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Sample records for 2d ft-icr ms

  1. 2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach.

    PubMed

    Floris, Federico; van Agthoven, Maria; Chiron, Lionel; Soulby, Andrew J; Wootton, Christopher A; Lam, Yuko P Y; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

    2016-09-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors through the modulation of precursor ion cyclotron radii prior to fragmentation. Previous results show that implementation of 2D FT-ICR MS with infrared multi-photon dissociation (IRMPD) and electron capture dissociation (ECD) has turned this method into a useful analytical tool. In this work, IRMPD tandem mass spectrometry of calmodulin (CaM) has been performed both in one-dimensional and two-dimensional FT-ICR MS using a top-down and bottom-up approach. 2D IRMPD FT-ICR MS is used to achieve extensive inter-residue bond cleavage and assignment for CaM, using its unique features for fragment identification in a less time- and sample-consuming experiment than doing the same thing using sequential MS/MS experiments. Graphical Abstract ᅟ. PMID:27431513

  2. 2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach

    NASA Astrophysics Data System (ADS)

    Floris, Federico; van Agthoven, Maria; Chiron, Lionel; Soulby, Andrew J.; Wootton, Christopher A.; Lam, Yuko P. Y.; Barrow, Mark P.; Delsuc, Marc-André; O'Connor, Peter B.

    2016-09-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors through the modulation of precursor ion cyclotron radii prior to fragmentation. Previous results show that implementation of 2D FT-ICR MS with infrared multi-photon dissociation (IRMPD) and electron capture dissociation (ECD) has turned this method into a useful analytical tool. In this work, IRMPD tandem mass spectrometry of calmodulin (CaM) has been performed both in one-dimensional and two-dimensional FT-ICR MS using a top-down and bottom-up approach. 2D IRMPD FT-ICR MS is used to achieve extensive inter-residue bond cleavage and assignment for CaM, using its unique features for fragment identification in a less time- and sample-consuming experiment than doing the same thing using sequential MS/MS experiments.

  3. Theory for spiralling ions for 2D FT-ICR and comparison with precessing magnetization vectors in 2D NMR.

    PubMed

    Sehgal, Akansha Ashvani; Pelupessy, Philippe; Rolando, Christian; Bodenhausen, Geoffrey

    2016-04-01

    Two-dimensional (2D) Fourier transform ion cyclotron resonance (FT-ICR) offers an approach to mass spectrometry (MS) that pursuits similar objectives as MS/MS experiments. While the latter must focus on one ion species at a time, 2D FT ICR can examine all possible correlations due to ion fragmentation in a single experiment: correlations between precursors, charged and neutral fragments. We revisited the original 2D FT-ICR experiment that has hitherto fallen short of stimulating significant analytical applications, probably because it is technically demanding. These shortcomings can now be overcome by improved FT-ICR instrumentation and computer hard- and software. We seek to achieve a better understanding of the intricacies of the behavior of ions during a basic two-dimensional ICR sequence comprising three simple monochromatic pulses. Through simulations based on Lorentzian equations, we have mapped the ion trajectories for different pulse durations and phases. PMID:26974979

  4. Analysis of Amino Acid Isotopomers using FT-ICR MS

    SciTech Connect

    Pingitore, Francesco; Tang, Yinjie; Kruppa, Gary H.; Keasling,Jay D.

    2006-10-08

    Fluxes through known metabolic pathways and the presence ofnovel metabolic reactions are often determined by feedingisotopically-labeled substrate to an organism and then determining theisotopomer distribution in amino acids in proteins. However, commonlyused techniques to measure the isotopomer distributions requirederivatization prior to analysis (gas chromatography-mass spectrometry(GC-MS)) or large sample sizes (nuclear magnetic resonance (NMR)spectroscopy). Here, we demonstrate the use of Fourier Transform-IonCyclotron Resonance Mass Spectrometry (FT-ICR MS) with direct infusionvia electrospray ionization to rapidly measure the amino acid isotopomerdistribution in a biomass hydrolysate of the soil bacterium Desulfovibriovulgaris Hildenborough. By applying high front-end resolution for theprecursor ion selection followed by sustained off-resonance irradiation -collision-induced dissociation (SORI-CID), it was possible to determineexactly and unambiguously the specific locations of the labeled atoms inthe amino acids, which usually requires a combination of 2-D 13C NMRspectroscopy and GC-MS. This method should be generally applicable toallbiomass samples and will allow more accurate determination of metabolicfluxes with less work and less sample.

  5. Application of Printed Circuit Board Technology to FT-ICR MS Analyzer Cell Construction and Prototyping

    NASA Astrophysics Data System (ADS)

    Leach, Franklin E.; Norheim, Randolph; Anderson, Gordon; Pasa-Tolic, Ljiljana

    2014-12-01

    Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) remains the mass spectrometry platform that provides the highest levels of performance for mass accuracy and resolving power, there is room for improvement in analyzer cell design as the ideal quadrupolar trapping potential has yet to be generated for a broadband MS experiment. To this end, analyzer cell designs have improved since the field's inception, yet few research groups participate in this area because of the high cost of instrumentation efforts. As a step towards reducing this barrier to participation and allowing for more designs to be physically tested, we introduce a method of FT-ICR analyzer cell prototyping utilizing printed circuit boards at modest vacuum conditions. This method allows for inexpensive devices to be readily fabricated and tested over short intervals and should open the field to laboratories lacking or unable to access high performance machine shop facilities because of the required financial investment.

  6. Monitoring the physicochemical degradation of coconut water using ESI-FT-ICR MS.

    PubMed

    Costa, Helber B; Souza, Lindamara M; Soprani, Letícia C; Oliveira, Bruno G; Ogawa, Elizângela M; Korres, Adriana M N; Ventura, José A; Romão, Wanderson

    2015-05-01

    Fresh and aged coconut water (CW) samples were introduced directly into the electrospray ionisation (ESI) source, and were combined with the Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) technique to characterise in situ chemical compounds produced during natural ageing (from 0 to 15 days) at room temperature (23 °C). The ESI-FT-ICR MS readings were acquired and the data were correlated to conventional methodologies: pH, total titratable acidity (TA), total soluble solids, microbial analyses, and ultraviolet visibility (UV-vis) spectroscopy analysis. In general, the pH and TA values changed after 3 days of storage making the CW unsuitable for consumption. The ESI(-)-FT-ICR data also showed a clear and evident change in the chemical profile of CW after 3 days of ageing in the m/z 150-250 and 350-450 regions. Initially, the relative intensity of the natural markers (the m/z 215 and 377 ions-sugar molecules) decreases as a function of ageing time, with the last marker disappearing after 3 days of ageing. New chemical species were then identified such as: citric (m/z 191), galacturonic (m/z 193), gluconic (m/z 195), and saccharic (m/z 209) acids. ESI(-)-FT-ICR MS is a powerful tool to predict the physicochemical properties of CW, such as the pH and TA, where species such as fructose, glucose, sucrose, and gluconic acid can be used as natural markers to monitor the quality of the fruits. PMID:25529663

  7. Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry Coupled to FT-ICR MS: Fundamentals and Applications.

    PubMed

    Benigni, Paolo; Fernandez-Lima, Francisco

    2016-07-19

    In the present paper, we describe the fundamentals and analytical advantages of Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry (OSA-TIMS) when coupled to ultrahigh resolution mass analyzers (e.g., FT-ICR MS). During TIMS analysis, ion packages are spatially resolved based on their mobilities along the TIMS analyzer axis and multiple strategies can be utilized during the trapping and elution of the ion population of interest. In the case of OSA-TIMS-FT-ICR MS, the TIMS operation sequence, trapping conditions, and operations are optimized to increase the signal-to-noise and the number of points across the mobility domain, which leads to more accurate mobility and mass measurements. Experimental results show that accurate ion-neutral collision cross sections (<1%) can be measured using OSA-TIMS-FT-ICR MS with high mobility resolving powers (RIMS up to 250), high mass accuracy (<1 ppm), and ultrahigh mass resolution (RMS up to 600-1200k at m/z 400) in a single analysis. The analytical advantages of OSA-TIMS over SA-TIMS were illustrated for the analysis of structural peptide isomers (SDGRG and GRGDS [M + H](+)), conformational isomers (AT-hook peptide 3 KRGRGRPRK [M + 2H](+2)), and a complex mixture of polyaromatic hydrocarbons (PAH) from coal tar. Baseline separation of the structural peptide isomers SDGRG and GRGDS, [M + H](+), was observed, and three conformations were identified for the AT-hook peptide 3 KRGRGRPRK [M + 2H](+2) during OSA-TIMS-FT-ICR MS. A 2-fold increase in the number of molecular features and a 2-6-fold signal-to-noise increase was observed for OSA-TIMS when compared with SA-TIMS during the PAH analysis. This work provides the proof-of-principle for further application of OSA-TIMS-FT-ICR MS for the unsupervised analysis of complex mixtures based on the characterization of the conformational space and the assignment of chemical formulas in a single analysis. PMID:27340830

  8. Improved protein identification using automated high mass measurement accuracy MALDI FT-ICR MS peptide mass fingerprinting

    NASA Astrophysics Data System (ADS)

    Horn, David M.; Peters, Eric C.; Klock, Heath; Meyers, Andrew; Brock, Ansgar

    2004-11-01

    A comparison between automated peptide mass fingerprinting systems using MALDI-TOF and MALDI FT-ICR MS is presented using 86 overexpressed proteins from Thermotoga maritima. The high mass measurement accuracy of FT-ICR MS greatly reduces the probability of an incorrect assignment of a protein in peptide mass fingerprinting by significantly decreasing the score and peptide sequence coverage of the highest ranked random protein match from the database. This improved mass accuracy led to the identification of all 86 proteins with the FT-ICR data versus 84 proteins using the TOF data against the T. maritima database. The beneficial effect of mass accuracy becomes much more evident with the addition of variable modifications and an increase in the size of the database used in the search. A search of the same data against the T. maritima database with the addition of a variable modification resulted in 77 identifications using MALDI-TOF and 84 identifications using MALDI FT-ICR MS. When searching the NCBInr database, the FT-ICR based system identified 82 of 86 proteins while the TOF based system could only identify 73. The MALDI FT-ICR based system has the further advantage of producing fewer unassigned masses in each peptide mass fingerprint, resulting in greatly reduced sequence coverage and score for the highest ranked random match and improving confidence in the correctly assigned top scoring protein. Finally, the use of rms error as a measure for instrumental mass accuracy is discussed.

  9. FT-ICR MS optimization for the analysis of intact proteins

    SciTech Connect

    Tolmachev, Aleksey V.; Robinson, Errol W.; Wu, Si; Pasa-Tolic, Ljiljana; Smith, Richard D.

    2009-10-15

    Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) remains the technique of choice for the analysis of intact proteins from complex biological systems, i.e. top-down proteomics. Recently, we have implemented a compensated open cylindrical ion trapping cell into a 12 T FT-ICR mass spectrometer. This new cell has previously demonstrated improved sensitivity, dynamic range, and mass measurement accuracy for the analysis of relatively small tryptic peptides. These improvements are due to the improved trapping potential of the cell which is significantly closer to the ideal harmonic trapping potential. Here we report the instrument optimization for the analysis of large macro-molecular ions, such as proteins. Also, presented are first principle theoretical considerations to account for different optimum conditions for the analysis of large macro-molecules. The proposed high energy ion loss mechanism is further supported by experimental results of bovine ubiquitin and serum albumin. We find that the analysis of large macro-molecules can be significantly improved by the further reduction of pressure in the ion trapping cell. This will reduce the impact of the high energy ion loss mechanism and enable increased sensitivity and mass measurement accuracy to be realized without compromising resolution. Further, these results appear to be applicable to FTMS in general, and the high energy ion loss mechanism applies to Orbitrap mass analyzers as well.

  10. Broad-Band FT-ICR MS for the Penning-Trap Mass Spectrometer MATS

    SciTech Connect

    Rodriguez, D.; Cakirli, R. B.; Schweikhard, L.; Stahl, S.; Ubieto-Diaz, M.

    2010-08-04

    Ion traps are known as ideal tools for precision measurements of fundamental particle properties. In particular, traps have been set up at Radioactive Ion Beam (RIB) facilities to investigate exotic nuclei. During the last decade this field of research has constantly grown, with currently almost a dozen ion-trap systems at RIB facilities in Europe and North America and several more planned at future accelerators projects. One of these, the Advanced Trapping System MATS will be installed at the low-energy branch for radioactive-ion beams at the Facility for Antiprotons and Ion Research (FAIR) in Darmstadt (Germany). One of the MATS features will be non-destructive ion detection based on Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry (FT-ICR MS). A prototype of the system has been developed at the Max-Planck-Institute for Nuclear Physics in Heidelberg (Germany) and recent results are outlined in this contribution.

  11. Application of Printed Circuit Board Technology to FT-ICR MS Analyzer Cell Construction and Prototyping

    SciTech Connect

    Leach, Franklin E.; Norheim, Randolph V.; Anderson, Gordon A.; Pasa-Tolic, Ljiljana

    2014-12-01

    Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS) remains themass spectrometry platform that provides the highest levels of performance for mass accuracy and resolving power, there is room for improvement in analyzer cell design as the ideal quadrupolar trapping potential has yet to be generated for a broadband MS experiment. To this end, analyzer cell designs have improved since the field’s inception, yet few research groups participate in this area because of the high cost of instrumentation efforts. As a step towards reducing this barrier to participation and allowing for more designs to be physically tested, we introduce a method of FT-ICR analyzer cell prototyping utilizing printed circuit boards at modest vacuum conditions. This method allows for inexpensive devices to be readily fabricated and tested over short intervals and should open the field to laboratories lacking or unable to access high performance machine shop facilities because of the required financial investment.

  12. FT-ICR MS optimization for the analysis of intact proteins.

    PubMed

    Tolmachev, Aleksey V; Robinson, Errol W; Wu, Si; Paša-Tolić, Ljiljana; Smith, Richard D

    2009-10-15

    Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) remains the technique of choice for the analysis of intact proteins from complex biological systems, i.e. top-down proteomics. Recently, we have implemented a compensated open cylindrical ion trapping cell into a 12 T FT-ICR mass spectrometer. This new cell has previously demonstrated improved sensitivity, dynamic range, and mass measurement accuracy for the analysis of relatively small tryptic peptides. These improvements are due to the modified trapping potential of the cell which closely approximates the ideal harmonic trapping potential. Here, we report the instrument optimization for the analysis of large macro-molecular ions, such as proteins. Single transient mass spectra of multiply charged bovine ubiquitin ions with sub-ppm mass measurement accuracy, improved signal intensity, and increased dynamic range were obtained using this new cell with increased post-excitation cyclotron radii. The increased cyclotron radii correspond to increased ion kinetic energy and collisions between neutrals and ions with sufficient kinetic energy can exceed a threshold of single collision ion fragmentation. A transition then occurs from relatively long signal lifetimes at low excitation radii to potentially shorter lifetimes, defined by the average ion-neutral collision time. The proposed high energy ion loss mechanism is evaluated and compared with experimental results for bovine ubiquitin and serum albumin. We find that the analysis of large macro-molecules can be significantly improved by the further reduction of pressure in the ion trapping cell. This reduces the high energy ion losses and can enable increased sensitivity and mass measurement accuracy to be realized without compromising resolution. Further, these results appear to be generally applicable to FTMS, and it is expected that the high energy ion loss mechanism also applies to Orbitrap mass analyzers. PMID:20473360

  13. Electrospray ionization FT-ICR/MS Investigation of Zinc Sulfate Clusters

    NASA Astrophysics Data System (ADS)

    Chen, K.; Lemke, K.

    2013-12-01

    Zinc sulfate (ZnSO4) is a common salt present in oxidized surface waters and may serve as a suitable model material to better understand precipitation/nucleation processes in aqueous fluids. In brief, precipitation of ZnSO4 commences with single molecule association (complexation) reactions and proceeds via a wide range of prenucleation clusters (ZnSO4)n and nanocrystalites ultimately toward bulk ZnSO4. Evidently, ZnSO4 growth will pass through the cluster-size domain, from which small ZnSO4 cluster subunits emerge with characteristic chain, sheet and 3-D structures. This experimental study focuses on small zinc sulfate clusters and provides a set of preliminary results pertaining to the stoichiometry, abundance and stability of these materials in aqueous environments. At present, very little is known with respect to the composition, structure and stability of ZnSO4 at the cluster level, however, electrospray ionization (ESI) mass spectrometry can provide detailed insight into the aforementioned features of ZnSO4. In addition, application of resonance techniques, such as high-resolution Fourier Transfer Ion Cyclotron Resonance Mass Spectrometry (FT-ICR/MS) provides detailed information with respect to the molecular composition of individual ion clusters at high resolution. Here we present the stoichiometries of zinc sulfate ion clusters identified using FT-ICR/MS. In 15mM dilute aqueous solution of zinc sulfate, singly-charged ion clusters [Znm(SO4)m-1(OH)●(H2O)n]+ with m=2, 3, 4 and 5 have been identified. In addition, a set of doubly-charged clusters with the general form [Znm(SO4)m-1●(H2O)n]2+ with 4≤m≤10 have been characterized. We will propose a scheme, in which singly-charged cluster species with m=4,5 are regarded to be of a critical-size from which stable doubly-charged ions begin to emerge. Upon passing the m~4-5 size-range, zinc sulfate clusters exhibit a strong affinity towards water with stable hepta-hydrates marking the upper range of

  14. Distributed computing strategies for processing of FT-ICR MS imaging datasets for continuous mode data visualization

    SciTech Connect

    Smith, Donald F.; Schulz, Carl; Konijnenburg, Marco; Kilic, Mehmet; Heeren, Ronald M.

