchical and Trans-dimensional Bayesian Inversion

NASA Astrophysics Data System (ADS)

Mustac, M.; Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.; Ford, S. R.; Sebastian, N.

2015-12-01

Conventional approaches to inverse problems suffer from non-linearity and non-uniqueness in estimations of seismic structures and source properties. Estimated results and associated uncertainties are often biased by applied regularizations and additional constraints, which are commonly introduced to solve such problems. Bayesian methods, however, provide statistically meaningful estimations of models and their uncertainties constrained by data information. In addition, hierarchical and trans-dimensional (trans-D) techniques are inherently implemented in the Bayesian framework to account for involved error statistics and model parameterizations, and, in turn, allow more rigorous estimations of the same. Here, we apply Bayesian methods throughout the entire inference process to estimate seismic structures and source properties in Northeast Asia including east China, the Korean peninsula, and the Japanese islands. Ambient noise analysis is first performed to obtain a base three-dimensional (3-D) heterogeneity model using continuous broadband waveforms from more than 300 stations. As for the tomography of surface wave group and phase velocities in the 5-70 s band, we adopt a hierarchical and trans-D Bayesian inversion method using Voronoi partition. The 3-D heterogeneity model is further improved by joint inversions of teleseismic receiver functions and dispersion data using a newly developed high-efficiency Bayesian technique. The obtained model is subsequently used to prepare 3-D structural Green's functions for the source characterization. A hierarchical Bayesian method for point source inversion using regional complete waveform data is applied to selected events from the region. The seismic structure and source characteristics with rigorously estimated uncertainties from the novel Bayesian methods provide enhanced monitoring and discrimination of seismic events in northeast Asia.

Robust design of mass-uncertain rolling-pendulum TMDs for the seismic protection of buildings

NASA Astrophysics Data System (ADS)

Matta, Emiliano; De Stefano, Alessandro

2009-01-01

Commonly used for mitigating wind- and traffic-induced vibrations in flexible structures, passive tuned mass dampers (TMDs) are rarely applied to the seismic control of buildings, their effectiveness to impulsive loads being conditional upon adoption of large mass ratios. Instead of recurring to cumbersome metal or concrete devices, this paper suggests meeting that condition by turning into TMDs non-structural masses sometimes available atop buildings. An innovative roof-garden TMD, for instance, sounds a promising tool capable of combining environmental and structural protection in one device. Unfortunately, the amount of these masses being generally variable, the resulting mass-uncertain TMD (MUTMD) appears prone to mistuning and control loss. In an attempt to minimize such adverse effects, robust analysis and synthesis against mass variations are applied in this study to MUTMDs of the rolling-pendulum type, a configuration characterized by mass-independent natural period. Through simulations under harmonic and recorded ground motions of increasing intensity, the performance of circular and cycloidal rolling-pendulum MUTMDs is evaluated on an SDOF structure in order to illustrate their respective advantages as well as the drawbacks inherent in their non-linear behavior. A possible implementation of a roof-garden TMD on a real building structure is described and its control efficacy numerically demonstrated, showing that in practical applications MUTMDs can become a good alternative to traditional TMDs.

Thermographic inspection of bond defects in Fiber Reinforced Polymer applied to masonry structures

NASA Astrophysics Data System (ADS)

Masini, N.; Aiello, M. A.; Capozzoli, L.; Vasanelli, E.

2012-04-01

Nowadays, externally bonded Fiber Reinforced Polymers (FRP) are extensively used for strengthening and repairing masonry and reinforced concrete existing structures; they have had a rapid spread in the area of rehabilitation for their many advantages over other conventional repair systems, such as lightweight, excellent corrosion and fatigue resistance, high strength, etc. FRP systems applied to masonry or concrete structures are typically installed using a wet-layup technique.The method is susceptible to cause flaws or defects in the bond between the FRP system and the substrate, which may reduce the effectiveness of the reinforcing systems and the correct transfer of load from the structure to the composite. Thus it is of primary importance to detect the presence of defects and to quantify their extension in order to eventually provide correct repair measurements. The IR thermography has been cited by the several guidelines as a good mean to qualitatively evaluate the presence of installation defects and to monitor the reinforcing system with time.The method is non-destructive and does not require contact with the composite or other means except air to detect the reinforcement. Some works in the literature have been published on this topic. Most of the researches aim at using the IR thermography technique to characterize quantitatively the defects in terms of depth, extension and type in order to have an experimental database on defect typology to evaluate the long term performances of the reinforcing system. Nevertheless, most of the works in the literature concerns with FRP applied to concrete structures without considering the case of masonry structures. In the present research artificial bond defects between FRP and the masonry substrate have been reproduced in laboratory and the IR multi temporal thermography technique has been used to detect them. Thermographic analysis has been carried out on two wall samples having limited dimensions (100 x 70 cm) both with and without plaster, reinforced with basalt and glass fiber strips for full height. Beneath FRP strips were simulated defects such as poor bonding or lack of adherence By statistical and algebraic operations, performed on thermographic multitemporal dataset, an attempt was made both to reduce the uncertainties of a typical IR active and passive test, but also to reconstruct exact geometrical shape of the simulated defects that characterize wall samples examined. Results are encouraging but more research is needed on this topic to establish a correct protocol to monitor the FRP performance with time and to quantitatively asses the presence and type of defect in the reinforcing system.

Responses of bat social groups to roost loss: More questions than answers

USGS Publications Warehouse

Silvis, Alexander; Abaid, Nicole; Ford, W. Mark; Britzke, Eric R.; Ortega, Jorge

2016-01-01

Though characterization of, and understanding determinants of, social structure in bats is increasing, little is known about how bat social groups respond to disturbance resulting in roost loss. Given that many species of bats roost in ephemeral or transitory resources such as plants, it is clear that bat social groups can tolerate some level of roost loss. Understanding responses of bat social groups to roost loss can provide insight into social structure that have applied conservation use. Herein, we review the existing literature on the effects of disturbance on bat social groups, and present a parameterizable agent-based model that can be used to explore the relationships among roost dynamics, population dynamics, and social behavior.

Evolutionary dynamics and the phase structure of the minority game

NASA Astrophysics Data System (ADS)

Yuan, Baosheng; Chen, Kan

2004-06-01

We show that a simple evolutionary scheme, when applied to the minority game (MG), changes the phase structure of the game. In this scheme each agent evolves individually whenever his wealth reaches the specified bankruptcy level, in contrast to the evolutionary schemes used in the previous works. We show that evolution greatly suppresses herding behavior, and it leads to better overall performance of the agents. Similar to the standard nonevolutionary MG, the dependence of the standard deviation σ on the number of agents N and the memory length m can be characterized by a universal curve. We suggest a crowd-anticrowd theory for understanding the effect of evolution in the MG.

Preventing Bacterial Infections using Metal Oxides Nanocoatings on Bone Implant

NASA Astrophysics Data System (ADS)

Duceac, L. D.; Straticiuc, S.; Hanganu, E.; Stafie, L.; Calin, G.; Gavrilescu, S. L.

2017-06-01

Nowadays bone implant removal is caused by infection that occurs around it possibly acquired after surgery or during hospitalization. The purpose of this study was to reveal some metal oxides applied as coatings on bone implant thus limiting the usual antibiotics-resistant bacteria colonization. Therefore ZnO, TiO2 and CuO were synthesized and structurally and morphologically analized in order to use them as an alternative antimicrobial agents deposited on bone implant. XRD, SEM, and FTIR characterization techniques were used to identify structure and texture of these nanoscaled metal oxides. These metal oxides nanocoatings on implant surface play a big role in preventing bacterial infection and reducing surgical complications.

Characterization of the bending stiffness of large space structure joints

NASA Technical Reports Server (NTRS)

Wu, K. Chauncey

1989-01-01

A technique for estimating the bending stiffness of large space structure joints is developed and demonstrated for an erectable joint concept. Experimental load-deflection data from a three-point bending test was used as input to solve a closed-form expression for the joint bending stiffness which was derived from linear beam theory. Potential error sources in both the experimental and analytical procedures are identified and discussed. The bending stiffness of a mechanically preloaded erectable joint is studied at three applied moments and seven joint orientations. Using this technique, the joint bending stiffness was bounded between 6 and 17 percent of the bending stiffness of the graphite/epoxy strut member.

Observations and analysis of self-similar branching topology in glacier networks

USGS Publications Warehouse

Bahr, D.B.; Peckham, S.D.

1996-01-01

Glaciers, like rivers, have a branching structure which can be characterized by topological trees or networks. Probability distributions of various topological quantities in the networks are shown to satisfy the criterion for self-similarity, a symmetry structure which might be used to simplify future models of glacier dynamics. Two analytical methods of describing river networks, Shreve's random topology model and deterministic self-similar trees, are applied to the six glaciers of south central Alaska studied in this analysis. Self-similar trees capture the topological behavior observed for all of the glaciers, and most of the networks are also reasonably approximated by Shreve's theory. Copyright 1996 by the American Geophysical Union.

Towards a minimally invasive sampling tool for high resolution tissue analytical mapping

NASA Astrophysics Data System (ADS)

Gottardi, R.

2015-09-01

Multiple spatial mapping techniques of biological tissues have been proposed over the years, but all present limitations either in terms of resolution, analytical capacity or invasiveness. Ren et al (2015 Nanotechnology 26 284001) propose in their most recent work the use of a picosecond infrared laser (PIRL) under conditions of ultrafast desorption by impulsive vibrational excitation (DIVE) to extract small amounts of cellular and molecular components, conserving their viability, structure and activity. The PIRL DIVE technique would then work as a nanobiopsy with minimal damage to the surrounding tissues, which could potentially be applied for high resolution local structural characterization of tissues in health and disease with the spatial limit determined by the laser focus.

Flexible ligand docking using a genetic algorithm

NASA Astrophysics Data System (ADS)

Oshiro, C. M.; Kuntz, I. D.; Dixon, J. Scott

1995-04-01

Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.

Enhancement of photocurrent in epitaxial lift-off thin-film GaInNAsSb solar cells due to light-confinement structure

NASA Astrophysics Data System (ADS)

Miyashita, Naoya; Behaghel, Benoît; Guillemoles, Jean-François; Okada, Yoshitaka

2018-07-01

This work focuses on the characterization of GaInNAsSb solar cells whose substrates are removed via the epitaxial lift-off (ELO) technique. As a result of the substrate removal, increases in the photocurrent and the interference feature were clearly observed. This is clear evidence of the light-confinement effect, whereby some of the unabsorbed photons at the rear metal contact were reflected back towards the front side of the ELO thin-film cell. We successfully demonstrated that the ELO technique can be applied for the GaInNAsSb cell, and the light management should add flexibility in designing the cell structures.

Development and Ground-Test Validation of Fiber Optic Sensor Attachment Techniques for Hot Structures Applications

NASA Technical Reports Server (NTRS)

Piazza, Anthony; Hudson, Larry D.; Richards, W. Lance

2005-01-01

Fiber Optic Strain Measurements: a) Successfully attached silica fiber optic sensors to both metallics and composites; b) Accomplished valid EFPI strain measurements to 1850 F; c) Successfully attached EFPI sensors to large scale hot-structures; and d) Attached and thermally validated FBG bond and epsilon(sub app). Future Development a) Improve characterization of sensors on C-C and C-SiC substrates; b) Apply application to other composites such as SiC-SiC; c) Assist development of interferometer based Sapphire sensor currently being conducted under a Phase II SBIR; and d) Complete combined thermal/mechanical testing of FBG on composite substrates in controlled laboratory environment.

“Agility” - Complexity Description in a New Dimension applied for Laser Cutting

NASA Astrophysics Data System (ADS)

Bartels, F.; Suess, B.; Wagner, A.; Hauptmann, J.; Wetzig, A.; Beyer, E.

How to describe or to compare the complexity of industrial upcoming part geometries in laser-cutting? This question is essential for defining machine dynamics or kinematic structures for efficient use of the technological cutting-potential which is given by modern beam sources. Solid-state lasers as well as CO2 lasers offer, especially in thin materials, the opportunity of high cutting velocities. Considering the mean velocity on cutting geometries, it is significantly below the technological limitations. The characterization of cutting geometries by means of the agility as well as the application for laser-cutting will be introduced. The identification of efficient dynamic constellations will be shown as basic principle for designing future machine structures.

Accelerated orbits in black hole fields: the static case

NASA Astrophysics Data System (ADS)

Bini, Donato; de Felice, Fernando; Geralico, Andrea

2011-11-01

We study non-geodesic orbits of test particles endowed with a structure, assuming the Schwarzschild spacetime as background. We develop a formalism which allows one to recognize the geometrical characterization of those orbits in terms of their Frenet-Serret parameters and apply it to explicit cases as those of spatially circular orbits which witness the equilibrium under conflicting types of interactions. In our general analysis, we solve the equations of motion offering a detailed picture of the dynamics having in mind a check with a possible astronomical setup. We focus on certain ambiguities which plague the interpretation of the measurements preventing one from identifying the particular structure carried by the particle.

Genomic characterization of EmsB microsatellite loci in Echinococcus multilocularis.

PubMed

Valot, Benoît; Knapp, Jenny; Umhang, Gérald; Grenouillet, Frédéric; Millon, Laurence

2015-06-01

EmsB is a molecular marker applied to Echinococcus multilocularis genotyping studies. This marker has largely been used to investigate the epidemiology of the parasite in different endemic foci. The present study has lifted the veil on the genetic structure of this microsatellite. By in silico analysis on the E. multilocularis genome the microsatellite was described in about 40 copies on the chromosome 5 of the parasite. Similar structure was found in the relative parasite Echinococcus granulosus, where the microsatellite was firstly described. The present study completes the first investigations made on the EmsB microsatellite origins and confirms the reliability of this highly discriminant molecular marker. Copyright © 2015 Elsevier B.V. All rights reserved.

Uniform 2 nm gold nanoparticles supported on iron oxides as active catalysts for CO oxidation reaction: structure-activity relationship

NASA Astrophysics Data System (ADS)

Guo, Yu; Gu, Dong; Jin, Zhao; Du, Pei-Pei; Si, Rui; Tao, Jing; Xu, Wen-Qian; Huang, Yu-Ying; Senanayake, Sanjaya; Song, Qi-Sheng; Jia, Chun-Jiang; Schüth, Ferdi

2015-03-01

Uniform Au nanoparticles (~2 nm) with narrow size-distribution (standard deviation: 0.5-0.6 nm) supported on both hydroxylated (Fe_OH) and dehydrated iron oxide (Fe_O) have been prepared by either deposition-precipitation (DP) or colloidal-deposition (CD) methods. Different structural and textural characterizations were applied to the dried, calcined and used gold-iron oxide samples. Transmission electron microscopy (TEM) and high-resolution TEM (HRTEM) showed high homogeneity in the supported Au nanoparticles. The ex situ and in situ X-ray absorption fine structure (XAFS) characterization monitored the electronic and short-range local structure of active gold species. The synchrotron-based in situ X-ray diffraction (XRD), together with the corresponding temperature-programmed reduction by hydrogen (H2-TPR), indicated a structural evolution of the iron-oxide supports, correlating to their reducibility. An inverse order of catalytic activity between DP (Au/Fe_OH < Au/Fe_O) and CD (Au/Fe_OH > Au/Fe_O) was observed. Effective gold-support interaction results in a high activity for gold nanoparticles, locally generated by the sintering of dispersed Au atoms on the oxide support in the DP synthesis, while a hydroxylated surface favors the reactivity of externally introduced Au nanoparticles on Fe_OH support for the CD approach. This work reveals why differences in the synthetic protocol translate to differences in the catalytic performance of Au/FeOx catalysts with very similar structural characteristics in CO oxidation.

Sequencing of a Patient with Balanced Chromosome Abnormalities and Neurodevelopmental Disease Identifies Disruption of Multiple High Risk Loci by Structural Variation

PubMed Central

Blake, Jonathon; Riddell, Andrew; Theiss, Susanne; Gonzalez, Alexis Perez; Haase, Bettina; Jauch, Anna; Janssen, Johannes W. G.; Ibberson, David; Pavlinic, Dinko; Moog, Ute; Benes, Vladimir; Runz, Heiko

2014-01-01

Balanced chromosome abnormalities (BCAs) occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD) and complex de novo BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (LINC00299, NUP205, PSMD14) that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor ZNF804A as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of ZNF804A in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception. PMID:24625750

Uniform 2 nm gold nanoparticles supported on iron oxides as active catalysts for CO oxidation reaction: Structure-activity relationship

DOE PAGES

Guo, Yu; Senanayake, Sanjaya; Gu, Dong; ...

2015-01-12

Uniform Au nanoparticles (~2 nm) with narrow size-distribution (standard deviation: 0.5–0.6 nm) supported on both hydroxylated (Fe_OH) and dehydrated iron oxide (Fe_O) have been prepared by either deposition-precipitation (DP) or colloidal-deposition (CD) methods. Different structural and textural characterizations were applied to the dried, calcined and used gold-iron oxide samples. The transmission electron microscopy (TEM) and high-resolution TEM (HRTEM) described the high homogeneity in the supported Au nanoparticles. The ex-situ and in-situ X-ray absorption fine structure (XAFS) characterization monitored the electronic and short-range local structure of active gold species. The synchrotron-based in-situ X-ray diffraction (XRD), together with the corresponding temperature-programmed reductionmore » by hydrogen (H₂-TPR), indicated a structural evolution of the iron-oxide supports, correlating to their reducibility. An inverse order of catalytic activity between DP (Au/Fe_OH < Au/Fe_O) and CD (Au/Fe_OH > Au/Fe_O) was observed. Effective gold-support interaction results in a high activity for gold nanoparticles, locally generated by the sintering of dispersed Au atoms on the oxide support in the DP synthesis, while a hydroxylated surface favors the reactivity of externally introduced Au nanoparticles on Fe_OH support for the CD approach. This work reveals why differences in the synthetic protocol translate to differences in the catalytic performance of Au/FeO x catalysts with very similar structural characteristics in CO oxidation.« less

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

PubMed

Parker, Brian J; Moltke, Ida; Roth, Adam; Washietl, Stefan; Wen, Jiayu; Kellis, Manolis; Breaker, Ronald; Pedersen, Jakob Skou

2011-11-01

Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. We have developed a comparative method, EvoFam, for genome-wide identification of families of regulatory RNA structures, based on primary sequence and secondary structure similarity. We apply EvoFam to a 41-way genomic vertebrate alignment. Genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural RNA elements. Known families identified include both noncoding RNAs, e.g., miRNAs and the recently identified MALAT1/MEN β lincRNA family; and cis-regulatory structures, e.g., iron-responsive elements. We also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as GO term enrichments. For some of these, detailed analysis has led to the formulation of specific functional hypotheses. Examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3'-UTR of MAT2A, a key metabolic gene that produces the primary human methyl donor S-adenosylmethionine; the other involving a tRNA-like structure in the intron of the tRNA maturation gene POP1. We experimentally validate the predicted MAT2A structures. Finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF, FOS, and CTLA4, which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding RNAs.

Determination of the pathological state of skin samples by optical polarimetry parameters

NASA Astrophysics Data System (ADS)

Fanjul-Vélez, F.; Ortega-Quijano, N.; Buelta, L.; Arce-Diego, J. L.

2008-11-01

Polarimetry is widely known to involve a series of powerful optical techniques that characterize the polarization behaviour of a sample. In this work, we propose a method for applying polarimetric procedures to the characterization of biological tissues, in order to differentiate between healthy and pathologic tissues on a polarimetric basis. Usually, medical morphology diseases are diagnosed based on histological alterations of the tissue. The fact that these alterations will be reflected in polarization information highlights the suitability of polarimetric procedures for diagnostic purposes. The analysis is mainly focused on the depolarization properties of the media, as long as the internal structure strongly affects the polarization state of the light that interacts with the sample. Therefore, a method is developed in order to determine the correlation between pathological ultraestructural characteristics and the subsequent variations in the polarimetric parameters of the backscattered light. This study is applied to three samples of porcine skin corresponding to a healthy region, a mole, and a cancerous region. The results show that the method proposed is indeed an adequate technique in order to achieve an early, accurate and effective cancer detection.

Characterization of a single-isomer carboxymethyl-beta-cyclodextrin in chiral capillary electrophoresis.

PubMed

Fejős, Ida; Varga, Erzsébet; Benkovics, Gábor; Malanga, Milo; Sohajda, Tamás; Szemán, Julianna; Béni, Szabolcs

2017-08-01

In this work, the synthesis, characterization, and chiral capillary electrophoretic study of heptakis-(2,3-di-O-methyl-6-O-carboxymethyl)-β-CD (HDMCM), a single-isomer carboxymethylated CD, are presented. The pH-dependent and selector concentration-dependent enantiorecognition properties of HDMCM were investigated and discussed herein. The enantioseparation was assessed applying a structurally diverse set of noncharged, basic, and zwitterionic racemates. The increase in the selector concentration and gross negative charge of HDMCM improved the enantioseparation that could be observed in the majority of the cases. HDMCM was also successfully applied as BGE additive in NACE using a methanol-based system in order to prove the separation selectivity features and to highlight the broad applicability of HDMCM. Over 25 racemates showed partial or baseline separation with HDMCM under the conditions investigated, among which optimal enantiomer migration order was found for the four stereoisomers of tadalafil, tapentadol, and dapoxetine, offering the possibility of a chiral CE method development for chiral purity profiling of these drugs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing the Complexities of Structural Changes in Layered Oxide Cathode Materials for Li-Ion Batteries during Fast Charge-Discharge Cycling and Heating.

PubMed

Hu, Enyuan; Wang, Xuelong; Yu, Xiqian; Yang, Xiao-Qing

2018-02-20

The rechargeable lithium-ion battery (LIB) is the most promising energy storage system to power electric vehicles with high energy density and long cycling life. However, in order to meet customers' demands for fast charging, the power performances of current LIBs need to be improved. From the cathode aspect, layer-structured cathode materials are widely used in today's market and will continue to play important roles in the near future. The high rate capability of layered cathode materials during charging and discharging is critical to the power performance of the whole cell and the thermal stability is closely related to the safety issues. Therefore, the in-depth understanding of structural changes of layered cathode materials during high rate charging/discharging and the thermal stability during heating are essential in developing new materials and improving current materials. Since structural changes take place from the atomic level to the whole electrode level, combination of characterization techniques covering multilength scales is quite important. In many cases, this means using comprehensive tools involving diffraction, spectroscopy, and imaging to differentiate the surface from the bulk and to obtain structural/chemical information with different levels of spatial resolution. For example, hard X-ray spectroscopy can yield the bulk information and soft X-ray spectroscopy can give the surface information; X-ray based imaging techniques can obtain spatial resolution of tens of nanometers, and electron-based microcopy can go to angstroms. In addition to challenges associated with different spatial resolution, the dynamic nature of structural changes during high rate cycling and heating requires characterization tools to have the capability of collecting high quality data in a time-resolved fashion. Thanks to the advancement in synchrotron based techniques and high-resolution electron microscopy, high temporal and spatial resolutions can now be achieved. In this Account, we focus on the recent works studying kinetic and thermal properties of layer-structured cathode materials, especially the structural changes during high rate cycling and the thermal stability during heating. Advanced characterization techniques relating to the rate capability and thermal stability will be introduced. The different structure evolution behavior of cathode materials cycled at high rate will be compared with that cycled at low rate. Different response of individual transition metals and the inhomogeneity in chemical distribution will be discussed. For the thermal stability, the relationship between structural changes and oxygen release will be emphatically pointed out. In all these studies being reviewed, advanced characterization techniques are critically applied to reveal complexities at multiscale in layer-structured cathode materials.

Redox properties of structural Fe in clay minerals: 3. Relationships between smectite redox and structural properties.

PubMed

Gorski, Christopher A; Klüpfel, Laura E; Voegelin, Andreas; Sander, Michael; Hofstetter, Thomas B

2013-01-01

Structural Fe in clay minerals is an important redox-active species in many pristine and contaminated environments as well as in engineered systems. Understanding the extent and kinetics of redox reactions involving Fe-bearing clay minerals has been challenging due to the inability to relate structural Fe(2+)/Fe(total) fractions to fundamental redox properties, such as reduction potentials (EH). Here, we overcame this challenge by using mediated electrochemical reduction (MER) and oxidation (MEO) to characterize the fraction of redox-active structural Fe (Fe(2+)/Fe(total)) in smectites over a wide range of applied EH-values (-0.6 V to +0.6 V). We examined Fe(2+)/Fe(total )- EH relationships of four natural Fe-bearing smectites (SWy-2, SWa-1, NAu-1, NAu-2) in their native, reduced, and reoxidized states and compared our measurements with spectroscopic observations and a suite of mineralogical properties. All smectites exhibited unique Fe(2+)/Fe(total) - EH relationships, were redox active over wide EH ranges, and underwent irreversible electron transfer induced structural changes that were observable with X-ray absorption spectroscopy. Variations among the smectite Fe(2+)/Fe(total) - EH relationships correlated well with both bulk and molecular-scale properties, including Fe(total) content, layer charge, and quadrupole splitting values, suggesting that multiple structural parameters determined the redox properties of smectites. The Fe(2+)/Fe(total) - EH relationships developed for these four commonly studied clay minerals may be applied to future studies interested in relating the extent of structural Fe reduction or oxidation to EH-values.