    2015-03-01

    High-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry imaging enables the spatial mapping and identification of biomolecules from complex surfaces. The need for long time-domain transients, and thus large raw file sizes, results in a large amount of raw data (“big data”) that must be processed efficiently and rapidly. This can be compounded by largearea imaging and/or high spatial resolution imaging. For FT-ICR, data processing and data reduction must not compromise the high mass resolution afforded by the mass spectrometer. The continuous mode “Mosaic Datacube” approach allows high mass resolution visualization (0.001 Da) of mass spectrometry imaging data, but requires additional processing as compared to featurebased processing. We describe the use of distributed computing for processing of FT-ICR MS imaging datasets with generation of continuous mode Mosaic Datacubes for high mass resolution visualization. An eight-fold improvement in processing time is demonstrated using a Dutch nationally available cloud service.

  15. Distributed computing strategies for processing of FT-ICR MS imaging datasets for continuous mode data visualization.

    PubMed

    Smith, Donald F; Schulz, Carl; Konijnenburg, Marco; Kilic, Mehmet; Heeren, Ron M A

    2015-03-01

    High-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry imaging enables the spatial mapping and identification of biomolecules from complex surfaces. The need for long time-domain transients, and thus large raw file sizes, results in a large amount of raw data ("big data") that must be processed efficiently and rapidly. This can be compounded by large-area imaging and/or high spatial resolution imaging. For FT-ICR, data processing and data reduction must not compromise the high mass resolution afforded by the mass spectrometer. The continuous mode "Mosaic Datacube" approach allows high mass resolution visualization (0.001 Da) of mass spectrometry imaging data, but requires additional processing as compared to feature-based processing. We describe the use of distributed computing for processing of FT-ICR MS imaging datasets with generation of continuous mode Mosaic Datacubes for high mass resolution visualization. An eight-fold improvement in processing time is demonstrated using a Dutch nationally available cloud service. PMID:25273594

  16. Probing the mechanisms of an air amplifier using a LTQ-FT-ICR-MS and fluorescence spectroscopy.

    PubMed

    Dixon, R Brent; Muddiman, David C; Hawkridge, Adam M; Fedorov, A G

    2007-11-01

    We report the first quantitative assessment of electrosprayed droplet/ion focusing enabled by the use of a voltage-assisted air amplifier between an electrospray ionization emitter and a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (ESI-LTQ-FT-ICR-MS). A solution of fluorescent dye was electrosprayed with a stainless steel mesh screen placed in front of the MS inlet capillary acting as a gas-permeable imaging plate for fluorescence spectroscopy. Without use of the air amplifier, no detectable FT-ICR signal was observed, as well as no detectable fluorescence on the screen upon imaging using a fluorescence scanner. When the air amplifier was turned ON while electrospraying the fluorescent dye, FT-ICR mass spectra with high signal to noise ratio were obtained with an average ion injection time of 21 ms for an AGC target value of 5 x 10(5). Imaging of the screen using a fluorescence scanner produced a distinct spot of cross-sectional area approximately 33.5 mm(2) in front of the MS inlet capillary. These experimental results provide direct evidence of aerodynamic focusing of electrosprayed droplets/ions enabled by an air amplifier, resulting in improved electrospray droplet/ion capture efficiency and reduced ion injection time. A second set of experiments was carried out to explore whether the air amplifier assists in desolvation. By electrospraying a mix of quaternary amines, ratios of increasingly hydrophobic molecules were obtained. Observation of the solvophobic effect associated with electrospray ionization resulted in a higher abundance of the hydrophobic molecule. This bias was eliminated when the air amplifier was turned ON and a response indicative of the respective component concentrations of the molecules in the bulk solution was observed. PMID:17855111

  17. Dissolved organic carbon (DOC) in soil extracts investigated by FT-ICR-MS

    NASA Astrophysics Data System (ADS)

    Hofmann, D.; Steffen, D.; Jablonowski, N. D.; Burauel, P.

    2012-04-01

    Soil drying and rewetting usually increases the release of xenobiotics like pesticides present in agricultural soils. Besides the effect on the release of two aged 14C-labeled pesticide residues we focus on the characterisation of simultaneously remobilized dissolved organic carbon (DOC) to gain new insights into structure and stability aspects of soil organic carbon fractions. The test soil (gleyic cambisol; Corg 1.2%, pH 7.2) was obtained from the upper soil layer of two individual outdoor lysimeter studies containing either environmentally long-term aged 14C residues of the herbicide ethidimuron (0-10 cm depth; time of aging: 9 years) or methabenzthiazuron (0-30 cm depth; time of aging: 17 years). Soil samples (10 g dry soil equivalents) were (A=dry/wet) previously dried (45°C) or (B=wet/wet) directly mixed with pure water (1+2, w:w), shaken (150 rpm, 1 h), and centrifuged (2000 g). This extraction procedure was repeated several individual times, for both setups. The first three individual extractions, respectively were used for further investigations. Salt was removed from samples prior analysis because of a possible quench effect in the electrospray (ESI) source by solid phase extraction (SPE) with Chromabond C18 Hydra-cartridges (Macherey-Nagel) and methanol as backextraction solvent. The so preconcentrated and desalted samples were introduced by flow injection analysis (FIA) in a fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS), equipped with an ESI source and a 7 T supra-conducting magnet (LTQ-FT Ultra, ThermoFisher Scientific). This technique is the key technique for complex natural systems attributed by their outstanding mass resolution (used 400.000 at m/z 400 Da) and mass accuracy (≤ 1ppm) by simultaneously providing molecular level details of thousands of compounds and was successful applied for the investigations of natural organic matter (NOM) different sources like marine and surface water, soil, sediment, bog and crude oil

  18. FT-ICR/MS and GC-EI/MS metabolomics networking unravels global potato sprout's responses to Rhizoctonia solani infection.

    PubMed

    Aliferis, Konstantinos A; Jabaji, Suha

    2012-01-01

    The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The developed bioanalytical and bioinformatics protocols provided a snapshot of the sprout's global metabolic network and its perturbations as a result of pathogen invasion. Mevalonic acid and deoxy-xylulose pathways were substantially up-regulated leading to the biosynthesis of sesquiterpene alkaloids such as the phytoalexins phytuberin, rishitin, and solavetivone, and steroidal alkaloids having solasodine and solanidine as their common aglycons. Additionally, the perturbation of the sprout's metabolism was depicted in fluctuations of the content of their amino acids pool and that of carboxylic and fatty acids. Components of the systemic acquired resistance (SAR) and hypersensitive reaction (HR) such as azelaic and oxalic acids were detected in increased levels in infected sprouts and strategies of the pathogen to overcome plant defense were proposed. Our metabolic approach has not only greatly expanded the multitude of metabolites previously reported in potato in response to pathogen invasion, but also enabled the identification of bioactive plant-derived metabolites providing valuable information that could be exploited in biotechnology, biomarker-assisted plant breeding, and crop protection for the development of new crop protection agents. PMID:22880040

  19. FT-ICR/MS and GC-EI/MS Metabolomics Networking Unravels Global Potato Sprout's Responses to Rhizoctonia solani Infection

    PubMed Central

    Aliferis, Konstantinos A.; Jabaji, Suha

    2012-01-01

    The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The developed bioanalytical and bioinformatics protocols provided a snapshot of the sprout's global metabolic network and its perturbations as a result of pathogen invasion. Mevalonic acid and deoxy-xylulose pathways were substantially up-regulated leading to the biosynthesis of sesquiterpene alkaloids such as the phytoalexins phytuberin, rishitin, and solavetivone, and steroidal alkaloids having solasodine and solanidine as their common aglycons. Additionally, the perturbation of the sprout's metabolism was depicted in fluctuations of the content of their amino acids pool and that of carboxylic and fatty acids. Components of the systemic acquired resistance (SAR) and hypersensitive reaction (HR) such as azelaic and oxalic acids were detected in increased levels in infected sprouts and strategies of the pathogen to overcome plant defense were proposed. Our metabolic approach has not only greatly expanded the multitude of metabolites previously reported in potato in response to pathogen invasion, but also enabled the identification of bioactive plant-derived metabolites providing valuable information that could be exploited in biotechnology, biomarker-assisted plant breeding, and crop protection for the development of new crop protection agents. PMID:22880040

  20. Comparison of collision-induced dissociation and electron-induced dissociation of phillyrin using FT-ICR MS

    NASA Astrophysics Data System (ADS)

    Lin, Zhenguang; Lin, Zhiwei; Mu, Yingdi; Yan, Dong

    2016-10-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry using collision-induced dissociation (CID) and electron capture dissociation (ECD) at high mass resolution was first applied to investigate the characteristic fragment ions of phillyrin. The CID experimental results demonstrated the elemental composition of fragment ions unambiguously, so a reasonable fragmentation pathway of phillyrin was proposed. The ECD fragmentation mechanism was believed to be fundamentally different from the CID method. ECD could be used not only in the biological field but also as a powerful complement to the structural identification of small molecular compounds. The characteristic fragmentation pathways were helpful in analyzing and interpreting the stability and property of the parent ion. The ESI FT-ICR MS using CID and ECD methods was applied to investigate the characteristic fragment ions of Phillyrin for the first time. The fragmentation process of phillyrin which formation of the peroxide bond by CID, was discussed in detail. These characteristic fragmentation pathways were helpful to analyze and interpret the stability and property of the parent ion. It was clearly demonstrated that ECD can be not only used to Biological field but also a powerful complement to the structure identification of small molecules.

  1. High-field FT-ICR-MS and aromaticity equivalent approach for structural identification of water soluble organic compounds (WSOC)

    NASA Astrophysics Data System (ADS)

    Harir, Mourad; Yassine, Mahmoud M.; Dabek-Zlotorzynska, Ewa; Hertkorn, Norbert; Schmitt-Kopplin, Philippe

    2015-04-01

    Organic aerosol (OA) makes up a large and often dominant fraction, (20 to 90%) of the submicron atmospheric particulate mass, and its effects are becoming increasingly important in determining climatic and health effects of atmospheric aerosols. Despite the abundance of OA, our understanding of the sources, formation processes and atmospheric properties of OA is limited. Atmospheric OA has both primary (directly emitted) and secondary (formed in the atmosphere from precursor gases) sources, which can be natural (e.g. vegetation) and/or anthropogenic (e.g. fossil-based vehicle exhaust or biomass burning). A significant fraction of OA contains as much as 20-70% of water soluble organic compounds (WSOC). The WSOC fraction is a very complex mixture of low volatility, polyfunctional aliphatic and aromatic compounds containing carboxyl, alcohol, carbonyl, sulfo, nitro, and other functionalities. This high degree of chemical complexity of atmospheric organics has inspired a number of sophisticated approaches that are capable of identifying and detecting a variety of different analytes in OA. Accordingly, one of the most challenging areas of atmospheric particulate matter (PM) analysis is to comprehend the molecular complexity of the OA, especially WSOC fraction, a significant component of atmospheric fine PM (PM2.5). The sources of WSOC are not well understood, especially the relative contributions of primary vs. secondary organic aerosol. Therefore, the molecular characterization of WSOC is important because it allows gaining insight into aerosol sources and underlying mechanisms of secondary organic aerosols (SOA) formation and transformation. In this abstract, molecular characterization of WSOC was achieved using high-field mass spectrometry FT-ICR-MS and aromaticity equivalent approach. Aromaticity equivalent (Xc), defined recently as a new parameter calculated from the assigned molecular formulas (complementary to the aromaticity index [1]), is introduced to improve

  2. Characterization of chemical constituents in Rhodiola Crenulate by high-performance liquid chromatography coupled with Fourier-transform ion cyclotron resonance mass spectrometer (HPLC-FT-ICR MS).

    PubMed

    Han, Fei; Li, Yanting; Mao, Xinjuan; Xu, Rui; Yin, Ran

    2016-05-01

    In this work, an approach using high-performance liquid chromatography coupled with diode-array detection and Fourier-transform ion cyclotron resonance mass spectrometer (HPLC-FT-ICR MS) for the identification and profiling of chemical constituents in Rhodiola crenulata was developed for the first time. The chromatographic separation was achieved on an Inertsil ODS-3 column (150 mm × 4.6 mm,3 µm) using a gradient elution program, and the detection was performed on a Bruker Solarix 7.0 T mass spectrometer equipped with electrospray ionization source in both positive and negative modes. Under the optimized conditions, a total of 48 chemical compounds, including 26 alcohols and their glycosides, 12 flavonoids and their glycosides, 5 flavanols and gallic acid derivatives, 4 organic acids and 1 cyanogenic glycoside were identified or tentatively characterized. The results indicated that the developed HPLC-FT-ICR MS method with ultra-high sensitivity and resolution is suitable for identifying and characterizing the chemical constituents in R. crenulata. And it provides a helpful chemical basis for further research on R. crenulata. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27194521

  3. Photochemical changes in water accommodated fractions of MC252 and surrogate oil created during solar exposure as determined by FT-ICR MS.

    PubMed

    Vaughan, Pamela P; Wilson, Tashiema; Kamerman, Rebecca; Hagy, Melissa E; McKenna, Amy; Chen, Huan; Jeffrey, Wade H

    2016-03-15

    To determine effects of photochemical weathering of petroleum, surrogate and Macondo (MC252) crude oils were exposed to solar radiation during the formation of Water Accommodated Fractions (WAFs) in sterile seawater. Samples were incubated in either unfiltered sunlight, with ultraviolet radiation blocked (Photosynthetically Active Radiation [PAR] only), or in darkness. WAFs were collected at two time points over the course of a week. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) analyses of water soluble species formed during exposure to sunlight were compared for the different treatments. Photochemical alterations resulted in differences in compound class distributions. In general, surrogate oil was photo-oxidized across a wider carbon number range compared to MC252. While photochemical differences were observed between MC252 and surrogate oils, microbial production in seawater responded similarly to both WAFs from both types of oils with the majority of the inhibition resulting from oil exposure to visible light. PMID:26774346

  4. The comparison of naturally weathered oil and artificially photo-degraded oil at the molecular level by a combination of SARA fractionation and FT-ICR MS.

    PubMed

    Islam, Ananna; Cho, Yunju; Yim, Un Hyuk; Shim, Won Joon; Kim, Young Hwan; Kim, Sunghwan

    2013-12-15

    Two sets of oil samples, one obtained from different weathering stages of the M/V Hebei Spirit oil spill site and the other prepared by an in vitro photo-degradation experiment, were analyzed and compared at the molecular level by atmospheric pressure photo-ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). For a more detailed comparison at the molecular level, the oil samples were separated into saturate, aromatic, resin, and asphaltene (SARA) fractions before MS analysis. Gravimetric analysis of the SARA fractions revealed a decreased weight percentage of the aromatic fraction and an increased resin fraction in both sets of samples. Molecular-level investigations of the SARA fractions showed a significant reduction in the S1 class in the saturate fraction and increase of S1O1 class compounds with high DBE values in resin fraction. Levels of N1 and N1O1 class compounds resulting in protonated ions (presumably basic nitrogen compounds) increased after degradation compared to compounds generating molecular ions (presumably non-basic nitrogen compounds). This study revealed changes occurring in heteroatom polar species of crude oils such as sulfur and nitrogen containing compounds that have not been easily detected with conventional GC based techniques. PMID:24231315

  5. Chemical Composition and Potential Environmental Impacts of Water-Soluble Polar Crude Oil Components Inferred from ESI FT-ICR MS

    PubMed Central

    Liu, Yina; Kujawinski, Elizabeth B.

    2015-01-01

    Polar petroleum components enter marine environments through oil spills and natural seepages each year. Lately, they are receiving increased attention due to their potential toxicity to marine organisms and persistence in the environment. We conducted a laboratory experiment and employed state-of-the-art Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to characterize the polar petroleum components within two operationally-defined seawater fractions: the water-soluble fraction (WSF), which includes only water-soluble molecules, and the water-accommodated fraction (WAF), which includes WSF and microscopic oil droplets. Our results show that compounds with higher heteroatom (N, S, O) to carbon ratios (NSO:C) than the parent oil were selectively partitioned into seawater in both fractions, reflecting the influence of polarity on aqueous solubility. WAF and WSF were compositionally distinct, with unique distributions of compounds across a range of hydrophobicity. These compositional differences will likely result in disparate impacts on environmental health and organismal toxicity, and thus highlight the need to distinguish between these often-interchangeable terminologies in toxicology studies. We use an empirical model to estimate hydrophobicity character for individual molecules within these complex mixtures and provide an estimate of the potential environmental impacts of different crude oil components. PMID:26327219

  6. Chemical Composition and Potential Environmental Impacts of Water-Soluble Polar Crude Oil Components Inferred from ESI FT-ICR MS.