A fluid–structure interaction model to characterize bone cell stimulation in parallel-plate flow chamber systems

PubMed Central

Vaughan, T. J.; Haugh, M. G.; McNamara, L. M.

2013-01-01

Bone continuously adapts its internal structure to accommodate the functional demands of its mechanical environment and strain-induced flow of interstitial fluid is believed to be the primary mediator of mechanical stimuli to bone cells in vivo. In vitro investigations have shown that bone cells produce important biochemical signals in response to fluid flow applied using parallel-plate flow chamber (PPFC) systems. However, the exact mechanical stimulus experienced by the cells within these systems remains unclear. To fully understand this behaviour represents a most challenging multi-physics problem involving the interaction between deformable cellular structures and adjacent fluid flows. In this study, we use a fluid–structure interaction computational approach to investigate the nature of the mechanical stimulus being applied to a single osteoblast cell under fluid flow within a PPFC system. The analysis decouples the contribution of pressure and shear stress on cellular deformation and for the first time highlights that cell strain under flow is dominated by the pressure in the PPFC system rather than the applied shear stress. Furthermore, it was found that strains imparted on the cell membrane were relatively low whereas significant strain amplification occurred at the cell–substrate interface. These results suggest that strain transfer through focal attachments at the base of the cell are the primary mediators of mechanical signals to the cell under flow in a PPFC system. Such information is vital in order to correctly interpret biological responses of bone cells under in vitro stimulation and elucidate the mechanisms associated with mechanotransduction in vivo. PMID:23365189

Characterization of physalins and fingerprint analysis for the quality evaluation of Physalis alkekengi L. var. franchetii by ultra-performance liquid chromatography combined with diode array detection and electrospray ionization tandem mass spectrometry.

PubMed

Zheng, Yunliang; Luan, Lianjun; Chen, Yong; Ren, Yiping; Wu, Yongjiang

2012-12-01

Physalins are important bioactive compounds from genus Physalis. They often occur as isomers, which makes the structural elucidation difficult. In the present study, the fragmentation behavior and UV characteristics of seven physalins from genus Physalis were firstly investigated using electrospray ionization tandem mass spectrometry (ESI-MS/MS) and diode array detection (DAD). Combined with ultra-performance liquid chromatography (UPLC) and DAD, the established approach to the structural identification of physalins by ESI-MS/MS was then applied to the analysis of Physalis alkekengi L. According to the UPLC retention behavior, the diagnostic UV spectra and the molecular structural information provided by MS/MS spectra, about 19 fingerprint peaks were identified, including 14 physalins and 5 other compounds. Finally, the established fingerprint method was applied to the analysis of 31 P. alkekengi L. samples collected from different locations, which reflected their similar chemical constituent properties. The proposed method provides a scientific and technical platform to the herbal industry for quality control and safety assurance of herbal preparations that contain this class of physalins. Copyright © 2012 Elsevier B.V. All rights reserved.

On the consistency of QCBED structure factor measurements for TiO 2 (Rutile)

DOE PAGES

Jiang, Bin; Zuo, Jian -Min; Friis, Jesper; ...

2003-09-16

The same Bragg reflection in TiO 2 from twelve different CBED patterns (from different crystals, orientations and thicknesses) are analysed quantitatively in order to evaluate the consistency of the QCBED method for bond-charge mapping. The standard deviation in the resulting distribution of derived X-ray structure factors is found to be an order of magnitude smaller than that in conventional X-ray work, and the standard error (0.026% for F X(110)) is slightly better than obtained by the X-ray Pendellosung method applied to silicon. This is sufficiently accuracy to distinguish between atomic, covalent and ionic models of bonding. We describe the importancemore » of extracting experimental parameters from CCD camera characterization, and of surface oxidation and crystal shape. Thus, the current experiments show that the QCBED method is now a robust and powerful tool for low order structure factor measurement, which does not suffer from the large extinction (multiple scattering) errors which occur in inorganic X-ray crystallography, and may be applied to nanocrystals. Our results will be used to understand the role of d electrons in the chemical bonding of TiO 2.« less

Characterization of Nanocrystalline Nickel-Cobalt Alloys Synthesized by Direct and Pulse Electrodeposition

NASA Astrophysics Data System (ADS)

Salehi, M.; Saidi, A.; Ahmadian, M.; Raeissi, K.

2014-01-01

Nanocrystalline Ni-Co alloys are electrodeposited by direct (DC) and pulse current (PC) in an electrolyte solution which consisted of nickel sulfate, cobalt sulfate and boric acid. Electrodeposition parameters including current density, electrolyte pH and pulse times in a single electrolyte bath were changed. XRD pattern showed that the structure of the alloys depends on Co content and the synthesis parameter and changed from single phase structure (fcc) to dual phase structure (fcc + hcp). The Co content in the deposited alloys declined from 70 at.% to 50 at.% by increasing in direct current from 70 mA/cm2 to 115 mA/cm2 and also decreased from 75 at.% to 33 at.% with decrease in pH values from 4 to 2. By applying PC the Co content changed from 76 at.% to 41 at.%. Magnetic properties measurements showed the saturation magnetization (Ms) increased with increasing the Co content. There was no significant effect on coercivity values (Hc) with change in Co content and about 40 Oe was obtained for all samples. The grain size of deposited alloys obtained between 24-58 nm and 15-21 nm by applying DC and PC, respectively.

Zn-Mn alloy coatings from acidic chloride bath: Effect of deposition conditions on the Zn-Mn electrodeposition-morphological and structural characterization

NASA Astrophysics Data System (ADS)

Loukil, N.; Feki, M.

2017-07-01

Zn-Mn alloy electrodeposition on steel electrode in chloride bath was investigated using cyclic voltammetric, chronopotentiometric and chronoamperometric techniques. Cyclic voltammetries (CV) reveal a deep understanding of electrochemical behaviors of each metal Zn, Mn, proton discharge and Zn-Mn co-deposition. The electrochemical results show that with increasing Mn2+ ions concentration in the electrolytic bath, Mn2+ reduction occurs at lower over-potential leading to an enhancement of Mn content into the Zn-Mn deposits. A dimensionless graph model was used to analyze the effect of Mn2+ ions concentration on Zn-Mn nucleation process. It was found that the nucleation process is not extremely affected by Mn2+ concentration. Nevertheless, it significantly depends on the applied potential. Several parameters such as Mn2+ ions concentration, current density and stirring were investigated with regard to the Mn content into the final Zn-Mn coatings. It was found that the Mn content increases with increasing the applied current density jimp and Mn2+ ions concentration in the electrolytic bath. However, stirring of the solution decreases the Mn content in the Zn-Mn coatings. The phase structure and surface morphology of Zn-Mn deposits are characterized by means of X-ray diffraction analysis and Scanning Electron Microscopy (SEM), respectively. The Zn-Mn deposited at low current density is tri-phasic and consisting of η-Zn, ζ-MnZn13 and hexagonal close packed ε-Zn-Mn. An increase in current density leads to a transition from crystalline to amorphous structure, arising from the hydroxide inclusions in the Zn-Mn coating at high current density.

A single molecule study of G-quadruplex and short duplex DNA structures

NASA Astrophysics Data System (ADS)

Roy, William A., Jr.

Given that certain conditions are met, a single stranded DNA/RNA (ssDNA/RNA) structure called G-quadruplex (GQ) can form in regions throughout the genome, including at the telomeres and internal regions of the chromosomes. These structures serve various functions depending on the region in which they form which include protecting the chromosome ends, interfering with telomere elongation in cancer cells, and regulating transcription and translation level gene expression. Due to their high stability, various cellular mechanisms, such as GQ destabilizing proteins, are employed to unfold these structures during DNA replication or repair. Yet, their distinct layered structure has made GQs an attractive drug target in cancer treatment as GQ stabilizing molecules could inhibit telomerase dependent telomere elongation, a mechanism occurring in the majority of cancer cells to avoid senescence and apoptosis. However, proteins or small molecules interact with GQ that is under the influence of various cellular tension mechanisms, including the tension applied by other nearby molecules or the tension due to DNA structure within the chromatin context. Therefore, it is important to characterize the stability of various GQs and their response to interacting molecules when subjected to a tensile force. We employed a novel DNA-based nano tension generator that utilizes the elastic properties of circularized short double-stranded DNA (dsDNA) oligonucleotides to apply tension on the GQ. Since this is a completely new approach, the majority of this thesis was dedicated to proof-of-principle studies that demonstrated the feasibility and functionality of the method.

Development of a method for urine bikunin/urinary trypsin inhibitor (UTI) quantitation and structural characterization: Application to type 1 and type 2 diabetes.

PubMed

Lepedda, Antonio Junior; Nieddu, Gabriele; Rocchiccioli, Silvia; Fresu, Pietro; De Muro, Pierina; Formato, Marilena

2013-12-01

Bikunin is a plasma proteinase inhibitor often associated with inflammatory conditions. It has a half-life of few minutes and it is rapidly excreted into urine as urinary trypsin inhibitor (UTI). UTI levels are usually low in healthy individuals but they can increase up to tenfold in both acute and chronic inflammatory diseases. This article describes a sensitive method for both direct UTI quantitation and structural characterization. UTI purification was performed by anion exchange micro-chromatography followed by SDS-PAGE. A calibration curve for protein quantitation was set up by using a purified UTI fraction. UTI identification and structural characterization was performed by Nano-LC-MS/MS analysis. The method was applied on urine samples from 9 patients with type 1 diabetes, 11 patients with type 2 diabetes, and 28 healthy controls, matched for age and sex with patients, evidencing higher UTI levels in both groups of patients with respect to controls (p < 0.001 and p = 0.001, respectively). Spearman's correlation tests highlighted no association between UTI levels and age in each group tested. Owing to the elevated sensitivity and specificity, the described method allows UTI quantitation from very low quantities of specimen. Furthermore, as UTI concentration is normalized for creatinine level, the analysis could be also performed on randomly collected urine samples. Finally, MS/MS analysis prospects the possibility of characterizing PTM sites potentially able to affect UTI localization, function, and pathophysiological activity. Preliminary results suggest that UTI levels could represent a useful marker of chronic inflammatory condition in type 1 and 2 diabetes. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and Characterization of Monodisperse Core-shell Lanthanide Upconversion Nanoparticles NaYF4: Yb,Tm/SiO2

NASA Astrophysics Data System (ADS)

Manurung, R. V.; Wiranto, G.; Hermida, I. D. P.

2018-05-01

Lanthanide up-converting luminescent nanoparticles (UCNPs) are exciting and promising materials for optical bioimaging, biosensor and theranostic due to their unique and advantageous optical and chemical properties. The UCNPs absorb low energy near-infrared (NIR) light and emit high-energy shorter wavelength photons (visible light). Their unique features allow them to overcome various problems associated with conventional imaging probes such as photostability, lack of toxicity, and to provide versatility for creating nanoplatforms with both imaging and therapeutic modalities. This paper reports synthesis and characterization of core-shell structured of NaYF4:Yb,Tm/SiO2 microspheres. The synthesis of lanthanide upconversion nanoparticles NaYF4:Yb,Tm was prepared by thermal decomposition process which involves dissolving organic precursors in high-boiling-point solvents oleic acid (OA) and octadecene (ODE). After that, the NaYF4:Yb,Tm phosphors was coated by silica via reverse microemulsion process to obtain core-shell structured NaYF4:Yb,Tm/SiO2. Scanning electron microscopy, transmission electron microscopy, specific area electron diffraction, and photoluminescence were applied to characterize these samples. The obtained core-shell structured NaYF4:Yb,Tm/SiO2 phosphors exhibit a perfect cubic morphology with narrow size distribution and smooth surface. Upon IR excitation at 980 nm, the NaYF4:Yb,Tm/SiO2 samples exhibit whitish blue upconversion (UC) luminescence, respectively. These phosphors show potential applications in the displaying on biological fields and biosensing.

Orbitrap mass spectrometry characterization of hybrid chondroitin/dermatan sulfate hexasaccharide domains expressed in brain.

PubMed

Robu, Adrian C; Popescu, Laurentiu; Munteanu, Cristian V A; Seidler, Daniela G; Zamfir, Alina D

2015-09-15

In the central nervous system, chondroitin/dermatan sulfate (CS/DS) glycosaminoglycans (GAGs) modulate neurotrophic effects and glial cell maturation during brain development. Previous reports revealed that GAG composition could be responsible for CS/DS activities in brain. In this work, for the structural characterization of DS- and CS-rich domains in hybrid GAG chains extracted from neural tissue, we have developed an advanced approach based on high-resolution mass spectrometry (MS) using nanoelectrospray ionization Orbitrap in the negative ion mode. Our high-resolution MS and multistage MS approach was developed and applied to hexasaccharides obtained from 4- and 14-week-old mouse brains by GAG digestion with chondroitin B and in parallel with AC I lyase. The expression of DS- and CS-rich domains in the two tissues was assessed comparatively. The analyses indicated an age-related structural variability of the CS/DS motifs. The older brain was found to contain more structures and a higher sulfation of DS-rich regions, whereas the younger brain was found to be characterized by a higher sulfation of CS-rich regions. By multistage MS using collision-induced dissociation, we also demonstrated the incidence in mouse brain of an atypical [4,5-Δ-GlcAGalNAc(IdoAGalNAc)2], presenting a bisulfated CS disaccharide formed by 3-O-sulfate-4,5-Δ-GlcA and 6-O-sulfate-GalNAc moieties. Copyright © 2015 Elsevier Inc. All rights reserved.

Dimensionless, Scale Invariant, Edge Weight Metric for the Study of Complex Structural Networks

PubMed Central

Colon-Perez, Luis M.; Spindler, Caitlin; Goicochea, Shelby; Triplett, William; Parekh, Mansi; Montie, Eric; Carney, Paul R.; Price, Catherine; Mareci, Thomas H.

2015-01-01

High spatial and angular resolution diffusion weighted imaging (DWI) with network analysis provides a unique framework for the study of brain structure in vivo. DWI-derived brain connectivity patterns are best characterized with graph theory using an edge weight to quantify the strength of white matter connections between gray matter nodes. Here a dimensionless, scale-invariant edge weight is introduced to measure node connectivity. This edge weight metric provides reasonable and consistent values over any size scale (e.g. rodents to humans) used to quantify the strength of connection. Firstly, simulations were used to assess the effects of tractography seed point density and random errors in the estimated fiber orientations; with sufficient signal-to-noise ratio (SNR), edge weight estimates improve as the seed density increases. Secondly to evaluate the application of the edge weight in the human brain, ten repeated measures of DWI in the same healthy human subject were analyzed. Mean edge weight values within the cingulum and corpus callosum were consistent and showed low variability. Thirdly, using excised rat brains to study the effects of spatial resolution, the weight of edges connecting major structures in the temporal lobe were used to characterize connectivity in this local network. The results indicate that with adequate resolution and SNR, connections between network nodes are characterized well by this edge weight metric. Therefore this new dimensionless, scale-invariant edge weight metric provides a robust measure of network connectivity that can be applied in any size regime. PMID:26173147

Dimensionless, Scale Invariant, Edge Weight Metric for the Study of Complex Structural Networks.

PubMed

Colon-Perez, Luis M; Spindler, Caitlin; Goicochea, Shelby; Triplett, William; Parekh, Mansi; Montie, Eric; Carney, Paul R; Price, Catherine; Mareci, Thomas H

2015-01-01

High spatial and angular resolution diffusion weighted imaging (DWI) with network analysis provides a unique framework for the study of brain structure in vivo. DWI-derived brain connectivity patterns are best characterized with graph theory using an edge weight to quantify the strength of white matter connections between gray matter nodes. Here a dimensionless, scale-invariant edge weight is introduced to measure node connectivity. This edge weight metric provides reasonable and consistent values over any size scale (e.g. rodents to humans) used to quantify the strength of connection. Firstly, simulations were used to assess the effects of tractography seed point density and random errors in the estimated fiber orientations; with sufficient signal-to-noise ratio (SNR), edge weight estimates improve as the seed density increases. Secondly to evaluate the application of the edge weight in the human brain, ten repeated measures of DWI in the same healthy human subject were analyzed. Mean edge weight values within the cingulum and corpus callosum were consistent and showed low variability. Thirdly, using excised rat brains to study the effects of spatial resolution, the weight of edges connecting major structures in the temporal lobe were used to characterize connectivity in this local network. The results indicate that with adequate resolution and SNR, connections between network nodes are characterized well by this edge weight metric. Therefore this new dimensionless, scale-invariant edge weight metric provides a robust measure of network connectivity that can be applied in any size regime.

Quantifying Standing Dead Tree Volume and Structural Loss with Voxelized Terrestrial Lidar Data

NASA Astrophysics Data System (ADS)

Popescu, S. C.; Putman, E.

2017-12-01

Standing dead trees (SDTs) are an important forest component and impact a variety of ecosystem processes, yet the carbon pool dynamics of SDTs are poorly constrained in terrestrial carbon cycling models. The ability to model wood decay and carbon cycling in relation to detectable changes in tree structure and volume over time would greatly improve such models. The overall objective of this study was to provide automated aboveground volume estimates of SDTs and automated procedures to detect, quantify, and characterize structural losses over time with terrestrial lidar data. The specific objectives of this study were: 1) develop an automated SDT volume estimation algorithm providing accurate volume estimates for trees scanned in dense forests; 2) develop an automated change detection methodology to accurately detect and quantify SDT structural loss between subsequent terrestrial lidar observations; and 3) characterize the structural loss rates of pine and oak SDTs in southeastern Texas. A voxel-based volume estimation algorithm, "TreeVolX", was developed and incorporates several methods designed to robustly process point clouds of varying quality levels. The algorithm operates on horizontal voxel slices by segmenting the slice into distinct branch or stem sections then applying an adaptive contour interpolation and interior filling process to create solid reconstructed tree models (RTMs). TreeVolX estimated large and small branch volume with an RMSE of 7.3% and 13.8%, respectively. A voxel-based change detection methodology was developed to accurately detect and quantify structural losses and incorporated several methods to mitigate the challenges presented by shifting tree and branch positions as SDT decay progresses. The volume and structural loss of 29 SDTs, composed of Pinus taeda and Quercus stellata, were successfully estimated using multitemporal terrestrial lidar observations over elapsed times ranging from 71 - 753 days. Pine and oak structural loss rates were characterized by estimating the amount of volumetric loss occurring in 20 equal-interval height bins of each SDT. Results showed that large pine snags exhibited more rapid structural loss in comparison to medium-sized oak snags in this study.

The ARTT motif and a unified structural understanding of substraterecognition in ADP ribosylating bacterial toxins and eukaryotic ADPribosyltransferases

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

Han, S.; Tainer, J.A.

2001-08-01

ADP-ribosylation is a widely occurring and biologically critical covalent chemical modification process in pathogenic mechanisms, intracellular signaling systems, DNA repair, and cell division. The reaction is catalyzed by ADP-ribosyltransferases, which transfer the ADP-ribose moiety of NAD to a target protein with nicotinamide release. A family of bacterial toxins and eukaryotic enzymes has been termed the mono-ADP-ribosyltransferases, in distinction to the poly-ADP-ribosyltransferases, which catalyze the addition of multiple ADP-ribose groups to the carboxyl terminus of eukaryotic nucleoproteins. Despite the limited primary sequence homology among the different ADP-ribosyltransferases, a central cleft bearing NAD-binding pocket formed by the two perpendicular b-sheet core hasmore » been remarkably conserved between bacterial toxins and eukaryotic mono- and poly-ADP-ribosyltransferases. The majority of bacterial toxins and eukaryotic mono-ADP-ribosyltransferases are characterized by conserved His and catalytic Glu residues. In contrast, Diphtheria toxin, Pseudomonas exotoxin A, and eukaryotic poly-ADP-ribosyltransferases are characterized by conserved Arg and catalytic Glu residues. The NAD-binding core of a binary toxin and a C3-like toxin family identified an ARTT motif (ADP-ribosylating turn-turn motif) that is implicated in substrate specificity and recognition by structural and mutagenic studies. Here we apply structure-based sequence alignment and comparative structural analyses of all known structures of ADP-ribosyltransfeases to suggest that this ARTT motif is functionally important in many ADP-ribosylating enzymes that bear a NAD binding cleft as characterized by conserved Arg and catalytic Glu residues. Overall, structure-based sequence analysis reveals common core structures and conserved active sites of ADP-ribosyltransferases to support similar NAD binding mechanisms but differing mechanisms of target protein binding via sequence variations within the ARTT motif structural framework. Thus, we propose here that the ARTT motif represents an experimentally testable general recognition motif region for many ADP-ribosyltransferases and thereby potentially provides a unified structural understanding of substrate recognition in ADP-ribosylation processes.« less

Structural Assembly of Multidomain Proteins and Protein Complexes Guided by the Overall Rotational Diffusion Tensor

PubMed Central

Ryabov, Yaroslav; Fushman, David

2008-01-01

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein’s rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning is also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of Lys48-linked di-ubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution. PMID:17550252

Three-Dimensional Bayesian Geostatistical Aquifer Characterization at the Hanford 300 Area using Tracer Test Data

NASA Astrophysics Data System (ADS)

Chen, X.; Murakami, H.; Hahn, M. S.; Hammond, G. E.; Rockhold, M. L.; Rubin, Y.

2010-12-01

Tracer testing under natural or forced gradient flow provides useful information for characterizing subsurface properties, by monitoring and modeling the tracer plume migration in a heterogeneous aquifer. At the Hanford 300 Area, non-reactive tracer experiments, in addition to constant-rate injection tests and electromagnetic borehole flowmeter (EBF) profiling, were conducted to characterize the heterogeneous hydraulic conductivity field. A Bayesian data assimilation technique, method of anchored distributions (MAD), is applied to assimilate the experimental tracer test data and to infer the three-dimensional heterogeneous structure of the hydraulic conductivity in the saturated zone of the Hanford formation. In this study, the prior information of the underlying random hydraulic conductivity field was obtained from previous field characterization efforts using the constant-rate injection tests and the EBF data. The posterior distribution of the random field is obtained by further conditioning the field on the temporal moments of tracer breakthrough curves at various observation wells. The parallel three-dimensional flow and transport code PFLOTRAN is implemented to cope with the highly transient flow boundary conditions at the site and to meet the computational demand of the proposed method. The validation results show that the field conditioned on the tracer test data better reproduces the tracer transport behavior compared to the field characterized previously without the tracer test data. A synthetic study proves that the proposed method can effectively assimilate tracer test data to capture the essential spatial heterogeneity of the three-dimensional hydraulic conductivity field. These characterization results will improve conceptual models developed for the site, including reactive transport models. The study successfully demonstrates the capability of MAD to assimilate multi-scale multi-type field data within a consistent Bayesian framework. The MAD framework can potentially be applied to combine geophysical data with other types of data in site characterization.

Transient rheology of stimuli responsive hydrogels: Integrating microrheology and microfluidics

NASA Astrophysics Data System (ADS)

Sato, Jun

Stimuli-responsive hydrogels have diverse potential applications in the field of drug delivery, tissue engineering, agriculture, cosmetics, gene therapy, and as sensors and actuators due to their unique responsiveness to external signals, such as pH, temperature, and ionic strength. Understanding the responsiveness of hydrogel structure and rheology to these stimuli is essential for designing materials with desirable performance. However, no instrumentation and well-defined methodology are available to characterize the structural and rheological responses to rapid solvent changes. In this thesis, a new microrheology set-up is described, which allows us to quantitatively measure the transient rheological properties and microstructure of a variety of solvent-responsive complex fluids. The device was constructed by integrating particle tracking microrheology and microfluidics and offers unique experimental capabilities for performing solvent-reponse measurements on soft fragile materials without applying external shear forces. Transient analysis methods to quantitatively obtain rheological properties were also constructed, and guidelines for the trade-off between statistical validity and temporal resolution were developed to accurately capture physical transitions. Employing the new device and methodology, we successfully quantified the transient rheological and microstructural responses during gel formation and break-up, and viscosity changes of solvent-responsive complex fluids. The analysis method was expanded for heterogeneous samples, incorporating methods to quantify the microrheology of samples with broad distributions of individual particle dynamics. Transient microrheology measurements of fragile, heterogeneous, self-assembled block copolypeptide hydrogels revealed that solvent exchange via convective mixing and dialysis can lead to significantly different gel properties and that commonly applied sample preparation protocols for the characterization of soft biomaterials could lead to erroneous conclusions about microstructural dynamics. Systematic investigations by varying key parameters, like molecular structure, gel concentration, salt concentration, and tracer particle size for microrheology, revealed that subtle variations in molecular architecture can cause major changes in response dynamics. Moreover, the results showed that the method can be applied for studying gel formation and breakup kinetics. The research in this thesis facilitates the design of solvent-responsive soft materials with appropriate microstructural dynamics for in vivo applications like tissue engineering and drug delivery, and can also be applied to study the effect of solvents on self-assembly mechanisms in other responsive soft materials, such as polymer solutions and colloidal dispersions.