    PubMed

    Liu, Yina; Kujawinski, Elizabeth B

    2015-01-01

    Polar petroleum components enter marine environments through oil spills and natural seepages each year. Lately, they are receiving increased attention due to their potential toxicity to marine organisms and persistence in the environment. We conducted a laboratory experiment and employed state-of-the-art Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to characterize the polar petroleum components within two operationally-defined seawater fractions: the water-soluble fraction (WSF), which includes only water-soluble molecules, and the water-accommodated fraction (WAF), which includes WSF and microscopic oil droplets. Our results show that compounds with higher heteroatom (N, S, O) to carbon ratios (NSO:C) than the parent oil were selectively partitioned into seawater in both fractions, reflecting the influence of polarity on aqueous solubility. WAF and WSF were compositionally distinct, with unique distributions of compounds across a range of hydrophobicity. These compositional differences will likely result in disparate impacts on environmental health and organismal toxicity, and thus highlight the need to distinguish between these often-interchangeable terminologies in toxicology studies. We use an empirical model to estimate hydrophobicity character for individual molecules within these complex mixtures and provide an estimate of the potential environmental impacts of different crude oil components. PMID:26327219

  7. Molecular-Scale Investigation with ESI-FT-ICR-MS on Fractionation of Dissolved Organic Matter Induced by Adsorption on Iron Oxyhydroxides.

    PubMed

    Lv, Jitao; Zhang, Shuzhen; Wang, Songshan; Luo, Lei; Cao, Dong; Christie, Peter

    2016-03-01

    Adsorption by minerals is a common geochemical process of dissolved organic matter (DOM) which may induce fractionation of DOM at the mineral-water interface. Here, we examine the molecular fractionation of DOM induced by adsorption onto three common iron oxyhydroxides using electrospray ionization coupled with Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). Ferrihydrite exhibited higher affinity to DOM and induced more pronounced molecular fractionation of DOM than did goethite or lepidocrocite. High molecular weight (>500 Da) compounds and compounds high in unsaturation or rich in oxygen including polycyclic aromatics, polyphenols and carboxylic compounds had higher affinity to iron oxyhydroxides and especially to ferrihydrite. Low molecular weight compounds and compounds low in unsaturation or containing few oxygenated groups (mainly alcohols and ethers) were preferentially maintained in solution. This study confirms that the double bond equivalence and the number of oxygen atoms are valuable parameters indicating the selective fractionation of DOM at mineral and water interfaces. The results of this study provide important information for further understanding the behavior of DOM in the natural environment. PMID:26815589

  8. A rapid and sensitive UHPLC-FT-ICR MS/MS method for identification of chemical constituents in Rhodiola crenulata extract, rat plasma and rat brain after oral administration.

    PubMed

    Han, Fei; Li, Yanting; Ma, Li; Liu, Tianfeng; Wu, Yawen; Xu, Rui; Song, Aihua; Yin, Ran

    2016-11-01

    A rapid and sensitive UHPLC-FT-ICR MS/MS method was developed for the first time to analyze the extract of Rhodiola crenulata and the constituents absorbed into rat blood and brain after oral administration. Under the optimized conditions, a total of 64 chemical constituents were identified or tentatively characterized in vitro in 30min, and also 24 and 9 chemical constituents were detected in rat plasma and brain respectively, by comparing the retention time, accurate mass and/or MS/MS data of blank and dosed sample. The results indicated that the developed UHPLC-FT-ICR MS/MS method was suitable for detection and identifying the chemical constituents in Rhodiola crenulata extract, rat plasma and rat brain, and it could be used as a powerful and reliable analytical strategy for rapid identification of chemical constituents in vitro and in vivo for other traditional Chinese herbal medicines (TCMs). Furthermore, the detected chemical constituents in rat brain could be speculated to be the pharmacodynamic substances of Rhodiola crenulata for Alzheimer's disease (AD) and it could also provide useful chemical information for further mass spectrometry imaging and bioactive substances research on Rhodiola crenulata. PMID:27591603

  9. High-resolution MALDI-FT-ICR MS imaging for the analysis of metabolites from formalin-fixed, paraffin-embedded clinical tissue samples.

    PubMed

    Buck, Achim; Ly, Alice; Balluff, Benjamin; Sun, Na; Gorzolka, Karin; Feuchtinger, Annette; Janssen, Klaus-Peter; Kuppen, Peter J K; van de Velde, Cornelis J H; Weirich, Gregor; Erlmeier, Franziska; Langer, Rupert; Aubele, Michaela; Zitzelsberger, Horst; Aichler, Michaela; Walch, Axel

    2015-09-01

    We present the first analytical approach to demonstrate the in situ imaging of metabolites from formalin-fixed, paraffin-embedded (FFPE) human tissue samples. Using high-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR MSI), we conducted a proof-of-principle experiment comparing metabolite measurements from FFPE and fresh frozen tissue sections, and found an overlap of 72% amongst 1700 m/z species. In particular, we observed conservation of biomedically relevant information at the metabolite level in FFPE tissues. In biomedical applications, we analysed tissues from 350 different cancer patients and were able to discriminate between normal and tumour tissues, and different tumours from the same organ, and found an independent prognostic factor for patient survival. This study demonstrates the ability to measure metabolites in FFPE tissues using MALDI-FT-ICR MSI, which can then be assigned to histology and clinical parameters. Our approach is a major technical, histochemical, and clinicopathological advance that highlights the potential for investigating diseases in archived FFPE tissues. PMID:25965788

  10. Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry: Theory and simulations.

    PubMed

    Nikolaev, Eugene N; Kostyukevich, Yury I; Vladimirov, Gleb N

    2016-01-01

    Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer offers highest resolving power and mass accuracy among all types of mass spectrometers. Its unique analytical characteristics made FT ICR important tool for proteomics, metabolomics, petroleomics, and investigation of complex mixtures. Signal acquisition in FT ICR MS takes long time (up to minutes). During this time ion-ion interaction considerably affects ion motion and result in decreasing of the resolving power. Understanding of those effects required complicated theory and supercomputer simulations but culminated in the invention of the ion trap with dynamic harmonization which demonstrated the highest resolving power ever achieved. In this review we summarize latest achievements in theory and simulation of FT ICR mass spectrometers. PMID:24515872

  11. Molecular formula assignment for dissolved organic matter (DOM) using high-field FT-ICR-MS: chemical perspective and validation of sulphur-rich organic components (CHOS) in pit lake samples.

    PubMed

    Herzsprung, Peter; Hertkorn, Norbert; von Tümpling, Wolf; Harir, Mourad; Friese, Kurt; Schmitt-Kopplin, Philippe

    2016-04-01

    Molecular formula assignment is one of the key challenges in processing high-field Fourier transform ion cyclotron resonance mass spectrometric (FT-ICR-MS) datasets. The number of potential solutions for an elemental formula increases exponentially with increasing molecular mass, especially when non-oxygen heteroatoms like N, S or P are included. A method was developed from the chemical perspective and validated using a Suwannee River Fulvic Acid (SRFA) dataset which is dominated by components consisting exclusively of C, H and O (78 % CHO). In order to get information on the application range and robustness of this method, we investigated a FT-ICR-MS dataset which was merged from 18 mine pit lake pore waters and 3 river floodplain soil waters. This dataset contained 50 % CHO and 18 % CHOS on average, whereas the former SRFA dataset contained only 1.5 % CHOS. The mass calculator was configured to allow up to five nitrogen atoms and up to one sulphur atom in assigning formulas to mass peaks. More than 50 % multiple-formula assignments were found for peaks with masses > 650 Da. Based on DBE - O frequency diagrams, many CHO, CHOS1, CHON1 and CHON1S1 molecular series were ultimately assigned to many m/z and considered to be reliable solutions. The unequivocal data pool could thus be enlarged by 523 (6.8 %) CHOS1 components. In contrast to the method validation with CHO-rich SRFA, validation with sulphur-rich pit lake samples showed that formulas with a higher number of non-oxygen heteroatoms can be more reliable assignments in many cases. As an example: CHOS molecular series were reliable and the CHO classes were unreliable amongst other molecular classes in many multiple-formula assignments from the sulphur-rich pit lake samples. Graphical abstract An exemplary frequency versus DBE - O diagram. CHOS components but not CHO (and not CHON2 or CHON2S) components were considered here reliable. PMID:26883969

  12. Automated microextraction sample preparation coupled on-line to FT-ICR-MS: application to desalting and concentration of river and marine dissolved organic matter.

    PubMed

    Morales-Cid, Gabriel; Gebefugi, Istvan; Kanawati, Basem; Harir, Mourad; Hertkorn, Norbert; Rosselló-Mora, Ramón; Schmitt-Kopplin, Philippe

    2009-10-01

    Sample preparation procedures are in most cases sample- and time-consuming and commonly require the use of a large amount of solvents. Automation in this regard can optimize the minimal-needed injection volume and the solvent consumption will be efficiently reduced. A new fully automated sample desalting and pre-concentration technique employing microextraction by packed sorbents (MEPS) cartridges is implemented and coupled to an ion cyclotron resonance Fourier-transform mass spectrometer (ICR-FT/MS). The performance of non-target mass spectrometric analysis is compared for the automated versus off-line sample preparation for several samples of aqueous natural organic matter. This approach can be generalized for any metabolite profiling or metabolome analysis of biological materials but was optimized herein using a well characterized but highly complex organic mixture: a surface water and its well-characterized natural organic matter and a marine sample having a highly salt charge and enabling to validate the presented automatic system for salty samples. The analysis of Suwannee River water showed selective C18-MEPS enrichment of chemical signatures with average H/C and O/C elemental ratios and loss of both highly polar and highly aromatic structures from the original sample. Automated on-line application to marine samples showed desalting and different chemical signatures from surface to bottom water. Relative comparison of structural footprints with the C18-concentration/desalting procedure however enabled to demonstrate that the surface water film was more concentrated in surface-active components of natural (fatty acids) and anthropogenic origin (sulfur-containing surfactants). Overall, the relative standard deviation distribution in terms of peak intensity was improved by automating the proposed on-line method. PMID:19685041

  13. Tracking the Magnetron Motion in FT-ICR Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Jertz, Roland; Friedrich, Jochen; Kriete, Claudia; Nikolaev, Evgeny N.; Baykut, Gökhan

    2015-08-01

    In Fourier transform ion cyclotron resonance spectrometry (FT-ICR MS) the ion magnetron motion is not usually directly measured, yet its contribution to the performance of the FT-ICR cell is important. Its presence is manifested primarily by the appearance of even-numbered harmonics in the spectra. In this work, the relationship between the ion magnetron motion in the ICR cell and the intensities of the second harmonic signal and its sideband peak in the FT-ICR spectrum is studied. Ion motion simulations show that during a cyclotron motion excitation of ions which are offset to the cell axis, a position-dependent radial drift of the cyclotron center takes place. This radial drift can be directed outwards if the ion is initially offset towards one of the detection electrodes, or it can be directed inwards if the ion is initially offset towards one of the excitation electrodes. Consequently, a magnetron orbit diameter can increase or decrease during a resonant cyclotron excitation. A method has been developed to study this behavior of the magnetron motion by acquiring a series of FT-ICR spectra using varied post-capture delay (PCD) time intervals. PCD is the delay time after the capture of the ions in the cell before the cyclotron excitation of the ion is started. Plotting the relative intensity of the second harmonic sideband peak versus the PCD in each mass spectrum leads to an oscillating "PCD curve". The position and height of minima and maxima of this curve can be used to interpret the size and the position of the magnetron orbit. Ion motion simulations show that an off-axis magnetron orbit generates even-numbered harmonic peaks with sidebands at a distance of one magnetron frequency and multiples of it. This magnetron offset is due to a radial offset of the electric field axis versus the geometric cell axis. In this work, we also show how this offset of the radial electric field center can be corrected by applying appropriate DC correction voltages to the

  14. Advanced characterisation of organic matter in oil sands and tailings sands used for land reclamation by Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS)

    NASA Astrophysics Data System (ADS)

    Noah, M.; Vieth-Hillebrand, A.; Wilkes, H.

    2012-04-01

    subsequent separation into asphaltenes, aliphatic hydrocarbons, aromatic hydrocarbons, neutral nitrogen, sulphur, oxygen (NSO) compounds and carboxylic acids. The asphaltene fractions are analysed using pyrolysis-GC, all other fractions are analysed by GC-MS. Additionally Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) is used to study the chemical composition of the samples on the molecular level using different ionisation methods.

  15. Ultrahigh-resolution FT-ICR mass spectrometry characterization of a-pinene ozonolysis SOA

    EPA Science Inventory

    Secondary organic aerosol (SOA) of α-pinene ozonolysis with and without hydroxyl radical scavenging hexane was characterized by ultrahigh-resolution. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Molecular formulas for more than 900 negative ions were i...

  16. Analysis of archaeological triacylglycerols by high resolution nanoESI, FT-ICR MS and IRMPD MS/MS: Application to 5th century BC-4th century AD oil lamps from Olbia (Ukraine)

    NASA Astrophysics Data System (ADS)

    Garnier, Nicolas; Rolando, Christian; Høtje, Jakob Munk; Tokarski, Caroline

    2009-07-01

    This work presents the precise identification of triacylglycerols (TAGs) extracted from archaeological samples using a methodology based on nanoelectrospray and Fourier transform mass spectrometry. The archaeological TAG identification needs adapted sample preparation protocols to trace samples in advanced degradation state. More precisely, the proposed preparation procedure includes extraction of the lipid components from finely grinded ceramic using dichloromethane/methanol mixture with additional ultrasonication treatment, and TAG purification by solid phase extraction on a diol cartridge. Focusing on the analytical approach, the implementation of "in-house" species-dependent TAG database was investigated using MS and InfraRed Multiphoton Dissociation (IRMPD) MS/MS spectra; several vegetal oils, dairy products and animal fats were studied. The high mass accuracy of the Fourier transform analyzer ([Delta]m below 2.5 ppm) provides easier data interpretation, and allows distinction between products of different origins. In details, the IRMPD spectra of the lithiated TAGs reveal fragmentation reactions including loss of free neutral fatty acid and loss of fatty acid as [alpha],[beta]-unsaturated moieties. Based on the developed preparation procedure and on the constituted database, TAG extracts from 5th century BC to 4th century AD Olbia lamps were analyzed. The structural information obtained succeeds in identifying that bovine/ovine fats were used as fuel used in these archaeological Olbia lamps.

  17. Molecular characterization and comparison of shale oils generated by different pyrolysis methods using FT-ICR mass spectrometry

    USGS Publications Warehouse

    Jin, J.M.; Kim, S.; Birdwell, J.E.

    2011-01-01

    Fourier transform ion cyclotron resonance mass spectrometry (FT ICR-MS) was applied in the analysis of shale oils generated using two different pyrolysis systems under laboratory conditions meant to simulate surface and in situ oil shale retorting. Significant variations were observed in the shale oils, particularly the degree of conjugation of the constituent molecules. Comparison of FT ICR-MS results to standard oil characterization methods (API gravity, SARA fractionation, gas chromatography-flame ionization detection) indicated correspondence between the average Double Bond Equivalence (DBE) and asphaltene content. The results show that, based on the average DBE values and DBE distributions of the shale oils examined, highly conjugated species are enriched in samples produced under low pressure, high temperature conditions and in the presence of water.

  18. Environmental Forensics: Molecular Insight into Oil Spill Weathering Helps Advance High Magnetic Field FT-ICR Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    McKenna, Amy

    2013-03-01

    The depletion of terrestrial global oil reserves has shifted oil exploration into offshore and ultra-deep water (> 5000 ft) oil reserves to meet global energy demands. Deep water reservoirs are currently in production in many parts of the world, including the Gulf of Mexico, but production is complicated by the water depth and thick salt caps that challenge reservoir characterization / production. The explosion aboard the Deepwater Horizon in April 2010 resulted in an estimated total release of ~5 million barrels (BP claims that they collected ~1M barrels, for a net release of 4 M) of light, sweet crude oil into the Gulf of Mexico and shifted attention toward the environmental risks associated with offshore oil production. The growing emphasis on deep water and ultra-deep water oil production poses a significant environmental threat, and increased regulations require that oil companies minimize environmental impact to prevent oil spills, and mitigate environmental damage when spills occur. Every oil spill is unique. The molecular transformations that occur to petroleum after contact with seawater depend on the physical and chemical properties of the spilled oil, environmental conditions, and deposition environment. Molecular-level knowledge of the composition, distribution, and total mass of released hydrocarbons is essential to disentangle photo- and bio-degradation, source identification, and long-term environmental impact of hydrocarbons released into the environment. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is unsurpassed in its ability to characterize complex mixtures at the level of elemental composition assignment. Only FT-ICR mass spectrometry can routinely achieve the required minimum resolving power necessary to elucidate molecular-level characterization of crude oil. Conversely, the spectral complexity of petroleum facilitates identification of systematic errors in the accumulation, transfer, excitation, and detection

  19. Characterization of dissolved organic nitrogen in wet deposition from Lake Erhai basin by using ultrahigh resolution FT-ICR mass spectrometry.