Predicted facies, sedimentary structures and potential resources of Jurassic petroleum complex in S-E sWestern Siberia (based on well logging data)

NASA Astrophysics Data System (ADS)

Prakojo, F.; Lobova, G.; Abramova, R.

2015-11-01

This paper is devoted to the current problem in petroleum geology and geophysics- prediction of facies sediments for further evaluation of productive layers. Applying the acoustic method and the characterizing sedimentary structure for each coastal-marine-delta type was determined. The summary of sedimentary structure characteristics and reservoir properties (porosity and permeability) of typical facies were described. Logging models SP, EL and GR (configuration, curve range) in interpreting geophysical data for each litho-facies were identified. According to geophysical characteristics these sediments can be classified as coastal-marine-delta. Prediction models for potential Jurassic oil-gas bearing complexes (horizon J11) in one S-E Western Siberian deposit were conducted. Comparing forecasting to actual testing data of layer J11 showed that the prediction is about 85%.

Elucidating the alkaline oxygen evolution reaction mechanism on platinum

DOE PAGES

Favaro, M.; Valero-Vidal, C.; Eichhorn, J.; ...

2017-03-07

Understanding the interplay between surface chemistry, electronic structure, and reaction mechanism of the catalyst at the electrified solid/liquid interface will enable the design of more efficient materials systems for sustainable energy production. The substantial progress in operando characterization, particularly using synchrotron based X-ray spectroscopies, provides the unprecedented opportunity to uncover surface chemical and structural transformations under various (electro)chemical reaction environments. In this work, we study a polycrystalline platinum surface under oxygen evolution conditions in an alkaline electrolyte by means of ambient pressure X-ray photoelectron spectroscopy performed at the electrified solid/liquid interface. We elucidate previously inaccessible aspects of the surface chemistrymore » and structure as a function of the applied potential, allowing us to propose a reaction mechanism for oxygen evolution on a platinum electrode in alkaline solutions.« less

Nanoscale measurements of unoccupied band dispersion in few-layer graphene

PubMed Central

Jobst, Johannes; Kautz, Jaap; Geelen, Daniël; Tromp, Rudolf M.; van der Molen, Sense Jan

2015-01-01

The properties of any material are fundamentally determined by its electronic band structure. Each band represents a series of allowed states inside a material, relating electron energy and momentum. The occupied bands, that is, the filled electron states below the Fermi level, can be routinely measured. However, it is remarkably difficult to characterize the empty part of the band structure experimentally. Here, we present direct measurements of unoccupied bands of monolayer, bilayer and trilayer graphene. To obtain these, we introduce a technique based on low-energy electron microscopy. It relies on the dependence of the electron reflectivity on incidence angle and energy and has a spatial resolution ∼10 nm. The method can be easily applied to other nanomaterials such as van der Waals structures that are available in small crystals only. PMID:26608712

Study Acoustic Emissions from Composites

NASA Technical Reports Server (NTRS)

Walker, James L.; Workman, Gary L.

1997-01-01

The nondestructive evaluation (NDE) of future propulsion systems utilizing advanced composite structures for the storage of cryogenic fuels, such as liquid hydrogen or oxygen, presents many challenges. Economic justification for these structures requires, light weight, reusable components with an infrastructure allowing periodic evaluation of structural integrity after enduring demanding stresses during operation. A major focus has been placed on the use of acoustic emission NDE to detect propagating defects, in service, necessitating an extensive study into characterizing the nature of acoustic signal propagation at very low temperatures and developing the methodology of applying AE sensors to monitor cryogenic components. This work addresses the question of sensor performance in the cryogenic environment. Problems involving sensor mounting, spectral response and durability are addressed. The results of this work provides a common point of measure from which sensor selection can be made when testing composite components at cryogenic temperatures.

Discovering Network Structure Beyond Communities

NASA Astrophysics Data System (ADS)

Nishikawa, Takashi; Motter, Adilson E.

2011-11-01

To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.

Enhanced magnetostriction derived from magnetic single domain structures in cluster-assembled SmCo films

NASA Astrophysics Data System (ADS)

Bai, Yulong; Yang, Bo; Guo, Fei; Lu, Qingshan; Zhao, Shifeng

2017-11-01

Cluster-assembled SmCo alloy films were prepared by low energy cluster beam deposition. The structure, magnetic domain, magnetization, and magnetostriction of the films were characterized. It is shown that the as-prepared films are assembled in compact and uniformly distributed spherical cluster nanoparticles, most of which, after vacuum in situ annealing at 700 K, aggregated to form cluster islands. These cluster islands result in transformations from superparamagnetic states to magnetic single domain (MSD) states in the films. Such MSD structures contribute to the enhanced magnetostrictive behaviors with a saturation magnetostrictive coefficient of 160 × 10-6 in comparison to 105 × 10-6 for the as-prepared films. This work demonstrates candidate materials that could be applied in nano-electro-mechanical systems, low power information storage, and weak magnetic detecting devices.

Leakage current suppression with a combination of planarized gate and overlap/off-set structure in metal-induced laterally crystallized polycrystalline-silicon thin-film transistors

NASA Astrophysics Data System (ADS)

Chae, Hee Jae; Seok, Ki Hwan; Lee, Sol Kyu; Joo, Seung Ki

2018-04-01

A novel inverted staggered metal-induced laterally crystallized (MILC) polycrystalline-silicon (poly-Si) thin-film transistors (TFTs) with a combination of a planarized gate and an overlap/off-set at the source-gate/drain-gate structure were fabricated and characterized. While the MILC process is advantageous for fabricating inverted staggered poly-Si TFTs, MILC TFTs reveal higher leakage current than TFTs crystallized by other processes due to their high trap density of Ni contamination. Due to this drawback, the planarized gate and overlap/off-set structure were applied to inverted staggered MILC TFTs. The proposed device shows drastic suppression of leakage current and pinning phenomenon by reducing the lateral electric field and the space-charge limited current from the gate to the drain.

Regulation of Complement and Contact System Activation via C1 Inhibitor Potentiation and Factor XIIa Activity Modulation by Sulfated Glycans – Structure-Activity Relationships

PubMed Central

Schoenfeld, Ann-Kathrin; Lahrsen, Eric; Alban, Susanne

2016-01-01

The serpin C1 inhibitor (C1-INH) is the only regulator of classical complement activation as well as the major regulator of the contact system. Its importance is demonstrated by hereditary angioedema (HAE), a severe disease with potentially life-threatening attacks due to deficiency or dysfunction of C1-INH. C1-INH replacement is the therapy of choice in HAE. In addition, C1-INH showed to have beneficial effects in other diseases characterized by inappropriate complement and contact system activation. Due to some limitations of its clinical application, there is a need for improving the efficacy of therapeutically applied C1-INH or to enhance the activity of endogenous C1-INH. Given the known potentiating effect of heparin on C1-INH, sulfated glycans (SG) may be such candidates. The aim of this study was to characterize suitable SG by evaluating structure-activity relationships. For this, more than 40 structurally distinct SG were examined for their effects on C1-INH, C1s and FXIIa. The SG turned out to potentiate the C1s inhibition by C1-INH without any direct influence on C1s. Their potentiating activity proved to depend on their degree of sulfation, molecular mass as well as glycan structure. In contrast, the SG had no effect on the FXIIa inhibition by C1-INH, but structure-dependently modulated the activity of FXIIa. Among the tested SG, β-1,3-glucan sulfates with a Mr ≤ 10 000 were identified as most promising lead candidates for the development of a glycan-based C1-INH amplifier. In conclusion, the obtained information on structural characteristics of SG favoring C1-INH potentiation represent an useful elementary basis for the development of compounds improving the potency of C1-INH in diseases and clinical situations characterized by inappropriate activation of complement and contact system. PMID:27783665

A small molecule-based strategy for endothelial differentiation and three-dimensional morphogenesis from human embryonic stem cells.

PubMed

Geng, Yijie; Feng, Bradley

2016-07-01

The emerging models of human embryonic stem cell (hESC) self-organizing organoids provide a valuable in vitro platform for studying self-organizing processes that presumably mimic in vivo human developmental events. Here we report that through a chemical screen, we identified two novel and structurally similar small molecules BIR1 and BIR2 which robustly induced the self-organization of a balloon-shaped three-dimensional structure when applied to two-dimensional adherent hESC cultures in the absence of growth factors. Gene expression analyses and functional assays demonstrated an endothelial identity of this balloon-like structure, while cell surface marker analyses revealed a VE-cadherin(+)CD31(+)CD34(+)KDR(+)CD43(-) putative endothelial progenitor population. Furthermore, molecular marker labeling and morphological examinations characterized several other distinct DiI-Ac-LDL(+) multi-cellular modules and a VEGFR3(+) sprouting structure in the balloon cultures that likely represented intermediate structures of balloon-formation.

Application of micro X-ray diffraction to investigate the reaction products formed by the alkali silica reaction in concrete structures

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

Dähn, R.; Arakcheeva, A.; Schaub, Ph.

Alkali–silica reaction (ASR) is one of the most important deterioration mechanisms in concrete leading to substantial damages of structures worldwide. Synchrotron-based micro-X-ray diffraction (micro-XRD) was employed to characterize the mineral phases formed in micro-cracks of concrete aggregates as a consequence of ASR. This particular high spatial resolution technique enables to directly gain structural information on ASR products formed in a 40-year old motorway bridge damaged due to ASR. Micro-X-ray-fluorescence was applied on thin sections to locate the reaction products formed in veins within concrete aggregates. Micro-XRD pattern were collected at selected points of interest along a vein by rotating themore » sample. Rietveld refinement determined the structure of the ASR product consisting of a new layered framework similar to mountainite and rhodesite. Furthermore, it is conceivable that understanding the structure of the ASR product may help developing new technical treatments inhibiting ASR.« less

Application of micro X-ray diffraction to investigate the reaction products formed by the alkali–silica reaction in concrete structures

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

Dähn, R., E-mail: rainer.daehn@psi.ch; Arakcheeva, A.; Schaub, Ph.

Alkali–silica reaction (ASR) is one of the most important deterioration mechanisms in concrete leading to substantial damages of structures worldwide. Synchrotron-based micro-X-ray diffraction (micro-XRD) was employed to characterize the mineral phases formed in micro-cracks of concrete aggregates as a consequence of ASR. This high spatial resolution technique enables to directly gain structural information on ASR products formed in a 40-year old motorway bridge damaged due to ASR. Micro-X-ray-fluorescence was applied on thin sections to locate the reaction products formed in veins within concrete aggregates. Micro-XRD pattern were collected at selected points of interest along a vein by rotating the sample.more » Rietveld refinement determined the structure of the ASR product consisting of a new layered framework similar to mountainite and rhodesite. It is conceivable that understanding the structure of the ASR product may help developing new technical treatments inhibiting ASR.« less

Cilia-like structures anchor the amphioxus notochord to its sheath.

PubMed

Bočina, Ivana; Ljubešić, Nikola; Saraga-Babić, Mirna

2011-01-01

Body stiffness is important during undulatory locomotion in fish. In amphioxus, the myosepta play an important role in transmission of muscular forces to the notochord. In order to define the specific supporting role of the notochord in amphioxus during locomotion, the ultrastructure of 10 adult amphioxus specimens was analyzed using transmission electron microscopy. Numerous cilia-like structures were found on the surface of each notochordal cell at the sites of their attachment to the notochordal sheath. Ultrastructurally, these structures consisted of the characteristic arrangement of peripheral and central microtubular doublets and were anchored to the inner layer of the notochordal sheath. Immunohistochemically, a positive reaction to applied dynein and β-tubulin antibodies characterized the area of the cilia-like structures. We propose that reduced back-and-forth movements of the cilia-like structures might contribute to the flow of the fluid content inside the notochord, thus modulating the stiffness of the amphioxus body during its undulatory locomotion. Copyright © 2009 Elsevier GmbH. All rights reserved.