    PubMed

    Feng, Shuang; Zhang, Li; Wang, Shengrui; Nadykto, Alexey B; Xu, Yisheng; Shi, Quan; Jiang, Bin; Qian, Weibin

    2016-08-01

    Dissolved Organic Nitrogen (DON) of wet deposition in Erhai basin (EWD) was characterized at the molecular level by using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). The structure and composition of DON were investigated by the combined ESI FT-ICR MS, UV-Vis absorbance and fluorescence techniques. The FT-ICR MS measurements indicate that a large (∼790) number of organic species present in the wet deposition, in which DON account for 18.3%, with most of DON containing a single nitrogen atom. The typical relative molecular mass of the DON species was found to be in the range of 200-400 Da. Approximately 57.2% of DON species are highly unsaturated (DBE (Double Bond Equivalent) > 5) with the nitrogen- and sulfur-containing species, which are probably represented mainly by active nitrooxy organosulfates, accounting for ∼ 19.3% of the total DON. The low average SUVA254 and A253/A203 values (0.02 and 0.06, respectively), indicates that the aromaticity of the EWD samples is particularly weak. The average values of E2/E3 and E4/E6 in the EWD samples were 6.84 and 1.84, respectively. This is a clear indication of the low degree of humification of EWD samples, in agreement with ESI FT-ICR MS measurements. Our study demonstrates that multiple experimental techniques combined with FT-ICR MS, UV-Vis absorbance and fluorescence can be efficiently used for in-depth studying the DON at the molecular level. Thus it allows us to achieve a deep and insightful understanding of the DON structure and composition. PMID:27192481

  20. Gas Chromatography Coupled to Atmospheric Pressure Chemical Ionization FT-ICR Mass Spectrometry for Improvement of Data Reliability.

    PubMed

    Schwemer, Theo; Rüger, Christopher P; Sklorz, Martin; Zimmermann, Ralf

    2015-12-15

    Atmospheric pressure chemical ionization (APCI) offers the advantage of molecular ion information with low fragmentation. Hyphenating APCI to gas chromatography (GC) and ultrahigh resolution mass spectrometry (FT-ICR MS) enables an improved characterization of complex mixtures. Data amounts acquired by this system are very huge, and existing peak picking algorithms are usually extremely time-consuming, if both gas chromatographic and ultrahigh resolution mass spectrometric data are concerned. Therefore, automatic routines are developed that are capable of handling these data sets and further allow the identification and removal of known ionization artifacts (e.g., water- and oxygen-adducts, demethylation, dehydrogenation, and decarboxylation). Furthermore, the data quality is enhanced by the prediction of an estimated retention index, which is calculated simply from exact mass data combined with a double bond equivalent correction. This retention index is used to identify mismatched elemental compositions. The approach was successfully tested for analysis of semivolatile components in heavy fuel oil and diesel fuel as well as primary combustion particles emitted by a ship diesel research engine. As a result, 10-28% of the detected compounds, mainly low abundant species, classically assigned by using only the mass spectrometric information, were identified as not valid and removed. Although GC separation is limited by the slow acquisition rate of the FT-ICR MS (<1 Hz), a database driven retention time comparison, as commonly used for low resolution GC/MS, can be applied for revealing isomeric information. PMID:26560682

  1. High resolution FT-ICR mass spectral analysis of bio-oil and residual water soluble organics produced by hydrothermal liquefaction of the marine microalga Nannochloropsis salina

    SciTech Connect

    Sudasinghe, Nilusha; Dungan, Barry; Lammers, Peter; Albrecht, Karl O.; Elliott, Douglas C.; Hallen, Richard T.; Schaub, Tanner

    2014-03-01

    We report a detailed compositional characterization of a bio-crude oil and aqueous by-product from hydrothermal liquefaction of Nannochloropsis salina by direct infusion Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) in both positive- and negative-ionization modes. The FT-ICR MS instrumentation approach facilitates direct assignment of elemental composition to >7000 resolved mass spectral peaks and three-dimensional mass spectral images for individual heteroatom classes highlight compositional diversity of the two samples and provide a baseline description of these materials. Aromatic nitrogen compounds and free fatty acids are predominant species observed in both the bio-oil and aqueous fraction. Residual organic compounds present in the aqueous fraction show distributions that are slightly lower in both molecular ring and/or double bond value and carbon number relative to those found in the bio-oil, albeit with a high degree of commonality between the two compositions.

  2. Size distributions and geometries of alkali halide nanoclusters probed using ESI FT-ICR mass spectrometry and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Lemke, K.; Sadjadi, S.; Seward, T.

    2010-12-01

    The structures and energetic properties of ionic alkali metal halide clusters play a significant role in our understanding of aqueous geochemical processes such as salt dissolution, precipitation and neutralization reactions. Mass spectrometric and quantum chemical studies of such systems offer new opportunities to study the size-dependent evolution of cluster structures, the occurrence of magic number species as well as their fundamental properties. The work here presents new results for the stability, abundance and structure of pure [Na(NaClm)]+ , [K(KCl)m]+ and mixed [Na(NaCl)p(KCl)q]+ metal halide clusters with m<23 and p+q<14, respectively, using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) in combination with the Gn and CBS-x multistep ab initio methods. Ion-cluster experiments were conducted on a modified 7T Bruker FT-ICR/MS equipped with electrospray ionization (ESI) sources and a custom-designed solvent gas inlet interface. In ESI FT-ICR/MS experiments performed with solutions containing NaCl and KCl salts (1mM; 80/20 CH3CN/H2O), singly and doubly charged salt clusters were generated up to a cluster size of [Na(NaCl)22]+, [K(KCl)17]+ and [K2(KCl)21,23]2+, respectively, including “magic number” clusters that correspond to the completed cluster cuboids with the dimensions 3x3x1 (m=4), 3x3x2+3 (m=10) 3x3x3 (m=13) and 3x3x5 (m=22) (see Figure). On the other hand, no pure clusters except [K(KCl)1-3]+ were generated when alkali halides were electrosprayed from 1mM NaCl/KCl solutions. Instead, mixed [Na(NaCl)p(KCl)q]+ clusters are generated up to p+q=14, which are the largest mixed alkali halide clusters yet generated in mass spectrometric experiments, including a suite of ionic species that are generated via CH3CN fragmentation and charge transfer in [Na(CH3CN)n]+ to yield the clusters [Na(NaCN)(CH3CN)n-1]+. We describe our ESI FT-ICR/MS experiments and discuss ion cluster abundances and extent of clustering

  3. Eugenia calycina Cambess extracts and their fractions: Their antimicrobial activity and the identification of major polar compounds using electrospray ionization FT-ICR mass spectrometry.

    PubMed

    Ferreira, Fernanda P S; Morais, Sandra R; Bara, Maria T F; Conceição, Edemilson C; Paula, José R; Carvalho, Thays C; Vaz, Boniek G; Costa, Helber B; Romão, Wanderson; Rezende, Maria H

    2014-10-01

    Eugenia calycina, which is described as "red pitanga or pitanga cherry of cerrado," is widely distributed in the Cerrado area of Brazil. Its leaf and bark extracts are used in folk medicine for many applications. In this study, the compositions of the major polar compounds of the bark and leaf extracts and their fractions were obtained from a liquid-liquid extraction using hexane, dichloromethane, ethyl acetate, and water. They were then evaluated using electrospray ionization negative FT-ICR mass spectrometry (ESI(-) FT-ICR MS), which revealed a large number of oxygen-containing compounds, such as flavonoids, terpenes, tanins, steroids, and fat acids. The biological activity of these extracts towards several bacterial and fungal strains was then evaluated. The highest activity was found using aqueous fractions, in which the ESI(-) FT-ICR MS analysis revealed compounds with a high content of oxygen (e.g., glycosed flavonoids, tannins, and polyphenolic compounds) against Cryptococcus sp. D (minimum inhibitory concentration [MIC]=15.62μg/mL). Strong activity was also found using the hexanic fractions-in which the ESI(-) FT-ICR MS analysis revealed that the compounds contained a decreased amount of oxygen (e.g., fat acids and steroids)-towards Cryptococcus gatti L48, Cryptococcus neoformans L3 (MIC=31.2μg/mL), and Cryptococcus sp. D (MIC=62.5μg/mL). Therefore, antimicrobial assays using the bark/leaf extracts of E. calycina present prospects for the research of active substances that may be used for the treatment of cryptococcosis, a disease that is common in immunosuppressed patients. PMID:25108373

  4. Extracting biomolecule collision cross sections from the high-resolution FT-ICR mass spectral linewidths.

    PubMed

    Jiang, Ting; Chen, Yu; Mao, Lu; Marshall, Alan G; Xu, Wei

    2016-01-14

    It is known that the ion collision cross section (CCS) may be calculated from the linewidth of a Fourier transform ion cyclotron resonance (FT-ICR) mass spectral peak at elevated pressure (e.g., ∼10(-6) Torr). However, the high mass resolution of FT-ICR is sacrificed in those experiments due to high buffer gas pressure. In this study, we describe a linewidth correction method to eliminate the windowing-induced peak broadening effect. Together with the energetic ion-neutral collision model previously developed by our group, this method enables the extraction of CCSs of biomolecules from high-resolution FT-ICR mass spectral linewidths, obtained at a typical operating buffer gas pressure of modern FT-ICR instruments (∼10(-10) Torr). CCS values of peptides including MRFA, angiotensin I, and bradykinin measured by the proposed method agree well with ion mobility measurements, and the unfolding of protein ions (ubiquitin) at higher charge states is also observed. PMID:26314765

  5. Ion-molecule reactions for the characterization of polyols and polyol mixtures by ESI/FT-ICR mass spectrometry.

    PubMed

    Watkins, Michael A; Winger, Brian E; Shea, Ryan C; Kenttämaa, Hilkka I

    2005-03-01

    A mass spectrometric method is described for the identification and counting of hydroxyl groups in an analyte. Analytes introduced into a FT-ICR mass spectrometer and ionized by positive mode ESI were allowed to react with the neutral reagent diethylmethoxyborane. This results in derivatization of the hydroxyl groups of the analytes by replacement of a proton with a diethylborenium ion. Protonated polyols react by consecutive derivatization reactions, wherein all, or nearly all, of the hydroxyls are derivatized. The polyol derivatization products are separated by 68 mass units in the mass spectrum. This 68 Da mass shift, along with 30 Da mass shifts arising from intramolecular derivatization of the primary derivatization products, makes it easy to count the number of functional groups present in the analyte. The utility of this method for the analysis of polyols as single-component solutions, as mixtures, or in HPLC effluent (LC-MS analysis) is demonstrated. PMID:15732922

  6. High mass accuracy and high mass resolving power FT-ICR secondary ion mass spectrometry for biological tissue imaging.

    PubMed

    Smith, Donald F; Kiss, Andras; Leach, Franklin E; Robinson, Errol W; Paša-Tolić, Ljiljana; Heeren, Ron M A

    2013-07-01

    Biological tissue imaging by secondary ion mass spectrometry has seen rapid development with the commercial availability of polyatomic primary ion sources. Endogenous lipids and other small bio-molecules can now be routinely mapped on the sub-micrometer scale. Such experiments are typically performed on time-of-flight mass spectrometers for high sensitivity and high repetition rate imaging. However, such mass analyzers lack the mass resolving power to ensure separation of isobaric ions and the mass accuracy for elemental formula assignment based on exact mass measurement. We have recently reported a secondary ion mass spectrometer with the combination of a C60 primary ion gun with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for high mass resolving power, high mass measurement accuracy, and tandem mass spectrometry capabilities. In this work, high specificity and high sensitivity secondary ion FT-ICR MS was applied to chemical imaging of biological tissue. An entire rat brain tissue was measured with 150 μm spatial resolution (75 μm primary ion spot size) with mass resolving power (m/Δm(50%)) of 67,500 (at m/z 750) and root-mean-square measurement accuracy less than two parts-per-million for intact phospholipids, small molecules and fragments. For the first time, ultra-high mass resolving power SIMS has been demonstrated, with m/Δm(50%) > 3,000,000. Higher spatial resolution capabilities of the platform were tested at a spatial resolution of 20 μm. The results represent order of magnitude improvements in mass resolving power and mass measurement accuracy for SIMS imaging and the promise of the platform for ultra-high mass resolving power and high spatial resolution imaging. PMID:23685962

  7. High Mass Accuracy and High Mass Resolving Power FT-ICR Secondary Ion Mass Spectrometry for Biological Tissue Imaging

    SciTech Connect

    Smith, Donald F.; Kiss, Andras; Leach, Franklin E.; Robinson, Errol W.; Pasa-Tolic, Ljiljana; Heeren, Ronald M.

    2013-07-01

    Biological tissue imaging by secondary ion mass spectrometry has seen rapid development with the commercial availability of polyatomic primary ion sources. Endogenous lipids and other small bio-molecules can now be routinely mapped on the micrometer scale. Such experiments are typically performed on time-of-flight mass spectrometers for high sensitivity and high repetition rate imaging. However, such mass analyzers lack the mass resolving power to ensure separation of isobaric ions and the mass accuracy for exact mass elemental formula assignment. We have recently reported a secondary ion mass spectrometer with the combination of a C60 primary ion gun with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for high mass resolving power, high mass measurement accuracy and tandem mass spectrometry capabilities. In this work, high specificity and high sensitivity secondary ion FT-ICR MS was applied to chemical imaging of biological tissue. An entire rat brain tissue was measured with 150 μm spatial resolution (75 μm primary ion spot size) with mass resolving power (m/Δm50%) of 67,500 (at m/z 750) and root-mean-square measurement accuracy less than two parts-per-million for intact phospholipids, small molecules and fragments. For the first time, ultra-high mass resolving power SIMS has been demonstrated, with m/Δm50% > 3,000,000. Higher spatial resolution capabilities of the platform were tested at a spatial resolution of 20 μm. The results represent order of magnitude improvements in mass resolving power and mass measurement accuracy for SIMS imaging and the promise of the platform for ultra-high mass resolving power and high spatial resolution imaging.

  8. Vacuum Ultraviolet Photodissociation and Fourier Transform-Ion Cyclotron Resonance (FT-ICR) Mass Spectrometry: Revisited.

    PubMed

    Shaw, Jared B; Robinson, Errol W; Paša-Tolić, Ljiljana

    2016-03-15

    We revisited the implementation of 193 nm ultraviolet photodissociation (UVPD) within the ion cyclotron resonance (ICR) cell of a Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer. UVPD performance characteristics were examined in the context of recent developments in the understanding of UVPD and in-cell tandem mass spectrometry. Efficient UVPD and photo-ECD of a model peptide and proteins within the ICR cell of a FT-ICR mass spectrometer are accomplished through appropriate modulation of laser pulse timing, relative to ion magnetron motion and the potential applied to an ion optical element upon which photons impinge. It is shown that UVPD yields efficient and extensive fragmentation, resulting in excellent sequence coverage for model peptide and protein cations. PMID:26882021

  9. Collision cross section measurements for biomolecules within a high-resolution FT-ICR cell: theory.

    PubMed

    Guo, Dan; Xin, Yi; Li, Dayu; Xu, Wei

    2015-04-14

    In this study, an energetic hard-sphere ion-neutral collision model was proposed to bridge-link ion collision cross section (CCS) with the image current collected from a high-resolution Fourier transform ion cyclotron resonance (FT-ICR) cell. By investigating the nonlinear effects induced by high-order electric fields and image charge forces, the energetic hard-sphere collision model was validated through experiments. Suitable application regions for the energetic hard-sphere collision model, as well as for the conventional Langevin and hard-sphere collision models, were also discussed. The energetic hard-sphere collision model was applied in the extraction of ion CCSs from high-resolution FT-ICR mass spectra. Discussions in the present study also apply to FT-Orbitraps and FT-quadrupole ion traps. PMID:25754983

  10. The Chemical Exhaust Hazards of Dichlorosilane Deposits Determined with FT-ICR Mass Spectrometry

    SciTech Connect

    JAREK, RUSSELL L.; THORNBERG, STEVEN M.

    1999-10-01

    Flammable deposits have been analyzed from the exhaust systems of tools employing dichlorosilane (DCS) as a processing gas. Exact mass determinations with a high-resolution Fourier-transform ion-cyclotron resonance (FT-ICR) mass spectrometer allowed the identification of various polysiloxane species present in such an exhaust flow. Ion-molecule reactions indicate the preferred reaction pathway of siloxane formation is through HCl loss, leading to the highly reactive polysiloxane that was detected in the flammable deposits.

  11. Hydrothermal liquefaction oil and hydrotreated product from pine feedstock characterized by heteronuclear two-dimensional NMR spectroscopy and FT-ICR mass spectrometry

    SciTech Connect

    Sudasinghe, Nilusha; Cort, John R.; Hallen, Richard; Olarte, Mariefel; Schmidt, Andrew; Schaub, Tanner

    2014-12-01

    Hydrothermal liquefaction (HTL) crude oil and hydrotreated product from pine tree farm waste (forest product residual, FPR) have been analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) in both positive- and negative-ionization modes and high-resolution twodimensional heteronuclear 1H-13C NMR spectroscopy. FT-ICR MS resolves thousands of compounds in complex oils and provides unparalleled compositional details for individual molecules for identification of compound class (heteroatom content), type (number of rings plus double bonds to carbon or double bond equivalents (DBE) and carbon number (degree of alkylation). Heteronuclear 1H-13C NMR spectroscopy provides one-bond and multiple-bond correlations between pairs of 1H and 13C chemical shifts that are characteristic of different organic functional groups. Taken together this information provides a picture of the chemical composition of these oils. Pyrolysis crude oil product from pine wood was characterized for comparison. Generally, pyrolysis oil is comprised of a more diverse distribution of heteroatom classes with higher oxygen number relative to HTL oil as shown by both positive- and negative-ion ESI FT-ICR MS. A total of 300 N1, 594 O1 and 267 O2 compounds were observed as products of hydrotreatment. The relative abundance of N1O1, N1O2, N1O3, N2, N2O1, N2O2 and O3 compounds are reduced to different degrees after hydrotreatment and other higher heteroatom containing species (O4-O10, N1O4, N1O5 and N2O3) are completely removed by hydrotreatment.

  12. Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures

    NASA Astrophysics Data System (ADS)

    Anderton, Christopher R.; Chu, Rosalie K.; Tolić, Nikola; Creissen, Alain; Paša-Tolić, Ljiljana

    2016-03-01

    The ability to visualize biochemical interactions between microbial communities using MALDI MSI has provided tremendous insights into a variety of biological fields. Matrix application using a sieve proved to be incredibly useful, but it has many limitations that include uneven matrix coverage and limitation in the types of matrices that could be employed in studies. Recently, there has been a concerted effort to improve matrix application for studying agar plated microbial cultures, many of which utilized automated matrix sprayers. Here, we describe the usefulness of using a robotic sprayer for matrix application. The robotic sprayer has two-dimensional control over where matrix is applied, and a heated capillary that allows for rapid drying of the applied matrix. This method provided a significant increase in MALDI sensitivity over the sieve method, as demonstrated by FT-ICR MS analysis, facilitating the ability to gain higher lateral resolution MS images of Bacillus subtilis than previously reported. This method also allowed for the use of different matrices to be applied to the culture surfaces.

  13. Oligomers, organosulfates, and nitroxy organosulfates in rainwater identified by ultra-high resolution electrospray ionization FT-ICR mass spectrometry

    NASA Astrophysics Data System (ADS)

    Altieri, K. E.; Turpin, B. J.; Seitzinger, S. P.

    2008-09-01

    Wet deposition is an important removal mechanism for atmospheric organic matter, and a potentially important input for receiving ecosystems, yet less than 50% of rainwater organic matter is considered chemically characterized. Precipitation samples collected in New Jersey, USA, were analyzed by negative ion ultra-high resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Elemental compositions of 552 unique molecular species were determined in the mass range 50 500 Da in the rainwater. Three main groups of organic compounds were identified: compounds containing carbon, hydrogen, and oxygen (CHO) only, sulfur (S) containing CHOS compounds, and S- and nitrogen containing CHONS compounds. Organic acids commonly identified in precipitation were detected, as well as linear alkylbenzene sulfonates, which are persistent pollutants commonly measured in river water, seawater, and sediments, but to our knowledge, not previously documented in atmospheric samples. Within the three main groups of compounds detected in the rainwater, oligomers, organosulfates, and nitroxy-organosulfates were identified. The majority of the compounds identified are products of atmospheric reactions and are known contributors to secondary organic aerosol (SOA) formed from gas phase, aerosol phase, and in-cloud reactions in the atmosphere. It is suggested that the large uncharacterized component of SOA is the main contributor to the large uncharacterized component of rainwater organic matter.

  14. Identification of Reactive and Refractory Components of Dissolved Organic Nitrogen by FT-ICR Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Cooper, W. T.; Podgorski, D. C.; Osborne, D. M.; Corbett, J.; Chanton, J.

    2010-12-01

    Dissolved organic nitrogen is an often overlooked but potentially significant bioavailable component of dissolved organic matter. Studies of bulk DON turnover have been reported, but the compositions of the reactive and refractory components of DON are largely unknown. Here we show the unique ability of atmospheric pressure photoionization (APPI) coupled to ultrahigh resolution mass spectrometry to identify the reactive and refractory components of DON. Figure 1 is an isolated 0.30 m/z window from an ultrahigh resolution APPI FT-ICR mass spectrum of DON in surface waters draining an agricultural area in South Florida. Using this optimized, negative-ion APPI strategy we have been able to identify the reactive and refractory components of DON in these nitrogen-rich waters. Similar results were observed with samples from soil porewaters in sedge-dominated fens and sphagnum-dominated bogs within the Glacial Lake Agassiz Peatlands (GLAP) of northern Minnesota. Surprisingly, microbes appear to initially use similar enzymatic pathways to degrade DON and DOC, often with little release of nitrogen. Figure 1. Isolated 0.30 m/z window at nominal mass 432 from negative-ion APPI FT-ICR mass spectrum of DOM from waters draining an agricultural area in South Florida. Peaks marked contain nitrogen.

  15. Rapid screening for potential epitopes reactive with a polycolonal antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry.

    PubMed

    Zhang, Qian; Noble, Kyle A; Mao, Yuan; Young, Nicolas L; Sathe, Shridhar K; Roux, Kenneth H; Marshall, Alan G

    2013-07-01

    The potential epitopes of a recombinant food allergen protein, cashew Ana o 2, reactive to polyclonal antibodies, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ana o 2 polyclonal antibodies were purified in the serum from a goat immunized with cashew nut extract. Antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen:polyclonal antibody (Ag:pAb) complexes. Complexed and uncomplexed (free) rAna o 2 were then subjected to HDX-MS analysis. Four regions protected from H/D exchange upon pAb binding are identified as potential epitopes and mapped onto a homologous model. PMID:23681851

  16. Rapid Screening for Potential Epitopes Reactive with a Polycolonal Antibody by Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zhang, Qian; Noble, Kyle A.; Mao, Yuan; Young, Nicolas L.; Sathe, Shridhar K.; Roux, Kenneth H.; Marshall, Alan G.

    2013-07-01

    The potential epitopes of a recombinant food allergen protein, cashew Ana o 2, reactive to polyclonal antibodies, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ana o 2 polyclonal antibodies were purified in the serum from a goat immunized with cashew nut extract. Antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen:polyclonal antibody (Ag:pAb) complexes. Complexed and uncomplexed (free) rAna o 2 were then subjected to HDX-MS analysis. Four regions protected from H/D exchange upon pAb binding are identified as potential epitopes and mapped onto a homologous model.

  17. Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry.

    PubMed

    Guan, Xiaoyan; Noble, Kyle A; Tao, Yeqing; Roux, Kenneth H; Sathe, Shridhar K; Young, Nicolas L; Marshall, Alan G

    2015-06-01

    The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution-phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX-MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope-contributing segments. PMID:26169135

  18. An online FT-ICR Penning-trap mass spectrometer for the DPS2-F section of the KATRIN experiment

    NASA Astrophysics Data System (ADS)

    Heck, M.; Ascher, P.; Cakirli, R. B.; Golzke, H.; Rodríguez, D.; Stahl, S.; Ubieto-Díaz, M.; Blaum, K.

    2014-09-01

    Two Fourier-transform ion-cyclotron resonance (FT-ICR) Penning-trap mass spectrometers will be installed in the pumping section of the KArlsruhe TRItium Neutrino (KATRIN) experiment. This experiment aims at determining the electron anti-neutrino mass m(νebar) with a sensitivity of 0.2 eV (90% C.L.) by high-resolution tritium β-spectroscopy. The tritium source creates various types of ions, which have to be reduced in order to reach the required low background level. The purpose of the FT-ICR mass spectrometers is the identification of the ion flux components as well as their abundance. Furthermore, the pumping efficiency of the differential pumping section DPS2-F can be determined since these Penning traps will be installed one at the entrance and one at the exit. In this paper the operation of the FT-ICR system is described. Experimental results are presented concerning the cryogenic broad-band amplifier system for the FT-ICR detection as well as the characterisation of the mass spectrometer with respect to, e.g., noise density and detection limit.

  19. An Electrically Compensated Trap Designed to 8th Order for FT-ICR Mass Spectrometry

    PubMed Central

    Brustkern, Adam M.; Rempel, Don L.; Gross, Michael L.

    2008-01-01

    We present the design, guided by theory to eighth order, and the first evaluation of a Fourier transform ion cyclotron resonance (FT-ICR) compensated trap. The purpose of the new trap is to reduce effects of the non-linear components of the trapping electric field; those non-liner components introduce variations in the cyclotron frequency of an ion based on its spatial position (its cyclotron and trapping mode amplitudes). This frequency spread leads to decreased mass resolving power and signal-to-noise. The reduction of the spread of cyclotron frequencies, as explicitly modeled in theory, serves as the basis for our design. The compensated trap shows improved signal-to-noise and at least a three-fold increase in mass resolving power compared to the uncompensated trap at the same trapping voltage. Resolving powers (FWHH) as high as 1.7 × 107 for the [M + H]+ of vasopressin at m/z 1084.5 in a 7.0-Tesla induction can be obtained when using trap compensation. PMID:18599306

  20. Metabolite Profiling of Methanosarcina Acetivorans (MA) with Direct Infusion to FT-ICR

    PubMed Central

    Showman, Lucas; Nikolau, Basil; Perera, Ann

    2012-01-01

    Methane producing organisms are of interest because they provide an efficient and cost-effective biofuel that can be distributed readily using existing infrastructure. Methanosarcina acetivorans (MA) is a methanogenic archaeon found in diverse anaerobic habitats including oil wells, trash dumps, deep sea hydrothermal vents, and oxygen depleted sediments beneath kelp beds. With the largest genome of all known methanogenic archaea containing 4721 predicted genes; MA is considered to be the most metabolically diverse methanogenic archaea. As with other organisms, accurate gene functional annotation of methanogens lags significantly behind the large body of sequence data, representing a sizable gap in understanding of the biology of these organisms. One particular poorly understood system in MA is the biotin network, where homology based gene annotations show an incomplete biotin biosynthetic pathway. In an effort to better understand the biotin network in MA, we are studying the metabolomic differences of MA grown under biotin containing and biotin depleted conditions. We are using high mass resolution capability that FT-ICR mass spectrometry provides to investigate the changes in metabolism. Preliminary data indicates that ether lipids play major role in this archaea metabolism.

  1. Gas phase investigations of sulfonium salts by electrospray ft-icr/ms

    NASA Astrophysics Data System (ADS)

    Katritzky, Alan R.; Shipkova, Petia A.; Watson, Clifford H.; Eyler, John R.; Kevill, Dennis N.

    1997-11-01

    Twelve sulfonium salts were studied by electrospray Fourier transform ion cyclotron resonance mass spectrometry. Collisionally activated dissociation, CAD, reactions, using neutral argon as the collision gas, were performed to investigate dissociation pathways in the gas phase and to study the stabilizing/destabilizing effects of electron donating/withdrawing substituents on the sulfonium ions. Ion-molecule reactions were attempted to identify SN2 reaction mechanisms, but to date we have detected exclusively SN1-type reactions in the gas phase. Literature reports on the mass spectrometry of sulfonium cations are reviewed.

  2. High molecular weight SOA formation during limonene ozonolysis: insights from ultrahigh-resolution FT-ICR mass spectrometry characterization

    NASA Astrophysics Data System (ADS)

    Kundu, S.; Fisseha, R.; Putman, A. L.; Rahn, T. A.; Mazzoleni, L. R.

    2012-01-01

    The detailed molecular composition of secondary organic aerosols (SOA) from limonene ozonolysis was studied using ultrahigh-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. High molecular weight (MW) compounds (m/z > 300) were found to constitute a significant number fraction of the identified SOA components. Double bond equivalents (DBE = the number of rings plus the number of double bonds) increased with MW. The O:C ratios and relative abundances of compounds decreased with increasing MW. The mass spectra of limonene contain 4 distinct clusters of negative ions: Group I (140 < m/z < 300), Group II (300 < m/z < 500), Group III (500 < m/z < 700) and Group IV (700 < m/z < 850). A number of CH2 and O homologous series of low MW SOA (Group 1) with carbon number 7-15 and oxygen number 3-9 were observed. Their occurrence can be explained with isomerization and elimination reactions of Criegee radicals, reactions between alkyl peroxy radicals, and scission of alkoxy radicals resulting from the Criegee radicals. Additionally, fragmentation analysis and observations of formaldehyde homologous series provide evidence for aerosol growth by the reactive uptake of generated gas-phase carbonyls in limonene ozonolysis. The decreasing O:C ratios between group of compounds indicated the importance of condensation (aldol and esterification) reaction pathways for high MW compound formation. However, the prominent DBE changes of 2 between the groups of compounds and selected fragmentation (MS/MS) analysis of Group II and Group III ions indicated a predominance of non-condensation (hydroperoxide, Criegee and hemi-acetal) reaction pathways. A reaction matrix created with the combination of low MW SOA, hydroperoxides, and Criegee radicals indicated higher frequencies for the hemi-acetal and condensation reaction pathways. Overall, the combined approach confirms the importance of non-condensation reaction pathways over condensation reaction pathways. Among

  3. High field FT-ICR mass spectrometry for molecular characterization of snow board from Moscow regions.

    PubMed

    Mazur, Dmitry M; Harir, Mourad; Schmitt-Kopplin, Philippe; Polyakova, Olga V; Lebedev, Albert T

    2016-07-01

    High field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry analysis of eight snow samples from Moscow city allowed us to identify more than 2000 various elemental compositions corresponding to regional air pollutants. The hierarchical cluster analysis (HCA) of the data showed good concordance of three main groups of samples with the main wind directions. The North-West group (A1) is represented by several homologous CHOS series of aliphatic organic aerosols. They may form as a result of enhanced photochemical reactions including oxidation of hydrocarbons with sulfonations due to higher amount of SO2 emissions in the atmosphere in this region. Group A2, corresponding to the South-East part of Moscow, contains large amount of oxidized hydrocarbons of different sources that may form during oxidation in atmosphere. These hydrocarbons appear correlated to emissions from traffic, neighboring oil refinery, and power plants. Another family of compounds specific for this region involves CHNO substances formed during oxidation processes including NOx and NO3 radical since emissions of NOx are higher in this part of the city. Group A3 is rich in CHO type of compounds with high H/C and low O/C ratios, which is characteristic of oxidized hydrocarbon-like organic aerosol. CHNO types of compounds in A3 group are probably nitro derivatives of condensed hydrocarbons such as PAH. This non-targeted profiling revealed site specific distribution of pollutants and gives a chance to develop new strategies in air quality control and further studies of Moscow environment. PMID:26994789

  4. Functional Groups and Structural Insights of Water-Soluble Organic Carbon using Ultrahigh Resolution FT-ICR Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Mazzoleni, L. R.; Habib, D.; Zhao, Y.; Dalbec, M.; Samburova, V.; Hallar, G.; Zielinska, B.; Lowenthal, D.

    2013-12-01

    Water-soluble organic carbon (WSOC) is a complex mixture of thousands of organic compounds which may have significant influence on the climate-relevant properties of atmospheric aerosols. An improved understanding of the molecular composition of WSOC is needed to evaluate the effect of aerosol composition upon aerosol physical properties. Products of gas phase, aqueous phase and particle phase reactions contribute to pre-existing aerosol organic mass or nucleate new aerosol particles. Thus, ambient aerosols carry a complex array of WSOC components with variable chemical signatures depending upon its origin and aerosol life-cycle processes. In this work, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to characterize aerosol WSOC collected during the summer of 2010 at the Storm Peak Laboratory (3210 m a.s.l.) near Steamboat Springs, CO. Approximately 4000 molecular formulas were assigned in the mass range of m/z 100-800 after negative-ion electrospray ionization. The observed trends indicate significant non-oxidative accretion reaction pathways for the formation of high molecular weight WSOC components closely associated with terpene ozonolysis secondary organic aerosol (SOA). The aerosol WSOC was further characterized using ultrahigh resolution tandem MS analysis with infrared multiphoton dissociation to determine the functional groups and structural properties of 1700 WSOC species up to m/z 600. Due to the complex nature of the WSOC, multiple precursor ions were simultaneously fragmented. The exact mass measurements of the precursor and product ions facilitated molecular formula assignments and matching of neutral losses. The most important neutral losses are CO2, H2O, CH3OH, HNO3, CH3NO3, SO3 and SO4. The presence and frequency of these losses indicate the type of functional groups contained in the precursor structures. Consistent with the acidic nature of WSOC compounds, the most frequently observed losses

  5. Chromatographic enrichment and subsequent separation of nickel and vanadyl porphyrins from natural seeps and molecular characterization by positive electrospray ionization FT-ICR mass spectrometry.