Optical Voltage Sensing Using DNA Origami

PubMed Central

2018-01-01

We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nanodevices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we assembled voltage responsive DNA origami structures labeled with a single pair of FRET dyes. The DNA structures were reversibly immobilized on a nanocapillary tip and underwent controlled structural changes upon application of an electric field. The applied field was monitored through a change in FRET efficiency. By exchanging the position of a single dye, we could tune the voltage sensitivity of our DNA origami structure, demonstrating the flexibility and versatility of our approach. The experimental studies were complemented by coarse-grained simulations that characterized voltage-dependent elastic deformation of the DNA nanostructures and the associated change in the distance between the FRET pair. Our work opens a novel pathway for determining the mechanical properties of DNA origami structures and highlights potential applications of dynamic DNA nanostructures as voltage sensors. PMID:29430924

Fabrication and Characterization of Large-Area Unpatterned and Patterned Plasmonic Gold Nanostructures

NASA Astrophysics Data System (ADS)

Do, Minh Thanh; Tong, Quang Cong; Luong, Mai Hoang; Lidiak, Alexander; Ledoux-Rak, Isabelle; Lai, Ngoc Diep

2016-05-01

We report fabrication of Au nanoisland films on different substrates by thermally annealing a sputtered Au nanolayer and investigation of their structure, morphology, and optical properties. It was found that high-temperature annealing leads to transformation of the initial, continuous film into the forms of hillock and isolated island film. The final nanoisland films exhibit remarkably enhanced and localized plasmon resonance spectra with respect to the original sputtered film. The strong dependence of the resonance band spectra of the resulting structures on the annealing temperature and supporting substrate is presented and analyzed, suggesting that both of these factors could be used to tune the optical spectroscopic properties of such structures. Moreover, we propose and demonstrate a novel and effective approach for fabrication of patterned Au structures by thermally annealing the Au layer deposited onto modulated-surface substrates. The experimental results indicate that this method could become a promising approach for manufacturing plasmonic array structures, which have been extensively investigated and widely applied in many fields.

Reconstructive structural phase transitions in dense Mg

NASA Astrophysics Data System (ADS)

Yao, Yansun; Klug, Dennis D.

2012-07-01

The question raised recently about whether the high-pressure phase transitions of Mg follow a hexagonal close-packed (hcp) → body centered cubic (bcc) or hcp → double hexagonal close-packed (dhcp) → bcc sequence at room temperature is examined by the use of first principles density functional methods. Enthalpy calculations show that the bcc structure replaces the hcp structure to become the most stable structure near 48 GPa, whereas the dhcp structure is never the most stable structure in the pressure range of interest. The characterized phase-transition mechanisms indicate that the hcp → dhcp transition is also associated with a higher enthalpy barrier. At room temperature, the structural sequence hcp → bcc is therefore more energetically favorable for Mg. The same conclusion is also reached from the simulations of the phase transitions using metadynamics methods. At room temperature, the metadynamics simulations predict the onset of a hcp → bcc transition at 40 GPa and the transition becomes more prominent upon further compression. At high temperatures, the metadynamics simulations reveal a structural fluctuation among the hcp, dhcp, and bcc structures at 15 GPa. With increasing pressure, the structural evolution at high temperatures becomes more unambiguous and eventually settles to a bcc structure once sufficient pressure is applied.

Reconstructive structural phase transitions in dense Mg.

PubMed

Yao, Yansun; Klug, Dennis D

2012-07-04

The question raised recently about whether the high-pressure phase transitions of Mg follow a hexagonal close-packed (hcp) → body centered cubic (bcc) or hcp → double hexagonal close-packed (dhcp) → bcc sequence at room temperature is examined by the use of first principles density functional methods. Enthalpy calculations show that the bcc structure replaces the hcp structure to become the most stable structure near 48 GPa, whereas the dhcp structure is never the most stable structure in the pressure range of interest. The characterized phase-transition mechanisms indicate that the hcp → dhcp transition is also associated with a higher enthalpy barrier. At room temperature, the structural sequence hcp → bcc is therefore more energetically favorable for Mg. The same conclusion is also reached from the simulations of the phase transitions using metadynamics methods. At room temperature, the metadynamics simulations predict the onset of a hcp → bcc transition at 40 GPa and the transition becomes more prominent upon further compression. At high temperatures, the metadynamics simulations reveal a structural fluctuation among the hcp, dhcp, and bcc structures at 15 GPa. With increasing pressure, the structural evolution at high temperatures becomes more unambiguous and eventually settles to a bcc structure once sufficient pressure is applied.

Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex.

PubMed

Haspel, Nurit; Geisbrecht, Brian V; Lambris, John; Kavraki, Lydia

2010-03-01

We present a novel multi-level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi-scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low-dimensional landscape to efficiently focus on important interactions and examine low energy regions. This methodology provides a more extensive sampling of the low energy landscape than an MD simulation starting from a single crystal structure as it explores multiple trajectories of the protein. This enables us to obtain a broader view of the dynamics of proteins and it can help in understanding complex binding, improving docking results and more. In this work, we apply the methodology to provide an extensive characterization of the bound complexes of the C3d fragment of human Complement component C3 and one of its powerful bacterial inhibitors, the inhibitory domain of Staphylococcus aureus extra-cellular fibrinogen-binding domain (Efb-C) and two of its mutants. We characterize several important interactions along the binding interface and define low free energy regions in the three complexes. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

A Bowman-Birk protease inhibitor purified, cloned, sequenced and characterized from the seeds of Maclura pomifera (Raf.) Schneid.

PubMed

Indarte, Martín; Lazza, Cristian M; Assis, Diego; Caffini, Néstor O; Juliano, María A; Avilés, Francesc X; Daura, Xavier; López, Laura M I; Trejo, Sebastián A

2017-02-01

A new BBI-type protease inhibitor with remarkable structural characteristics was purified, cloned, and sequenced from seeds of Maclura pomifera , a dicotyledonous plant belonging to the Moraceae family. In this work, we report a Bowman-Birk inhibitor (BBI) isolated, purified, cloned, and characterized from Maclura pomifera seeds (MpBBI), the first of this type from a species belonging to Moraceae family. MpBBI was purified to homogeneity by RP-HPLC, total RNA was extracted from seeds of M. pomifera, and the 3'RACE-PCR method was applied to obtain the cDNA, which was cloned and sequenced. Peptide mass fingerprinting (PMF) analysis showed correspondence between the in silico-translated protein and MpBBI, confirming that it corresponds to a new plant protease inhibitor. The obtained cDNA encoded a polypeptide of 65 residues and possesses 10 cysteine residues, with molecular mass of 7379.27, pI 6.10, and extinction molar coefficient of 9105 M -1  cm -1 . MpBBI inhibits strongly trypsin with K i in the 10 -10 M range and was stable in a wide array of pH and extreme temperatures. MpBBI comparative modeling was applied to gain insight into its 3D structure and highlighted some distinguishing features: (1) two non-identical loops, (2) loop 1 (CEEESRC) is completely different from any known BBI, and (3) the amount of disulphide bonds is also different from any reported BBI from dicot plants.

Boletus edulis loaded with γ-Fe2O3 nanoparticles as a magnetic sorbent for preconcentration of Co(II) and Sn(II) prior to their determination by ICP-OES.

PubMed

Ozdemir, Sadin; Serkan Yalcin, M; Kilinc, Ersin; Soylak, Mustafa

2017-12-20

The authors show that the fungus Boletus edulis loaded with γ-Fe 2 O 3 nanoparticles is a viable sorbent for magnetic solid phase extraction of trace levels of Co(II) and Sn(II). The surface structure of immobilized magnetized B. edulis was characterized by FT-IR, SEM and EDX. Experimental parameters were optimized. Following elution with 1 M HCl, the ions were quantified by ICP-OES. The limits of detection are 21 pg·mL -1 for Co(II), and 19 pg·mL -1 for Sn(II). The preconcentration factors are 100 for both ions. The sorption capacities of the sorbent are 35.8 mg·g -1 for Co(II) and 29.6 mg·g -1 for Sn(II). The method was applied to the analysis of certificated reference materials and gave ≥95% recoveries with low RSDs. It was also successfully applied to the quantification of Co(II) and Sn(II) in spiked environmental and food samples. Graphical abstract The fungus Boletus edulis loaded with γ-Fe 2 O 3 nanoparticles is a viable biosorbent for magnetic solid phase extraction (MSPE) of trace levels of Co(II) and Sn(II). The surface structure of immobilized magnetized B. edulis was characterized by FT-IR, SEM and EDX. Experimental parameters were optimized.

Graph characterization via Ihara coefficients.

PubMed

Ren, Peng; Wilson, Richard C; Hancock, Edwin R

2011-02-01

The novel contributions of this paper are twofold. First, we demonstrate how to characterize unweighted graphs in a permutation-invariant manner using the polynomial coefficients from the Ihara zeta function, i.e., the Ihara coefficients. Second, we generalize the definition of the Ihara coefficients to edge-weighted graphs. For an unweighted graph, the Ihara zeta function is the reciprocal of a quasi characteristic polynomial of the adjacency matrix of the associated oriented line graph. Since the Ihara zeta function has poles that give rise to infinities, the most convenient numerically stable representation is to work with the coefficients of the quasi characteristic polynomial. Moreover, the polynomial coefficients are invariant to vertex order permutations and also convey information concerning the cycle structure of the graph. To generalize the representation to edge-weighted graphs, we make use of the reduced Bartholdi zeta function. We prove that the computation of the Ihara coefficients for unweighted graphs is a special case of our proposed method for unit edge weights. We also present a spectral analysis of the Ihara coefficients and indicate their advantages over other graph spectral methods. We apply the proposed graph characterization method to capturing graph-class structure and clustering graphs. Experimental results reveal that the Ihara coefficients are more effective than methods based on Laplacian spectra.

An electrical impedance tomography (EIT) multi-electrode needle-probe device for local assessment of heterogeneous tissue impeditivity.

PubMed

Meroni, Davide; Maglioli, Camilla Carpano; Bovio, Dario; Greco, Francesco G; Aliverti, Andrea

2017-07-01

Electrical Impedance Tomography (EIT) is an image reconstruction technique applied in medicine for the electrical imaging of living tissues. In literature there is the evidence that a large resistivity variation related to the differences of the human tissues exists. As a result of this interest for the electrical characterization of the biological samples, recently the attention is also focused on the identification and characterization of the human tissue, by studying the homogeneity of its structure. An 8 electrodes needle-probe device has been developed with the intent of identifying the structural inhomogeneities under the surface layers. Ex-vivo impeditivity measurements, by placing the needle-probe in 5 different patterns of fat and lean porcine tissue, were performed, and impeditivity maps were obtained by EIDORS open source software for image reconstruction in electrical impedance. The values composing the maps have been analyzed, pointing out a good tissue discrimination, and the conformity with the real images. We conclude that this device is able to perform impeditivity maps matching to reality for position and orientation. In all the five patterns presented is possible to identify and replicate correctly the heterogeneous tissue under test. This new procedure can be helpful to the medical staff to completely characterize the biological sample, in different unclear situations.

Limestone characterization to model damage from acidic precipitation: Effect of pore structure on mass transfer

USGS Publications Warehouse

Leith, S.D.; Reddy, M.M.; Irez, W.F.; Heymans, M.J.

1996-01-01

The pore structure of Salem limestone is investigated, and conclusions regarding the effect of the pore geometry on modeling moisture and contaminant transport are discussed based on thin section petrography, scanning electron microscopy, mercury intrusion porosimetry, and nitrogen adsorption analyses. These investigations are compared to and shown to compliment permeability and capillary pressure measurements for this common building stone. Salem limestone exhibits a bimodal pore size distribution in which the larger pores provide routes for convective mass transfer of contaminants into the material and the smaller pores lead to high surface area adsorption and reaction sites. Relative permeability and capillary pressure measurements of the air/water system indicate that Salem limestone exhibits high capillarity end low effective permeability to water. Based on stone characterization, aqueous diffusion and convection are believed to be the primary transport mechanisms for pollutants in this stone. The extent of contaminant accumulation in the stone depends on the mechanism of partitioning between the aqueous and solid phases. The described characterization techniques and modeling approach can be applied to many systems of interest such as acidic damage to limestone, mass transfer of contaminants in concrete and other porous building materials, and modeling pollutant transport in subsurface moisture zones.

Selective Laser Melting: a regular unit cell approach for the manufacture of porous, titanium, bone in-growth constructs, suitable for orthopedic applications.

PubMed

Mullen, Lewis; Stamp, Robin C; Brooks, Wesley K; Jones, Eric; Sutcliffe, Christopher J

2009-05-01

In this study, a novel porous titanium structure for the purpose of bone in-growth has been designed, manufactured and evaluated. The structure was produced by Selective Laser Melting (SLM); a rapid manufacturing process capable of producing highly intricate, functionally graded parts. The technique described utilizes an approach based on a defined regular unit cell to design and produce structures with a large range of both physical and mechanical properties. These properties can be tailored to suit specific requirements; in particular, functionally graded structures with bone in-growth surfaces exhibiting properties comparable to those of human bone have been manufactured. The structures were manufactured and characterized by unit cell size, strand diameter, porosity, and compression strength. They exhibited a porosity (10-95%) dependant compression strength (0.5-350 Mpa) comparable to the typical naturally occurring range. It is also demonstrated that optimized structures have been produced that possesses ideal qualities for bone in-growth applications and that these structures can be applied in the production of orthopedic devices. (c) 2008 Wiley Periodicals, Inc.