    PubMed

    Putman, Jonathan C; Rowland, Steven M; Corilo, Yuri E; McKenna, Amy M

    2014-11-01

    We report a novel chromatographic method to enrich and separate nickel and vanadyl porphyrins from a natural seep sample and combine molecular level characterization by positive-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Vanadyl and nickel porphyrin model compound elution from primary secondary amine (PSA) stationary phase combined with UV-vis spectroscopy confirms enrichment and subsequent fractionation of nickel and vanadyl porphyrins into polarity-based subfractions. A more than 100-fold increase in signal-to-noise ratio for nickel porphyrins enables unequivocal elemental composition assignment confirmed by isotopic fine structure for all isotopes >1% relative abundance, and the first mass spectral identification of (61)Ni porphyrin isotopologues derived from natural seeps. Oxygen-containing vanadyl porphyrins and sulfur-containing vanadyl porphyrins are isolated in the same fraction simultaneously from the same sample. We provide the first chromatographic evidence of carboxylic acid functionalities peripheral to the porphyrin core, in agreement with previous studies. PMID:25286139

  6. Ion/molecule reactions of 2-chloro- and 2-bromopropene radical cations with methanol and ethanol--FT-ICR spectrometry and DFT calculations

    NASA Astrophysics Data System (ADS)

    Grützmacher, Hans-Friedrich; Büchner, Michael; Zipse, Hendrik

    2005-02-01

    Continuing the studies of ion/molecule reactions of haloalkene radical cations with nucleophiles, the reactions of the radical cations of 2-chloropropene, 1+, and 2-bromopropene. 2+, with methanol and ethanol, respectively, have been investigated by FT-ICR spectrometry and by computational analysis using DFT calculation (BHLYP/6-311 + G(2d,p)//BHLYP/6-31 + G(d) level). Only slow reactions (reaction efficiency <1%) are observed for 1+/methanol and 2+/methanol. Slow proton transfer is the main process for 1+/methanol besides minor addition of methanol to 1+ followed by loss of HCl or Cl. Addition of methanol accompanied by loss of Br is the exclusive process observed for 2+/methanol. In contrast, both 1+ and 2+ react efficiently with ethanol yielding protonated acetaldehyde as the exclusive (1+) or by far dominant (2+) primary reaction product. The computational analysis of these ion/molecule reactions shows that in the case of 1+/methanol and 2+/methanol all processes are either endothermic or blocked by large activation energies. Nonetheless, addition of methanol to the ionized CC double bond of 1+ or 2+ is exothermic, yielding in each case a pair of isomeric [beta]-distonic methoxonium ions. A new reaction mechanism has been found for the HX (X = Cl, Br) elimination from the less stable isomer of the distonic intermediates. Further, an energetically favorable transition state has been detected for hydrogen atom transfer from the [alpha]-CH2 group of alcohol to the halogenoalkene radical cations. These findings lead to a revised mechanism of the oxidation process and provide a plausible explanation for the excessive H/D exchange between 1+ and CD3OH during their slow reaction.

  7. Spatial Segmentation of MALDI FT-ICR MSI Data: A Powerful Tool to Explore the Head and Neck Tumor In Situ Lipidome

    NASA Astrophysics Data System (ADS)

    Krasny, Lukas; Hoffmann, Franziska; Ernst, Günther; Trede, Dennis; Alexandrov, Theodore; Havlicek, Vladimir; Guntinas-Lichius, Orlando; von Eggeling, Ferdinand; Crecelius, Anna C.

    2015-01-01

    Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI MSI) is a well-established analytical technique for determining spatial localization of lipids in biological samples. The use of Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometers for the molecular imaging of endogenous compounds is gaining popularity, since the high mass accuracy and high mass resolving power enables accurate determination of exact masses and, consequently, a more confident identification of these molecules. The high mass resolution FT-ICR imaging datasets are typically large in size. In order to analyze them in an appropriate timeframe, the following approach has been employed: the FT-ICR imaging datasets were spatially segmented by clustering all spectra by their similarity. The resulted spatial segmentation maps were compared with the histologic annotation. This approach facilitates interpretation of the full datasets by providing spatial regions of interest. The application of this approach, which has originally been developed for MALDI-TOF MSI datasets, to the lipidomic analysis of head and neck tumor tissue revealed new insights into the metabolic organization of the carcinoma tissue.

  8. Characterization of polyesters prepared from three different phthalic acid isomers by CID-ESI-FT-ICR and PSD-MALDI-TOF mass spectrometry.

    PubMed

    Laine, Olli; Laitinen, Tuomo; Vainiotalo, Pirjo

    2002-08-15

    Polyesters prepared from the same diol, 2-butyl-2-ethyl-1,3-propanediol, but different phthalic acid isomers, phthalic, isophthalic, and terephthalic acid, were characterized by collision-induced dissociation electrospray ionization Fourier transform ion cyclotron resonance (CID-ESI-FT-ICR) and postsource-decay matrix-assisted laser desorption/ionization time-of-flight (PSD-MALDI-TOF) mass spectrometry. Sodiated dihydroxyl-terminated polyester oligomers containing five repeating units at m/z 1634 were selected as precursor ions for dissociation studies. Two main mechanisms occurred in the fragmentation of all of the polyesters, since dissociation of the oligomers was initiated by hydrogen rearrangement or transesterification reactions. Polyesters prepared from different phthalic acid isomers could be distinguished by their fragmentation behavior. Polyester prepared from phthalic acid was easily identified by using both CID-ESI-FT-ICR and PSD-MALDI-TOF mass spectrometry. However, distinguishing between the polyesters prepared from isophthalic and terephthalic acid succeeded marginally only with CID-ESI-FT-ICR mass spectrometry. Molecular dynamics calculations were used to obtain an idea of the fragmentation behavior of the polyesters. The low-energy structures of the precursor ions were determined, and the coordination of the oxygen atoms of the polyester oligomers to the sodium cation was examined more closely. Both the experimental and the theoretical studies showed that the sodium ion affinity of polyester changed with the phthalic acid isomer. PMID:12199599

  9. Atmospheric organic matter in clouds: exact masses and molecular formula identification using ultrahigh resolution FT-ICR mass spectrometry

    NASA Astrophysics Data System (ADS)

    Zhao, Y.; Hallar, A. G.; Mazzoleni, L. R.

    2013-08-01

    cyclotron resonance (FT-ICR) mass spectrometry provides an unambiguous identification of the cloud water organic composition in the Rocky Mountain area which could help to improve the understanding of aqueous phase processes.

  10. High molecular weight SOA formation during limonene ozonolysis: insights from ultrahigh-resolution FT-ICR mass spectrometry characterization

    NASA Astrophysics Data System (ADS)

    Kundu, S.; Fisseha, R.; Putman, A. L.; Rahn, T. A.; Mazzoleni, L. R.

    2012-06-01

    The detailed molecular composition of laboratory generated limonene ozonolysis secondary organic aerosol (SOA) was studied using ultrahigh-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Approximately 1200 molecular formulas were identified in the SOA over the mass range of 140 to 850 Da. Four characteristic groups of high relative abundance species were observed; they indicate an array of accretion products that retain a large fraction of the limonene skeleton. The identified molecular formulas of each of the groups are related to one another by CH2, O and CH2O homologous series. The CH2 and O homologous series of the low molecular weight (MW) SOA (m/z < 300) are explained with a combination of functionalization and fragmentation of radical intermediates and reactive uptake of gas-phase carbonyls. They include isomerization and elimination reactions of Criegee radicals, reactions between alkyl peroxy radicals, and scission of alkoxy radicals resulting from the Criegee radicals. The presence of compounds with 10-15 carbon atoms in the first group (e.g. C11H18O6) provides evidence for SOA formation by the reactive uptake of gas-phase carbonyls during limonene ozonolysis. The high MW compounds (m/z > 300) were found to constitute a significant number fraction of the identified SOA components. The formation of high MW compounds was evaluated by molecular formula trends, fragmentation analysis of select high MW compounds and a comprehensive reaction matrix including the identified low MW SOA, hydroperoxides and Criegee radicals as building blocks. Although the formation of high MW SOA may occur via a variety of radical and non-radical reaction channels, the combined approach indicates a greater importance of the non-condensation reactions over aldol and ester condensation reaction channels. Among these hemi-acetal reactions appear to be most dominant followed by hydroperoxide and Criegee reaction channels.

  11. Comparison of collision-induced dissociation and electron-induced dissociation of phillyrin using FT-ICR MS.

    PubMed

    Lin, Zhenguang; Lin, Zhiwei; Mu, Yingdi; Yan, Dong

    2016-10-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry using collision-induced dissociation (CID) and electron capture dissociation (ECD) at high mass resolution was first applied to investigate the characteristic fragment ions of phillyrin. The CID experimental results demonstrated the elemental composition of fragment ions unambiguously, so a reasonable fragmentation pathway of phillyrin was proposed. The ECD fragmentation mechanism was believed to be fundamentally different from the CID method. ECD could be used not only in the biological field but also as a powerful complement to the structural identification of small molecular compounds. The characteristic fragmentation pathways were helpful in analyzing and interpreting the stability and property of the parent ion. PMID:27258687

  12. Atmospheric organic matter in clouds: exact masses and molecular formula identification using ultrahigh-resolution FT-ICR mass spectrometry

    NASA Astrophysics Data System (ADS)

    Zhao, Y.; Hallar, A. G.; Mazzoleni, L. R.

    2013-12-01

    cyclotron resonance (FT-ICR) mass spectrometry provides an unambiguous identification of the cloud water organic anion composition in the Rocky Mountain area that could help to improve the understanding of aqueous-phase processes.

  13. Characterizing the secondary organic aerosol products of ozone and α-pinene using ultrahigh-resolution FT-ICR mass spectrometry

    NASA Astrophysics Data System (ADS)

    Putman, A.; Offenberg, J. H.; Fisseha, R.; Kundu, S.; Rahn, T.; Mazzoleni, L. R.

    2011-12-01

    Three samples of secondary organic aerosol (SOA) were generated by reacting a-pinene and ozone in the presence of variable concentrations of hydroxyl radical scavenging cyclohexane and were characterized by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS). The reactions were performed in the presence of different concentrations of hydroxyl radical scavenger. This provided an opportunity to examine the molecular level differences of SOA. More than 900 chemical formulas for negative ions were identified over the mass range of 100 to 820 u. The experimental reproducibility of the SOA composition and the technical reproducibility of the mass spectra were evaluated. Similar chemical formulas with similar relative abundances were observed in all three experiments. A few exceptions were particular high relative abundance signals such as m/z 357, 367 and 539, whose production efficiency increased in the presence of cyclohexane, and m/z 185, 199, 215, 231 and 261, whose production efficiency decreased in the presence of cyclohexane. In general, the composition of a-pinene SOA was only slightly influenced by the concentration of the hydroxyl radical scavenger, cyclohexane. The negative ion spectra of the SOA contained four groups of peaks over the following mass ranges: 150 < n < 300, 300 < n < 475, 475 < n < 600, 600 < n < 850. As the molecular weight increased, a variety of changes occurred. The number of individual compounds within one nominal mass increased. The range of oxygen to carbon and hydrogen ratios decreased from group I to IV. Likewise, the mean values of oxygen to carbon decreased from 0.55 to 0.42. The mean value of hydrogen to carbon, approximately 1.5, did not change with respect to molecular weight, although the range of values did decrease. The chemical formulas of groups I and II with the highest relative abundances contained 5-7 and 7-10 oxygen atoms and double bond equivalents (DBE) of 3-4 and 5

  14. Enhancement of MS2D Bartington point measurement of soil magnetic susceptibility

    NASA Astrophysics Data System (ADS)

    Fabijańczyk, Piotr; Zawadzki, Jarosław

    2015-04-01

    Field magnetometry is fast method used to assess the potential soil pollution. The most popular device used to measure the soil magnetic susceptibility on the soil surface is a MS2D Bartington. Single reading using MS2D device of soil magnetic susceptibility is low time-consuming but often characterized by considerable errors related to the instrument or environmental and lithogenic factors. Typically, in order to calculate the reliable average value of soil magnetic susceptibility, a series of MS2D readings is performed in the sample point. As it was analyzed previously, such methodology makes it possible to significantly reduce the nugget effect of the variograms of soil magnetic susceptibility that is related to the micro-scale variance and measurement errors. The goal of this study was to optimize the process of taking a series of MS2D readings, whose average value constitutes a single measurement, in order to take into account micro-scale variations of soil magnetic susceptibility in proper determination of this parameter. This was done using statistical and geostatistical analyses. The analyses were performed using field MS2D measurements that were carried out in the study area located in the direct vicinity of the Katowice agglomeration. At 150 sample points 10 MS2D readings of soil magnetic susceptibility were taken. Using this data set, series of experimental variograms were calculated and modeled. Firstly, using single random MS2D reading for each sample point, and next using the data set increased by adding one more MS2D reading, until their number reached 10. The parameters of variogram: nugget effect, sill and range of correlation were used to determine the most suitable number of MS2D readings at sample point. The distributions of soil magnetic susceptibility at sample point were also analyzed in order to determine adequate number of readings enabling to calculate reliable average soil magnetic susceptibility. The research leading to these results has

  15. Water Nanodroplets as a Reaction Medium: FT-ICR Studies of the Stability, Structure and Reactivity of Hydrated Ions and Ionic Water Clusters

    NASA Astrophysics Data System (ADS)

    Bondybey, Vladimir E.

    2001-03-01

    With the help of a versatile ion source coupling laser vaporization with supersonic expansion, ionic clusters of the type X^±(H_2O)n are easily generated, and if desired, they can be mass selected in a Fourier Transform Ion Cyclotron (FT-ICR) mass spectrometer. The central ion, X^± can be for instance H^+ or OH^-, a free electron, or an ionized metal such as Na^+, Ag^+, Mg^+, or Al^+. Such "nanodroplets" solvated with up to 200 molecules of water or other ligands slowly fragment in the collision-free environment of the FT-ICR trap. They lose in a controlled way the solvent molecules, one by one on a millisecond timescale. The products of reactions which occur in the nanodroplet as a result of the loss of the stabilizing ligand can in the high-resolution mass spectrometer be unambiguously identified. In this way, a variety of solution processes such as ionic dissolution, fragmentation, neutralization, precipitation, reduction-oxidation reactions, or acid-base catalyzed reactions can be investigated in molecular, microscopic detail. Small droplets and particles are important for a variety of atmospheric processes and reactions occurring both in the troposphere and the stratosphere. This suggests the possibility of preparing such nano-droplets of suitable composition, and using them as a model system for investigating a large variety of reactions important for atmospheric chemistry. In the present talk, we will describe our apparatus and external source, and discuss a variety of results obtained recently with it in our laboratory. The aldol condensation of acetaldehyde as an example of an acid-base catalyzed reaction and the precipitation of AgCl show that a number of well-known reactions in solution have their counterpart on a single molecule level in the cluster. The competition between electron detachment and water loss of hydrated electrons e^-(H_2O)_n, n=13-36, provides interesting and unexpected insights into the coupling dynamics of the electron to its water

  16. Identification of Acetaminophen Adducts of Rat Liver Microsomal Proteins using 2D-LC-MS/MS.

    PubMed

    Golizeh, Makan; LeBlanc, André; Sleno, Lekha

    2015-11-16

    Xenobiotic metabolism in the liver can give rise to reactive metabolites that covalently bind to proteins, and determining which proteins are targeted is important in drug discovery and molecular toxicology. However, there are difficulties in the analysis of these modified proteins in complex biological matrices due to their low abundance. In this study, an analytical approach was developed to systematically identify target proteins of acetaminophen (APAP) in rat liver microsomes (RLM) using two-dimensional chromatography and high-resolution tandem mass spectrometry. In vitro microsomal incubations, with and without APAP, were digested and subjected to strong cation exchange (SCX) fractionation prior to reverse-phase UHPLC-MS/MS. Four data processing strategies were combined into an efficient label-free workflow meant to eliminate potential false positives, using peptide spectral matching, statistical differential analysis, product ion screening, and a custom-built delta-mass filtering tool to pinpoint potential modified peptides. This study revealed four proteins, involved in important cellular processes, to be covalently modified by APAP. Data are available via ProteomeXchange with identifier PXD002590. PMID:26510387

  17. Evaluation of sample preparation techniques for mass measurements of PCR products using ESI-FT-ICR mass spectrometry.

    PubMed

    Null, Allison P; George, Laura T; Muddiman, David C

    2002-04-01

    Elimination of PCR buffer components and alkali metal cations (i.e., Na+, K+) is of critical importance to allow for accurate mass measurements of PCR products for genotyping and sequencing applications. Ethanol precipitation followed by microdialysis has been repeatedly shown to efficiently desalt PCR products for analysis by mass spectrometry and is considered the gold standard. Alternative cleanup techniques that are compatible with automation are explored here with the intent of expanding the bottleneck that exists between the production of PCR products and analysis by electrospray ionization mass spectrometry (ESI-MS). Numerous combinations of approaches were evaluated that included PCR purification kits and alcohol precipitations. The data shown here support alternative approaches to an ethanol precipitation followed by microdialysis that have comparable desalting efficiency and can be utilized for cleanup of PCR products generated from single reactions. PMID:11951971

  18. New Approach for Studying Slow Fragmentation Kinetics in FT-ICR: Surface-Induced Dissociation Combined with Resonant Ejection

    SciTech Connect

    Laskin, Julia; Futrell, Jean H.