Electric Potential and Electric Field Imaging with Dynamic Applications & Extensions

NASA Technical Reports Server (NTRS)

Generazio, Ed

2017-01-01

The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field made be used for volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e- Sensor enhancements (ephemeral e-Sensor) are discussed. Critical design elements of current linear and real-time two-dimensional (2D) measurement systems are highlighted, and the development of a three dimensional (3D) EFI system is presented. Demonstrations for structural, electronic, human, and memory applications are shown. Recent work demonstrates that phonons may be used to create and annihilate electric dipoles within structures. Phonon induced dipoles are ephemeral and their polarization, strength, and location may be quantitatively characterized by EFI providing a new subsurface Phonon-EFI imaging technology. Results from real-time imaging of combustion and ion flow, and their measurement complications, will be discussed. Extensions to environment, Space and subterranean applications will be presented, and initial results for quantitative characterizing material properties are shown. A wearable EFI system has been developed by using fundamental EFI concepts. These new EFI capabilities are demonstrated to characterize electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, manufacturing quality control, crime scene forensics, design and materials selection for advanced sensors, combustion science, on-orbit space potential, container inspection, remote characterization of electronic circuits and level of activation, dielectric morphology of structures, tether integrity, organic molecular memory, atmospheric science, weather prediction, earth quake prediction, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

MicroRaman, PXRD, EDS and microscopic investigation of magnesium calcite biomineral phases. The case of sea urchin biominerals

NASA Astrophysics Data System (ADS)

Borzęcka-Prokop, B.; Wesełucha-Birczyńska, A.; Koszowska, E.

2007-02-01

This study concerns Mg-calcite characterization (and in particular molecular structure and microstructural studies of mineral phases) of a sea urchin mineralised test and spines. Sea urchins are spiny sea animals (kingdom Animalia, phylum Echinodermata, class Echinoidea). Microscopic observations, SEM, EDS, PXRD and spectroscopic microRaman methods have been applied to characterize the biomineral parts of the sea urchin. The latter technique is very useful in research of biological systems and especially suitable for monitoring differences within biomineral phases exhibiting varieties of morphological forms. Crystalline magnesium calcium carbonate, Mg xCa 1- xCO 3 (magnesian calcite; space group R-3 cH; a = 4.9594(8) Å, c = 16.886(6) Å), has been identified as the predominant biomineral component.

A study of the stress wave factor technique for evaluation of composite materials

NASA Technical Reports Server (NTRS)

Duke, J. C., Jr.; Henneke, E. G., II; Kiernan, M. T.; Grosskopf, P. P.

1989-01-01

The acousto-ultrasonic approach for nondestructive evaluation provides a measurement procedure for quantifying the integrated effect of globally distributed damage characteristic of fiber reinforced composite materials. The evaluation procedure provides a stress wave factor that correlates closely with several material performance parameters. The procedure was investigated for a variety of materials including advanced composites, hybrid structure bonds, adhesive bonds, wood products, and wire rope. The research program focused primarily on development of fundamental understanding and applications advancements of acousto-ultrasonics for materials characterization. This involves characterization of materials for which detection, location, and identification of imperfections cannot at present be analyzed satisfactorily with mechanical performance prediction models. In addition to presenting definitive studies on application potentials, the understanding of the acousto-ultrasonic method as applied to advanced composites is reviewed.

Silicon nanowires reliability and robustness investigation using AFM-based techniques

NASA Astrophysics Data System (ADS)

Bieniek, Tomasz; Janczyk, Grzegorz; Janus, Paweł; Grabiec, Piotr; Nieprzecki, Marek; Wielgoszewski, Grzegorz; Moczała, Magdalena; Gotszalk, Teodor; Buitrago, Elizabeth; Badia, Montserrat F.; Ionescu, Adrian M.

2013-07-01

Silicon nanowires (SiNWs) have undergone intensive research for their application in novel integrated systems such as field effect transistor (FET) biosensors and mass sensing resonators profiting from large surface-to-volume ratios (nano dimensions). Such devices have been shown to have the potential for outstanding performances in terms of high sensitivity, selectivity through surface modification and unprecedented structural characteristics. This paper presents the results of mechanical characterization done for various types of suspended SiNWs arranged in a 3D array. The characterization has been performed using techniques based on atomic force microscopy (AFM). This investigation is a necessary prerequisite for the reliable and robust design of any biosensing system. This paper also describes the applied investigation methodology and reports measurement results aggregated during series of AFM-based tests.

A 3D-Printable Polymer-Metal Soft-Magnetic Functional Composite-Development and Characterization.

PubMed

Khatri, Bilal; Lappe, Karl; Noetzel, Dorit; Pursche, Kilian; Hanemann, Thomas

2018-01-25

In this work, a 3D printed polymer-metal soft-magnetic composite was developed and characterized for its material, structural, and functional properties. The material comprises acrylonitrile butadiene styrene (ABS) as the polymer matrix, with up to 40 vol. % stainless steel micropowder as the filler. The composites were rheologically analyzed and 3D printed into tensile and flexural test specimens using a commercial desktop 3D printer. Mechanical characterization revealed a linearly decreasing trend of the ultimate tensile strength (UTS) and a sharp decrease in Young's modulus with increasing filler content. Four-point bending analysis showed a decrease of up to 70% in the flexural strength of the composite and up to a two-factor increase in the secant modulus of elasticity. Magnetic hysteresis characterization revealed retentivities of up to 15.6 mT and coercive forces of up to 4.31 kA/m at an applied magnetic field of 485 kA/m. The composite shows promise as a material for the additive manufacturing of passive magnetic sensors and/or actuators.

A 3D-Printable Polymer-Metal Soft-Magnetic Functional Composite—Development and Characterization

PubMed Central

Lappe, Karl; Noetzel, Dorit; Pursche, Kilian; Hanemann, Thomas

2018-01-01

In this work, a 3D printed polymer–metal soft-magnetic composite was developed and characterized for its material, structural, and functional properties. The material comprises acrylonitrile butadiene styrene (ABS) as the polymer matrix, with up to 40 vol. % stainless steel micropowder as the filler. The composites were rheologically analyzed and 3D printed into tensile and flexural test specimens using a commercial desktop 3D printer. Mechanical characterization revealed a linearly decreasing trend of the ultimate tensile strength (UTS) and a sharp decrease in Young’s modulus with increasing filler content. Four-point bending analysis showed a decrease of up to 70% in the flexural strength of the composite and up to a two-factor increase in the secant modulus of elasticity. Magnetic hysteresis characterization revealed retentivities of up to 15.6 mT and coercive forces of up to 4.31 kA/m at an applied magnetic field of 485 kA/m. The composite shows promise as a material for the additive manufacturing of passive magnetic sensors and/or actuators. PMID:29370112

Subcortical structure segmentation using probabilistic atlas priors

NASA Astrophysics Data System (ADS)

Gouttard, Sylvain; Styner, Martin; Joshi, Sarang; Smith, Rachel G.; Cody Hazlett, Heather; Gerig, Guido

2007-03-01

The segmentation of the subcortical structures of the brain is required for many forms of quantitative neuroanatomic analysis. The volumetric and shape parameters of structures such as lateral ventricles, putamen, caudate, hippocampus, pallidus and amygdala are employed to characterize a disease or its evolution. This paper presents a fully automatic segmentation of these structures via a non-rigid registration of a probabilistic atlas prior and alongside a comprehensive validation. Our approach is based on an unbiased diffeomorphic atlas with probabilistic spatial priors built from a training set of MR images with corresponding manual segmentations. The atlas building computes an average image along with transformation fields mapping each training case to the average image. These transformation fields are applied to the manually segmented structures of each case in order to obtain a probabilistic map on the atlas. When applying the atlas for automatic structural segmentation, an MR image is first intensity inhomogeneity corrected, skull stripped and intensity calibrated to the atlas. Then the atlas image is registered to the image using an affine followed by a deformable registration matching the gray level intensity. Finally, the registration transformation is applied to the probabilistic maps of each structures, which are then thresholded at 0.5 probability. Using manual segmentations for comparison, measures of volumetric differences show high correlation with our results. Furthermore, the dice coefficient, which quantifies the volumetric overlap, is higher than 62% for all structures and is close to 80% for basal ganglia. The intraclass correlation coefficient computed on these same datasets shows a good inter-method correlation of the volumetric measurements. Using a dataset of a single patient scanned 10 times on 5 different scanners, reliability is shown with a coefficient of variance of less than 2 percents over the whole dataset. Overall, these validation and reliability studies show that our method accurately and reliably segments almost all structures. Only the hippocampus and amygdala segmentations exhibit relative low correlation with the manual segmentation in at least one of the validation studies, whereas they still show appropriate dice overlap coefficients.

MEFA (multiepitope fusion antigen)-Novel Technology for Structural Vaccinology, Proof from Computational and Empirical Immunogenicity Characterization of an Enterotoxigenic Escherichia coli (ETEC) Adhesin MEFA

PubMed Central

Duan, Qiangde; Lee, Kuo Hao; Nandre, Rahul M; Garcia, Carolina; Chen, Jianhan; Zhang, Weiping

2017-01-01

Vaccine development often encounters the challenge of virulence heterogeneity. Enterotoxigenic Escherichia coli (ETEC) bacteria producing immunologically heterogeneous virulence factors are a leading cause of children’s diarrhea and travelers’ diarrhea. Currently, we do not have licensed vaccines against ETEC bacteria. While conventional methods continue to make progress but encounter challenge, new computational and structure-based approaches are explored to accelerate ETEC vaccine development. In this study, we applied a structural vaccinology concept to construct a structure-based multiepitope fusion antigen (MEFA) to carry representing epitopes of the seven most important ETEC adhesins [CFA/I, CFA/II (CS1–CS3), CFA/IV (CS4–CS6)], simulated antigenic structure of the CFA/I/II/IV MEFA with computational atomistic modeling and simulation, characterized immunogenicity in mouse immunization, and examined the potential of structure-informed vaccine design for ETEC vaccine development. A tag-less recombinant MEFA protein (CFA/I/II/IV MEFA) was effectively expressed and extracted. Molecular dynamics simulations indicated that this MEFA immunogen maintained a stable secondary structure and presented epitopes on the protein surface. Empirical data showed that mice immunized with the tagless CFA/I/II/IV MEFA developed strong antigen-specific antibody responses, and mouse serum antibodies significantly inhibited in vitro adherence of bacteria expressing these seven adhesins. These results revealed congruence of antigen immunogenicity between computational simulation and empirical mouse immunization and indicated this tag-less CFA/I/II/IV MEFA potentially an antigen for a broadly protective ETEC vaccine, suggesting a potential application of MEFA-based structural vaccinology for vaccine design against ETEC and likely other pathogens. PMID:28944092

Determining the structure-mechanics relationships of dense microtubule networks with confocal microscopy and magnetic tweezers-based microrheology.

PubMed

Yang, Yali; Valentine, Megan T

2013-01-01

The microtubule (MT) cytoskeleton is essential in maintaining the shape, strength, and organization of cells. Its spatiotemporal organization is fundamental for numerous dynamic biological processes, and mechanical stress within the MT cytoskeleton provides an important signaling mechanism in mitosis and neural development. This raises important questions about the relationships between structure and mechanics in complex MT structures. In vitro, reconstituted cytoskeletal networks provide a minimal model of cell mechanics while also providing a testing ground for the fundamental polymer physics of stiff polymer gels. Here, we describe our development and implementation of a broad tool kit to study structure-mechanics relationships in reconstituted MT networks, including protocols for the assembly of entangled and cross-linked MT networks, fluorescence imaging, microstructure characterization, construction and calibration of magnetic tweezers devices, and mechanical data collection and analysis. In particular, we present the design and assembly of three neodymium iron boron (NdFeB)-based magnetic tweezers devices optimized for use with MT networks: (1) high-force magnetic tweezers devices that enable the application of nano-Newton forces and possible meso- to macroscale materials characterization; (2) ring-shaped NdFeB-based magnetic tweezers devices that enable oscillatory microrheology measurements; and (3) portable magnetic tweezers devices that enable direct visualization of microscale deformation in soft materials under applied force. Copyright © 2013 Elsevier Inc. All rights reserved.

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

PubMed

Neuwald, Andrew F; Altschul, Stephen F

2016-12-01

Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes' theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu).

Multiscale Characterization of Engineered Cardiac Tissue Architecture.