    2015-02-01

    We introduce a new approach for studying the kinetics of large ion fragmentation in the gas phase by coupling surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer with resonant ejection of selected fragment ions using a relatively short (5 ms) ejection pulse. The approach is demonstrated for singly protonated angiotensin III ions excited by collisions with a self-assembled monolayer of alkylthiol on gold (HSAM). The overall decomposition rate and rate constants of individual reaction channels are controlled by varying the kinetic energy of the precursor ion in a range of 65–95 eV. The kinetics of peptide fragmentation are probed by varying the delay time between resonant ejection and fragment ion detection at a constant total reaction time. RRKM modeling indicates that the shape of the kinetics plots is strongly affected by the shape and position of the energy deposition function (EDF) describing the internal energy distribution of the ion following ion-surface collision. Modeling of the kinetics data provides detailed information on the shape of the EDF and energy and entropy effects of individual reaction channels.

  19. Reproducibility of an Integrated Quantitation Method Coupling 2D GeLC-MS/MS with the emPAI for Comparative Proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2D gel mapping, most protein spots consist of multiple proteins posing a significant challenge for the proper interpretation of gel-based comparative experiments. Previously we introduced an approach integrating 2-D difference gel electrophoresis and LC-MS/MS analysis with the exponentially modif...

  20. Identification by FT-ICR-MS of Camelus dromedarius α-lactalbumin variants as the result of nonenzymatic deamidation of Asn-16 and Asn-45.

    PubMed

    Si Ahmed Zennia, Saliha; Mati, Abderrahmane; Saulnier, Franck; Verdier, Yann; Chiappetta, Giovanni; Mulliert, Guillermo; Miclo, Laurent; Vinh, Joëlle; Girardet, Jean-Michel

    2015-11-15

    Nonenzymatic deamidation of asparaginyl residues can occur spontaneously under physiological conditions principally when a glycyl residue is at the carboxyl side of Asn and leads to formation of aspartyl and isoaspartyl residues. This modification can change the biological activity of proteins or peptides and trigger an auto-immune response. The α-lactalbumins of members of the Camelidae family are the only of described α-lactalbumins that carry two AsnGly sequences. In the present study, high-resolution mass spectrometry, which enables accurate mass measurement has shown that Asn(16) and Asn(45) underwent a nonenzymatic deamidation, the sequence Asn(45)-Gly(46) being deamidated spontaneously at near-neutral and basic pH and Asn(16)-Gly(17) rather at basic pH. The 16-17 sequence was probably stabilized at near-neutral pH by hydrogen bonds according to the molecular modelisation performed with the camel protein. PMID:25977031

  1. Unraveling the venom proteome of the bumblebee (Bombus terrestris) by integrating a combinatorial peptide ligand library approach with FT-ICR MS.

    PubMed

    Van Vaerenbergh, Matthias; Debyser, Griet; Smagghe, Guy; Devreese, Bart; de Graaf, Dirk C

    2015-08-01

    Within the Apidae, the largest family of bees with over 5600 described species, the honeybee is the sole species with a well studied venom proteome. So far, only little research has focused on bumblebee venom. Recently, the genome sequence of the European large earth bumblebee (Bombus terrestris) became available and this allowed the first in-depth proteomic analysis of its venom composition. We identified 57 compounds, with 52 of them never described in bumblebee venom. Remarkably, 72% of the detected compounds were found to have a honeybee venom homolog, which reflects the similar defensive function of both venoms and the high degree of homology between both genomes. However, both venoms contain a selection of species-specific toxins, revealing distinct damaging effects that may have evolved in response to species-specific attackers. Further, this study extends the list of potential venom allergens. The availability of both the honeybee and bumblebee venom proteome may help to develop a strategy that solves the current issue of false double sensitivity in allergy diagnosis, which is caused by cross-reactivity between both venoms. A correct diagnosis is important as it is recommended to perform an immunotherapy with venom of the culprit species. PMID:26071081

  2. The investigation of the bitumen from ancient Greek amphora using FT ICR MS, H/D exchange and novel spectrum reduction approach.

    PubMed

    Kostyukevich, Yury; Solovyov, Sergey; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

    2016-06-01

    Recently Russian archeologists have discovered on Taman peninsula an ancient (V B.C.) Greek amphora full of dense bitumen. This is the oldest amphora in the world that contains bitumen. We report the investigation of this bitumen using ultrahigh resolution Fourier transform mass spectrometry. Also we used recently developed in-ESI source Hydrogen/Deuterium exchange approach for the structural characterization of the individual molecules and estimation of the biodegradation of the bitumen. The increase of number of the labile hydrogens compared to the non-degraded oil can serve as an additional evidence of the degradation of bitumen via oxidation. For the facilitation of the spectrum processing we have developed the special iterative spectrum reduction approach. It was observed that molecules that have only oxygen heteroatoms possess two -OH groups what is unusual for the petroleum. Based on this we suggested that the bitumen degraded during its being in amphora for 2500 years. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27270866

  3. Determination and removal of impurities in 2-D LC-MS of peptides.

    PubMed

    Mihailova, Albena; Lundanes, Elsa; Greibrokk, Tyge

    2006-03-01

    Problems occurring during operation of a 2-D LC-MS system for separation and identification of neuropeptides, such as contamination of the used salts and column bleed, are described. When using polysulfoethyl aspartamide, which is widely used as a strong cation exchange stationary phase in the first dimension, interfering peaks were observed in the second-dimension reversed-phase chromatograms. The observed peaks, found to be caused by column bleeding, had abundance above the threshold value and influenced the quality of the analyses. The origin of the peaks was verified and appropriate measures are proposed. Additionally, peaks caused by polyethylene glycols (PEGs), covering approximately 5 min of feasible chromatographic time in every fraction, were observed. The commercial ammonium formate salts used to prepare the first-dimension mobile phase were found to contain PEG impurities, and in subsequent work the salt solutions were prepared from formic acid and ammonia to avoid any additional contaminations. PMID:16583696

  4. Isolation, LC-MS/MS and 2D-NMR characterization of alkaline degradants of tenofovir disoproxil fumarate.

    PubMed

    Anandgaonkar, Vaibhav; Gupta, Abhishek; Kona, Srinivas; Talluri, M V N Kumar

    2015-03-25

    The present work describes the preparative isolation and characterization of two alkaline degradation products of tenofovir disoproxil fumarate (TDF). Tenofovir disoproxil is a prodrug of tenofovir (antiviral agent) and co-crystal form of this prodrug with fumaric acid is tenofovir disoproxil fumarate. The drug is subjected to alkaline degradation with 0.1N sodium hydroxide for 2 min at room temperature. The two degradants were detected by high performance liquid chromatography (HPLC) at relative retention of 0.26 and 0.73 with respect to the drug. HPLC method involves gradient elution on Kromasil Eternity column (150 mm × 2.1 mm, 2.5 μm) using ammonium acetate (10mM) - acetonitrile as mobile phase at flow rate of 0.3 mL/min and UV detection at 260 nm. Two degradation products were isolated by preparative HPLC and further characterized by LC-MS, (1)H NMR, (13)C NMR and 2D-NMR. On the basis of this spectral data, the structure of two DPs are confirmed as methyl hydrogen ({[1-(6-amino-9H-purin-9-yl)propan-2-yl]oxy}methyl)phosphonate for DP-I and dimethyl ({[1-(6-amino-9H-purin-9-yl)propan-2-yl]oxy}methyl)phosphonate for DP-II. PMID:25594895

  5. Improvement of Capture Compound Mass Spectrometry Technology (CCMS) for the Profiling of Human Kinases by Combination with 2D LC-MS/MS

    PubMed Central

    Fischer, Jenny J.; Graebner, Olivia; Dreger, Mathias; Glinski, Mirko; Baumgart, Sabine; Koester, Hubert

    2011-01-01

    An increasingly popular and promising field in functional proteomics is the isolation of proteome subsets based on small molecule-protein interactions. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate captured protein conjugates from complex biological samples for direct protein identification by liquid chromatography/mass spectrometry (nLC-MS/MS). In this study we used staurosporine as a selectivity group for analysis in HepG2 cells derived from human liver. In the present study, we combined the functional isolation of kinases with different separation workflows of automated split-free nanoflow liquid chromatography prior to mass spectrometric analysis. Two different CCMS setups, CCMS technology combined with 1D LC-MS and 2D LC-MS, were compared regarding the total number of kinase identifications. By extending the chromatographic separation of the tryptic digested captured proteins from 1D LC linear gradients to 2D LC we were able to identify 97 kinases. This result is similar to the 1D LC setup we previously reported but this time 4 times less input material was needed. This makes CCMS of kinases an even more powerful tool for the proteomic profiling of this important protein family. PMID:21941435

  6. In-Depth Characterization and Spectral Library Building of Glycopeptides in the Tryptic Digest of a Monoclonal Antibody Using 1D and 2D LC-MS/MS.

    PubMed

    Dong, Qian; Yan, Xinjian; Liang, Yuxue; Stein, Stephen E

    2016-05-01

    This work presents a detailed analysis of glycopeptides produced in the tryptic digestion of an IgG1 reference material. Analysis was done by nanospray ESI LC-MS/MS over a wide range of HCD collision energies with both conventional 1D separation for various digestion conditions and a 20 fraction 2D-LC study of a single digest. An extended version of NIST-developed software for analysis of "shotgun" proteomics served to identify the glycopeptides from their precursor masses and product ions for peptides with up to three missed cleavages. A peptide with a single missed cleavage, TKPREEQYNSTYR, was dominant and led to the determination of almost all glycans reported in this study. The 2D studies found a total of 247 glycopeptide ions and 60 glycans of different masses, including 30 glycans found in the 1D studies. This significantly larger number of glycans than found in any other glycoanalysis of therapeutic glycoproteins is due to both the improved separation of sialylated versus asialylated species in the first (high-pH) dimension and the ability to inject large amounts of glycosylated peptides in the 2D studies. Systematic variations in retention with glycan size were also noted. Energy-dependent changes in HCD fragmentation confirmed the proposed glycan structures and led to a peak-annotated mass spectral library to aid the analysis of glycopeptides derived from IgG1 drugs. PMID:26990841

  7. Nucleotide-induced conformational changes of tetradecameric GroEL mapped by H/D exchange monitored by FT-ICR mass spectrometry

    PubMed Central

    Zhang, Qian; Chen, Jin; Kuwajima, Kunihiro; Zhang, Hui-Min; Xian, Feng; Young, Nicolas L.; Marshall, Alan G.

    2013-01-01

    Here we employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) to access E. coli chaperonin GroEL conformation. The ~800 kDa tetradecameric GroEL plays an essential role in the proper folding of many proteins. Previous studies of the structural dynamics of GroEL upon ATP binding have been inconsistent, showing either minimal or major allosteric changes. Our results, based on the native, non-mutated, protein under physiological conditions in solution demonstrate substantial changes in conformation and/or flexibility upon ATP binding. We capture the pivotal step in its functional cycle by use of a non-hydrolyzable ATP analog, ATPγS, to mimic the ATP-bound GroEL state. Comparison of HDX-MS results for apo GroEL and GroEL-ATPγS enables the characterization of the nucleotide-regulated conformational changes throughout the entire protein with high sequence resolution. The 14-mer GroEL complex is the largest protein assembly yet accessed by HDX-MS, with sequence resolution of segments of as few as five amino acids. PMID:23409238

  8. Experimental Investigations of the Internal Energy of Molecules Evaporated via Laser-induced Acoustic Desorption into a Fourier-transform Ion Cyclotron Resonance Mass Spectrometer (LIAD/FT-ICR)

    PubMed Central

    Shea, Ryan C.; Petzold, Christopher J.; Liu, Ji-ang; Kenttämaa, Hilkka I.

    2008-01-01

    The internal energy of neutral gas-phase organic and biomolecules, evaporated by means of laser-induced acoustic desorption (LIAD) into a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR), was investigated through several experimental approaches. The desorbed molecules were demonstrated not to undergo degradation during the desorption process by collecting LIAD-evaporated molecules and subjecting them to analysis by electrospray ionization/quadrupole ion trap mass spectrometry. Previously established gas-phase basicity (GB) values were remeasured for LIAD-evaporated organic molecules and biomolecules with the use of the bracketing method. No endothermic reactions were observed. The remeasured basicity values are in close agreement with the values reported in the literature. The amount of internal energy deposited during LIAD is concluded to be less than a few kcal/mol. Chemical ionization with a series of proton transfer reagents was employed to obtain a breakdown curve for a protonated dipeptide, val-pro, evaporated by LIAD. Comparison of this breakdown curve with a previously published analogous curve obtained by using substrate-assisted laser desorption (SALD) to evaporate the peptide suggests that the molecules evaporated via LIAD have less internal energy than those evaporated via SALD. PMID:17263513

  9. Analysis of pharmaceutical impurities using multi-heartcutting 2D LC coupled with UV-charged aerosol MS detection.

    PubMed

    Zhang, Kelly; Li, Yi; Tsang, Midco; Chetwyn, Nik P

    2013-09-01

    To overcome challenges in HPLC impurity analysis of pharmaceuticals, we developed an automated online multi-heartcutting 2D HPLC system with hyphenated UV-charged aerosol MS detection. The first dimension has a primary column and the second dimension has six orthogonal columns to enhance flexibility and selectivity. The two dimensions were interfaced by a pair of switching valves equipped with six trapping loops that allow multi-heartcutting of peaks of interest in the first dimension and also allow "peak parking." The hyphenated UV-charged aerosol MS detection provides comprehensive detection for compounds with and without UV chromophores, organics, and inorganics. It also provides structural information for impurity identification. A hidden degradation product that co-eluted with the drug main peak was revealed by RP × RP separation and thus enabled the stability-indicating method development. A poorly retained polar component with no UV chromophores was analyzed by RP × hydrophilic interaction liquid chromatography separation with charged aerosol detection. Furthermore, using this system, the structures of low-level impurities separated by a method using nonvolatile phosphate buffer were identified and tracked by MS in the second dimension. PMID:23821312

  10. Gold chloride clusters with Au(III) and Au(I) probed by FT-ICR mass spectrometry and MP2 theory.

    PubMed

    Lemke, Kono H

    2014-05-01

    Microsolvated clusters of gold chloride are probed by electrospray ionization mass spectrometry (ESI-MS) and scalar relativistic electronic structure calculations. Electrospray ionization of aqueous AuCl3 leads to mononuclear clusters of types [AuCl2](+)(H2O)n (n = 0-4), [AuOHCl](+)(H2O)n (n = 0-1) and [AuCl2](+)(HCl)2(H2O)n (n = 0-4). In addition, strong ion signals due to dinuclear [Au2Cl5-xOHx](+)(H2O)n (x = 0-1) are present in ESI mass spectra of aqueous AuCl3, with the abundance of individual dinuclear species controlled by the concentration-dependent variation of the precursor complexes [AuCl2-xOHx](+)(H2O)n and AuCl3. Equilibrium structures, energies and thermodynamic properties of mono- and dinuclear gold clusters have been predicted using MP2 and CCSD(T) theory, and these data have been applied to examine the influence of microsolvation on cluster stability. Specifically, results from CCSD(T) calculations indicate that non-covalently bound ion-neutral complexes Au(+)(Cl2)(H2O)n, with formal Au(I), are the dominant forms of mononuclear gold with n = 0-2, while higher hydrates (n > 2) are covalently bound [AuCl2](+)(H2O)n complexes in which gold exists as Au(III). MP2 calculations show that the lowest energy structure of dinuclear gold is an ion-molecule cluster [Au2Cl(Cl2)2](+) consisting of a single-bridged digold-chloronium ion bound end-on to two dichlorine ligands, with two higher energy isomers, single-bridged [Au2Cl3(Cl2)](+) and double-bridged [Au2Cl5](+) clusters. Finally, AuAu interactions in the singly-bridged clusters [Au2Cl(Cl2)2](+)(H2O)n and [Au2Cl3(Cl2)](+)(H2O)n are examined employing a wide range of computational tools, including natural bond order (NBO) analysis and localized orbital locator (LOL) profiles. PMID:24643288

  11. Uncoiling collagen: a multidimensional mass spectrometry study.

    PubMed

    Simon, H J; van Agthoven, M A; Lam, P Y; Floris, F; Chiron, L; Delsuc, M-A; Rolando, C; Barrow, M P; O'Connor, P B