PubMed

Drew, Nancy K; Johnsen, Nicholas E; Core, Jason Q; Grosberg, Anna

2016-11-01

In a properly contracting cardiac muscle, many different subcellular structures are organized into an intricate architecture. While it has been observed that this organization is altered in pathological conditions, the relationship between length-scales and architecture has not been properly explored. In this work, we utilize a variety of architecture metrics to quantify organization and consistency of single structures over multiple scales, from subcellular to tissue scale as well as correlation of organization of multiple structures. Specifically, as the best way to characterize cardiac tissues, we chose the orientational and co-orientational order parameters (COOPs). Similarly, neonatal rat ventricular myocytes were selected for their consistent architectural behavior. The engineered cells and tissues were stained for four architectural structures: actin, tubulin, sarcomeric z-lines, and nuclei. We applied the orientational metrics to cardiac cells of various shapes, isotropic cardiac tissues, and anisotropic globally aligned tissues. With these novel tools, we discovered: (1) the relationship between cellular shape and consistency of self-assembly; (2) the length-scales at which unguided tissues self-organize; and (3) the correlation or lack thereof between organization of actin fibrils, sarcomeric z-lines, tubulin fibrils, and nuclei. All of these together elucidate some of the current mysteries in the relationship between force production and architecture, while raising more questions about the effect of guidance cues on self-assembly function. These types of metrics are the future of quantitative tissue engineering in cardiovascular biomechanics.

Scaling up the Single Transducer Thickness-Independent Ultrasonic Imaging Method for Accurate Characterization of Microstructural Gradients in Monolithic and Composite Tubular Structures

NASA Technical Reports Server (NTRS)

Roth, Don J.; Carney, Dorothy V.; Baaklini, George Y.; Bodis, James R.; Rauser, Richard W.

1998-01-01

Ultrasonic velocity/time-of-flight imaging that uses back surface reflections to gauge volumetric material quality is highly suited for quantitative characterization of microstructural gradients including those due to pore fraction, density, fiber fraction, and chemical composition variations. However, a weakness of conventional pulse-echo ultrasonic velocity/time-of-flight imaging is that the image shows the effects of thickness as well as microstructural variations unless the part is uniformly thick. This limits this imaging method's usefulness in practical applications. Prior studies have described a pulse-echo time-of-flight-based ultrasonic imaging method that requires using a single transducer in combination with a reflector plate placed behind samples that eliminates the effect of thickness variation in the image. In those studies, this method was successful at isolating ultrasonic variations due to material microstructure in plate-like samples of silicon nitride, metal matrix composite, and polymer matrix composite. In this study, the method is engineered for inspection of more complex-shaped structures-those having (hollow) tubular/curved geometry. The experimental inspection technique and results are described as applied to (1) monolithic mullite ceramic and polymer matrix composite 'proof-of-concept' tubular structures that contain machined patches of various depths and (2) as-manufactured monolithic silicon nitride ceramic and silicon carbide/silicon carbide composite tubular structures that might be used in 'real world' applications.

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

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

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems.

PubMed

Foster, Clay A; West, Ann H

2017-01-01

Two-component signaling (TCS) is the primary means by which bacteria, as well as certain plants and fungi, respond to external stimuli. Signal transduction involves stimulus-dependent autophosphorylation of a sensor histidine kinase and phosphoryl transfer to the receiver domain of a downstream response regulator. Phosphorylation acts as an allosteric switch, inducing structural and functional changes in the pathway's components. Due to their transient nature, phosphorylated receiver domains are challenging to characterize structurally. In this work, we provide a methodology for simulating receiver domain phosphorylation to predict conformations that are nearly identical to experimental structures. Using restrained molecular dynamics, phosphorylated conformations of receiver domains can be reliably sampled on nanosecond timescales. These simulations also provide data on conformational dynamics that can be used to identify regions of functional significance related to phosphorylation. We first validated this approach on several well-characterized receiver domains and then used it to compare the upstream and downstream components of the fungal Sln1 phosphorelay. Our results demonstrate that this technique provides structural insight, obtained in the absence of crystallographic or NMR information, regarding phosphorylation-induced conformational changes in receiver domains that regulate the output of their associated signaling pathway. To our knowledge, this is the first time such a protocol has been described that can be broadly applied to TCS proteins for predictive purposes. Proteins 2016; 85:155-176. © 2016 Wiley Periodicals, Inc. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Permanently densified SiO2 glasses: a structural approach.

PubMed

Martinet, C; Kassir-Bodon, A; Deschamps, T; Cornet, A; Le Floch, S; Martinez, V; Champagnon, B

2015-08-19

Densified silica can be obtained by different pressure and temperature paths and for different stress conditions, hydrostatic or including shear. The density is usually the macroscopic parameter used to characterize the different compressed silica samples. The aim of our present study is to compare structural modifications for silica glass, densified from several routes. For this, densified silica glasses are prepared from cold and high temperature (up to 1020 °C) compressions. The different densified glasses obtained in our study are characterized by micro-Raman spectroscopy. Intertetrahedral angles from the main band relative to the bending mode decrease and their values are larger for densified samples from high temperature compression than those samples from cold compression. The relative amount of 3-membered rings deduced from the D2 line area increases as a function of density for cold compression. The temperature increase during the compression process induces a decrease of the 3 fold ring population. Moreover, 3 fold rings are more deformed and stressed for densified samples at room temperature at the expense of those densified at high temperature. Temperature plays a main role in the reorganization structure during the densification and leads to obtaining a more relaxed structure with lower stresses than glasses densified from cold compression. The role of hydrostatic or non-hydrostatic applied stresses on the glass structure is discussed. From the Sen and Thorpe central force model, intertetrahedral angle average value and their distribution are estimated.

Synthesis and Technological Innovation of Applying Oxide Nanomaterials in Wastewater Treatment by Flotation

NASA Astrophysics Data System (ADS)

Covaliu, C. I.; Moga, I. C.; Matache, M. G.; Paraschiv, G.; Gageanu, I.; Vasile, E.

2018-06-01

The appearance and development of nanotechnology gave new and efficient modalities for pollutants removal from wastewaters by using new compounds called nanomaterials which possess unique structural and morphological properties. In this paper we investigated the application of CoFe2O4 nanomaterial for increasing the efficiency of oily wastewater treatment by flotation. CoFe2O4 nanomaterial was prepared by precipitation method. Prior testing their application in wastewater treatment by flotation, the oxide nanomaterial was structural and morphological characterized by XRD and TEM analyses. The influence of CoFe2O4nanomaterial on oily wastewater depollution by flotation process was investigated by measuring the following parameters: treatment efficiency [%] and the stability of froth.

Temperature and field dependent electronic structure and magnetic properties of LaCoO3 and GdCoO3

NASA Astrophysics Data System (ADS)

Ovchinnikov, S. G.; Orlov, Yu. S.; Dudnikov, V. A.

2012-10-01

The transformation of the band structure of LaCoO3 in the applied magnetic field has been theoretically studied. If the field is below its critical value BC≈65 T, the dielectric band gap decreases with the field, thus giving rise to negative magnetoresistance that is highest at T≈300÷500 K. The critical field is related to the crossover between the low- and high-spin terms of Co3+ ions. The spin crossover results in an insulator-metal transition induced by an increase in the magnetic field. Similar calculations have been done for GdCoO3 which is characterized by large spin gap∼2000 K.

Passive control of aerodynamically forced vibrations of supersonic turbomachine rotors by splitter blades

NASA Technical Reports Server (NTRS)

Fleeter, S.; Topp, D. A.; Hoyniak, D.

1986-01-01

An aeroelastic model is developed to examine the use of splitter blades as a passive detuning mechanism for flow induced forced response of unstalled supersonic turbomachine rotors. The splitters introduce aerodynamic and structural detuning to the rotor design. The relationship between aerodynamic and structural detuning and the location and chord lengths of splitters is analyzed. The model is applied to the flow induced response of four 12-blade rotors with Verdon's (1973) Cascade B flow geometry. The data reveal that for gusts characterized by forward and backward traveling waves the splitters generally decrease the maximum amplitudes of response; however, for some gust load interblade phase angles, such as -180 deg and 120 deg the splitters did not reduce the amplitudes of response.

Engineering AAV receptor footprints for gene therapy.

PubMed

Madigan, Victoria J; Asokan, Aravind

2016-06-01

Adeno-associated viruses (AAV) are currently at the forefront of human gene therapy clinical trials as recombinant vectors. Significant progress has been made in elucidating the structure, biology and tropisms of different naturally occurring AAV isolates in the past decade. In particular, a spectrum of AAV capsid interactions with host receptors have been identified and characterized. These studies have enabled a better understanding of key determinants of AAV cell recognition and entry in different hosts. This knowledge is now being applied toward engineering new, lab-derived AAV capsids with favorable transduction profiles. The current review conveys a structural perspective of capsid-glycan interactions and provides a roadmap for generating synthetic strains by engineering AAV receptor footprints. Copyright © 2016 Elsevier B.V. All rights reserved.

Bonding and Microstructural Stability in Ni55Ti45 Studied by Experimental and Theoretical Methods

NASA Technical Reports Server (NTRS)

Stott, Amanda C.; Brauer, Jonathan I.; Garg, Anita; Pepper, Stephen V.; Abel, Phillip B.; DellaCorte, Christopher; Noebe, Ronald D.; Glennon, Glenn; Bylaska, Eric; Dixon, David A.

2010-01-01

Spiral orbit tribometry friction tests performed on Ni-rich Ni55Ti45 titanium ball bearings indicate that this alloy is a promising candidate for future aerospace bearing applications. Microstructural characterization of the bearing specimens was performed using transmission electron microscopy and energy dispersive spectroscopy, with NiTi, Ni4Ti3, Ni3Ti, and Ni2Ti4Ox phases identified within the microstructure of the alloy. Density functional theory was applied to predict the electronic structure of the NixTiy phases, including the band structure and site projected density of states. Ultraviolet photoemission spectroscopy was used to verify the density of states results from the density functional theory calculations, with good agreement observed between experiment and theory.

Giant self-biased magnetoelectric coupling in co-fired textured layered composites

NASA Astrophysics Data System (ADS)

Yan, Yongke; Zhou, Yuan; Priya, Shashank

2013-02-01

Co-fired magnetostrictive/piezoelectric/magnetostrictive laminate structure with silver inner electrode was synthesized and characterized. We demonstrate integration of textured piezoelectric microstructure with the cost-effective low-temperature co-fired layered structure to achieve strong magnetoelectric coupling. Using the co-fired composite, a strategy was developed based upon the hysteretic response of nickel-copper-zinc ferrite magnetostrictive materials to achieve peak magnetoelectric response at zero DC bias, referred as self-biased magnetoelectric response. Fundamental understanding of self-bias phenomenon in composites with single phase magnetic material was investigated by quantifying the magnetization and piezomagnetic changes with applied DC field. We delineate the contribution arising from the interfacial strain and inherent magnetic hysteretic behavior of copper modified nickel-zinc ferrite towards self-bias response.

Halloysite clay nanotubes for controlled release of protective agents.

PubMed

Abdullayev, Elshad; Lvov, Yuri

2011-11-01

Halloysite is a naturally occurring clay mineral with submicron sized hollow cylindrical morphology. Halloysite morphology, structure and properties were characterized by using SEM, TEM, XRD, FT-IR spectroscopy, surface electrokinetic (zeta) potential and nitrogen adsorption isotherms. Comparison of the halloysite structure with imogolite was also provided. Halloysite toxicological studies revealed that it is environmentally friendly and biocompatible material. Due to its unique tubular shape and availability in thousands of tons halloysite has potential to be applied as nanocontainers for encapsulation of chemically and biologically active agents such as medicines, pharmaceuticals, antiseptics, corrosion inhibitors, antifouling agents, and doped with them plastics producing smart polymeric nanocomposites with improved mechanical strength. Finally possibility to synthesize metal nanorods within the halloysite lumen was demonstrated.

Multimodal and synthetic aperture approach to full-field 3D shape and displacement measurements

NASA Astrophysics Data System (ADS)

Kujawińska, M.; Sitnik, R.

2017-08-01

Recently most of the measurement tasks in industry, civil engineering and culture heritage applications require archiving, characterization and monitoring of 3D objects and structures and their performance under changing conditions. These requirements can be met if multimodal measurement (MM) strategy is applied. It rely on effective combining structured light method and 3D digital image correlation with laser scanning/ToF, thermal imaging, multispectral imaging and BDRF measurements. In the case of big size and/or complicated objects MM have to be combined with hierarchical or synthetic aperture (SA) measurements. The new solutions in MM and SA strategies are presented and their applicability is shown at interesting cultural heritage and civil engineering applications.