    2016-01-01

    Mass spectrometry can be used to determine structural information about ions by activating precursors and analysing the resulting series of fragments. Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) is a technique that correlates the mass-to-charge (m/z) ratio of fragment and precursor ions in a single spectrum. 2D FT-ICR MS records the fragmentation of all ions in a sample without the need for isolation. To analyse specific precursors, horizontal cross-sections of the spectrum (fragment ion scans) are taken, providing an alternative to conventional tandem mass spectrometry (MS/MS) experiments. In this work, 2D FT-ICR MS has been used to study the tryptic digest of type I collagen, a large protein. Fragment ion scans have been extracted from the 2D FT-ICR MS spectrum for precursor m/z ratios: 951.81, 850.41, 634.34, and 659.34, and 2D FT-ICR MS spectra are compared with a set of 1D MS/MS spectra using different fragmentation methods. The results show that two-dimensional mass spectrometry excells at MS/MS of complex mixtures, simplifying spectra by eliminating contaminant peaks, and aiding the identification of species in the sample. Currently, with desktop computers, 2D FT-ICR MS is limited by data processing power, a limitation which should be alleviated using cluster parallel computing. In order to explore 2D FT-ICR MS for collagen, with reasonable computing time, the resolution in the fragment ion dimension is limited to 256k data points (compared to 4M data points in 1D MS/MS spectra), but the vertical precursor ion dimension has 4096 lines, so the total data set is 1G data points (4 Gbytes). The fragment ion coverage obtained with a blind, unoptimized 2D FT-ICR MS experiment was lower than conventional MS/MS, but MS/MS information is obtained for all ions in the sample regardless of selection and isolation. Finally, although all 2D FT-ICR MS peak assignments were made with the aid of 1D FT-ICR MS data, these results

  12. Mapping and Identification of the Urine Proteome of Prostate Cancer Patients by 2D PAGE/MS

    PubMed Central

    Kiprijanovska, Sanja; Stavridis, Sotir; Stankov, Oliver; Komina, Selim; Petrusevska, Gordana; Polenakovic, Momir; Davalieva, Katarina

    2014-01-01

    Proteome analysis of the urine has shown that urine contains disease-specific information for a variety of urogenital system disorders, including prostate cancer (PCa). The aim of this study was to determine the protein components of urine from PCa patients. Urine from 8 patients with clinically and histologically confirmed PCa was analyzed by conventional 2D PAGE. The MS identification of the most prominent 125 spots from the urine map revealed 45 distinct proteins. According to Gene Ontology, the identified proteins are involved in a variety of biological processes, majority of them are secreted (71%), and half of them are enzymes or transporters. Comparison with the normal urine proteome revealed 11 proteins distinctive for PCa. Using Ingenuity Pathways Analysis, we have found 3 proteins (E3 ubiquitin-protein ligase rififylin, tumor protein D52, and thymidine phosphorylase) associated with cellular growth and proliferation (p = 8.35 × 10−4 − 3.41 × 10−2). The top network of functional associations between 11 proteins was Cell Death and Survival, Cell-To-Cell Signaling and Interaction, and System Development and Function (p = 10−30). In summary, we have created an initial proteomic map of PCa patient's urine. The results from this study provide some leads to understand the molecular bases of prostate cancer. PMID:25215235

  13. A Group of Novel Serum Diagnostic Biomarkers for Multidrug-Resistant Tuberculosis by iTRAQ-2D LC-MS/MS and Solexa Sequencing

    PubMed Central

    Wang, Chong; Liu, Chang-Ming; Wei, Li-Liang; Shi, Li-Ying; Pan, Zhi-Fen; Mao, Lian-Gen; Wan, Xiao-Chen; Ping, Ze-Peng; Jiang, Ting-Ting; Chen, Zhong-Liang; Li, Zhong-Jie; Li, Ji-Cheng

    2016-01-01

    The epidemic of pulmonary tuberculosis (TB), especially multidrug-resistance tuberculosis (MDR-TB) presented a major challenge for TB treatment today. We performed iTRAQ labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) and Solexa sequencing among MDR-TB patients, drug-sensitive tuberculosis (DS-TB) patients, and healthy controls. A total of 50 differentially expressed proteins and 43 differentially expressed miRNAs (fold change >1.50 or <0.60, P<0.05) were identified in the MDR-TB patients compared to both DS-TB patients and healthy controls. We found that 22.00% of differentially expressed proteins and 32.56% of differentially expressed miRNAs were related, and could construct a network mainly in complement and coagulation cascades. Significant differences in CD44 antigen (CD44), coagulation factor XI (F11), kininogen-1 (KNG1), miR-4433b-5p, miR-424-5p, and miR-199b-5p were found among MDR-TB patients, DS-TB patients and healthy controls (P<0.05) by enzyme-linked immunosorbent assay (ELISA) and SYBR green qRT-PCR validation. A strong negative correlation, consistent with the target gene prediction, was found between miR-199b-5p and KNG1 (r=-0.232, P=0.017). Moreover, we established the MDR-TB diagnostic model based on five biomarkers (CD44, KNG1, miR-4433b-5p, miR-424-5p, and miR-199b-5p). Our study proposes potential biomarkers for MDR-TB diagnosis, and also provides a new experimental basis to understand the pathogenesis of MDR-TB. PMID:26884721

  14. Comparative proteome analysis of brown adipose tissue in obese C57BL/6J mice using iTRAQ-coupled 2D LC-MS/MS.

    PubMed

    Li, Juan; Zhao, Wei-Gang; Shen, Zhu-Fang; Yuan, Tao; Liu, Shuai-Nan; Liu, Quan; Fu, Yong; Sun, Wei

    2015-01-01

    High-fat diet (HFD) leads to the development of obesity accompanied by insulin resistance, which increases the risk of type 2 diabetes mellitus and cardiovascular disease. Brown adipose tissue (BAT) plays an essential role in energy metabolism, thus it will give us promising treatment targets through elucidating underlying mechanisms of BAT in obesity. In this study, female C57BL/6J mice were fed HFD or normal diet (ND) for 22 weeks. Hyperinsulinemic-euglycemic clamp was performed to evaluate insulin sensitivity, which was independently correlated with obesity. Using isobaric tag for relative and absolute quantification (iTRAQ) coupled with 2D LC-MS/MS, we quantitated 3048 proteins in BAT. As compared HFD with ND, we obtained 727 differentially expressed proteins. Functional analysis found that those proteins were mainly assigned to the pathway of mitochondrial function. In this pathway, carnitine O-palmitoyltransferase 2 (CPT2), uncoupling protein 1 (UCP1) and apoptosis-inducing factor 1 (AIF1) were up-regulated significantly by HFD, and they were confirmed by western blotting. The results indicated that HFD might induce the apoptosis of brown adipocytes via the up-regulated AIF1. Meanwhile, HFD also stimulated fatty acid β-oxidation and raised compensatory energy consuming through the increases of CPT2 and UCP1, respectively. However, the apoptosis of brown adipocytes might weaken the compensatory energy expenditure, and finally contribute to overweight/obesity. So, preventing the apoptosis of brown adipocytes may be the key target to treat obesity. PMID:25747866

  15. Digit (2D:4D) ratio is associated with muscle mass (MM) and strength (MS) in older adults: possible effect of in utero androgen exposure.

    PubMed

    Halil, Meltem; Gurel, Esin Ileri; Kuyumcu, Mehmet Emin; Karaismailoglu, Serkan; Yesil, Yusuf; Ozturk, Zeynel Abidin; Yavuz, Burcu Balam; Cankurtaran, Mustafa; Ariogul, Servet

    2013-01-01

    Decline in MM and MS with aging, defined as sarcopenia, is related with physical disability, poor quality of life and death. Its mechanisms are not fully understood. Testosterone increases muscle protein synthesis. However, the effects of in utero androgen exposure to MM and MS in older adults have not been studied. In utero androgen exposure is inversely related with 2D:4D ratio. The aim of this study was to investigate the relationship between 2D:4D ratio as an indicator of in utero androgen exposure and MM and MS in elderly patients. A total of 151 older adults were included. Calf-circumference (CC) and skeletal muscle mass index (SMI) were used for the assessment of MM and hand grip strength for the assessment of MS. Mean age ± SD of the patients was 73.72 ± 6.23. Fifty-two (34.4%) of patients were male, 99 (65.6%) were female. Right and left 2D:4D were significantly and negatively correlated with hand grip strength (r=-0.365, p=0.018 and r=-0.434, p=0.005, respectively), CC (r=-0.422, p=0.002 and r=-0.459, p=0.001, respectively) and SMI (r=-0.354, p=0.018 and r=-0.348, p=0.022, respectively) in men. In women, right and left 2D:4D were significantly and negatively correlated with hand grip strength (r=-0.252, p=0.022 and r=-0.234, p=0.033, respectively), CC (r=-0.229, p=0.024 and r=-0.302, p=0.003, respectively) and SMI (r=-0.382, p<0.001 and r=-0.431, p<0.001, respectively). In this study, we found that 2D:4D ratio was significantly and negatively correlated with parameters depicting MM and MS which may suggest the possible role of in utero androgen exposure in the development of MM and MS loss in the elderly. PMID:23219021

  16. Isolation and characterization of a potential process related impurity of phenazopyridine HCl by preparative HPLC followed by MS-MS and 2D-NMR spectroscopy.

    PubMed

    Rao, R Nageswara; Maurya, Pawan K; Raju, A Narasa

    2009-07-12

    During the process development of phenazopyridine HCl bulk drug, a potential impurity was detected in the routine impurity profiles by HPLC. Using MS-MS and multidimensional NMR techniques, the trace level impurity was unambiguously identified to be 3-phenyl-5-phenylazo-pyridine-2,6-diamine after its isolation from phenazopyridine HCl by semi-preparative HPLC. The formation of the impurity was discussed. To our knowledge, it is a novel impurity not reported elsewhere. PMID:19376664

  17. Isolation and Identification of Dipeptidyl Peptidase IV-Inhibitory Peptides from Trypsin/Chymotrypsin-Treated Goat Milk Casein Hydrolysates by 2D-TLC and LC-MS/MS.

    PubMed

    Zhang, Ying; Chen, Ran; Ma, Huiqin; Chen, Shangwu

    2015-10-14

    New dipeptidyl peptidase IV (DPP-IV)-inhibitory peptides from trypsin/chymotrypsin-treated goat milk casein hydrolysates were isolated and identified by two-dimensional silica thin-layer chromatography (2D-TLC) combined to nano LC-MS/MS. 2D-TLC with chloroform/methanol/25% ammonia (2:2:1) and n-butanol/acetic acid/water (4:1:1) as the first- and second-dimension eluents, respectively, in analytical and semipreparative scales, was set up and verified by reversed-phase high-performance liquid chromatography (RP-HPLC) to be feasible and efficient to separate the hydrolysates. Five new DPP-IV-inhibitory peptides, four relatively large oligopeptides (MHQPPQPL, SPTVMFPPQSVL, VMFPPQSVL, and INNQFLPYPY), and AWPQYL were identified, and INNQFLPYPY showed a notable IC50 value of 40.08 μM as an uncompetitive inhibitor. Interactive effects on DPP-IV inhibition were also observed among separated fractions and pure synthetic peptide mixtures with concentration-dependent activity. The study gives new insights into goat casein hydrolysates with identified DPP-IV-inhibitory peptides efficiently isolated by 2D-TLC, which provides a simple and cost-efficient separation process and is compatible with liquid chromatography-tandem mass spectrometry (LC-MS/MS) identification. PMID:26323964

  18. Towards analytically useful two-dimensional Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    van Agthoven, Maria A; Delsuc, Marc-André; Bodenhausen, Geoffrey; Rolando, Christian

    2013-01-01

    Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) achieves high resolution and mass accuracy, allowing the identification of the raw chemical formulae of ions in complex samples. Using ion isolation and fragmentation (MS/MS), we can obtain more structural information, but MS/MS is time- and sample-consuming because each ion must be isolated before fragmentation. In 1987, Pfändler et al. proposed an experiment for 2D FT-ICR MS in order to fragment ions without isolating them and to visualize the fragmentations of complex samples in a single 2D mass spectrum, like 2D NMR spectroscopy. Because of limitations of electronics and computers, few studies have been conducted with this technique. The improvement of modern computers and the use of digital electronics for FT-ICR hardware now make it possible to acquire 2D mass spectra over a broad mass range. The original experiments used in-cell collision-induced dissociation, which caused a loss of resolution. Gas-free fragmentation modes such as infrared multiphoton dissociation and electron capture dissociation allow one to measure high-resolution 2D mass spectra. Consequently, there is renewed interest to develop 2D FT-ICR MS into an efficient analytical method. Improvements introduced in 2D NMR spectroscopy can also be transposed to 2D FT-ICR MS. We describe the history of 2D FT-ICR MS, introduce recent improvements, and present analytical applications to map the fragmentation of peptides. Finally, we provide a glossary which defines a few keywords for the 2D FT-ICR MS field. PMID:23076397

  19. A direct sensitivity comparison between flow-modulated comprehensive 2D and 1D GC in untargeted and targeted MS-based experiments.

    PubMed

    Tranchida, Peter Q; Franchina, Flavio A; Zoccali, Mariosimone; Bonaccorsi, Ivana; Cacciola, Francesco; Mondello, Luigi

    2013-09-01

    The present contribution is focused on the measurement of the analytical sensitivity attained in untargeted/targeted MS/MS experiments, performed using flow-modulator comprehensive 2D and 1D GC. The comprehensive 2D experiment was performed by diverting part of the high flow (circa 80%) to flush the accumulation loop (about 28 mL/min) to waste, to reduce the gas flow entering the ion source. 1D analyses were performed through: (i) unmodulated and (ii) single column applications. An equivalent temperature program was applied in the modulated and unmodulated analyses, while a faster one was employed in the single column one. In all application types, the (same) triple quadrupole instrument was operated in the full-scan and multiple reaction monitoring modes. A genuine sweet orange oil and the same sample spiked with 20 phytosanitary compounds were employed to reach the research objective. The results highlight the problems related to the flow modulation-MS combination. Specifically, it was found that sensitivity was on average three to four times higher in unmodulated and optimized single-column applications. PMID:23868497

  20. Accurate GM atrophy quantification in MS using lesion-filling with co-registered 2D lesion masks☆

    PubMed Central

    Popescu, V.; Ran, N.C.G.; Barkhof, F.; Chard, D.T.; Wheeler-Kingshott, C.A.; Vrenken, H.

    2014-01-01

    Background In multiple sclerosis (MS), brain atrophy quantification is affected by white matter lesions. LEAP and FSL-lesion_filling, replace lesion voxels with white matter intensities; however, they require precise lesion identification on 3DT1-images. Aim To determine whether 2DT2 lesion masks co-registered to 3DT1 images, yield grey and white matter volumes comparable to precise lesion masks. Methods 2DT2 lesion masks were linearly co-registered to 20 3DT1-images of MS patients, with nearest-neighbor (NNI), and tri-linear interpolation. As gold-standard, lesion masks were manually outlined on 3DT1-images. LEAP and FSL-lesion_filling were applied with each lesion mask. Grey (GM) and white matter (WM) volumes were quantified with FSL-FAST, and deep gray matter (DGM) volumes using FSL-FIRST. Volumes were compared between lesion mask types using paired Wilcoxon tests. Results Lesion-filling with gold-standard lesion masks compared to native images reduced GM overestimation by 1.93 mL (p < .001) for LEAP, and 1.21 mL (p = .002) for FSL-lesion_filling. Similar effects were achieved with NNI lesion masks from 2DT2. Global WM underestimation was not significantly influenced. GM and WM volumes from NNI, did not differ significantly from gold-standard. GM segmentation differed between lesion masks in the lesion area, and also elsewhere. Using the gold-standard, FSL-FAST quantified as GM on average 0.4% of the lesion area with LEAP and 24.5% with FSL-lesion_filling. Lesion-filling did not influence DGM volumes from FSL-FIRST. Discussion These results demonstrate that for global GM volumetry, precise lesion masks on 3DT1 images can be replaced by co-registered 2DT2 lesion masks. This makes lesion-filling a feasible method for GM atrophy measurements in MS. PMID:24567908

  1. Comparative Proteomics Profile of Lipid-Cumulating Oleaginous Yeast: An iTRAQ-Coupled 2-D LC-MS/MS Analysis

    PubMed Central

    Shi, Jiahua; Feng, Huixing; Lee, Jaslyn; Ning Chen, Wei

    2013-01-01

    Accumulation of intracellular lipid in oleaginous yeast cells has been studied for providing an alternative supply for energy, biofuel. Numerous studies have been conducted on increasing lipid content in oleaginous yeasts. However, few explore the mechanism of the high lipid accumulation ability of oleaginous yeast strains at the proteomics level. In this study, a time-course comparative proteomics analysis was introduced to compare the non-oleaginous yeast Saccharomyces cerevisiae, with two oleaginous yeast strains, Cryptococcus albidus and Rhodosporidium toruloides at different lipid accumulation stages. Two dimensional LC-MS/MS approach has been applied for protein profiling together with isobaric tag for relative and absolute quantitation (iTRAQ) labelling method. 132 proteins were identified when three yeast strains were all at early lipid accumulation stage; 122 and 116 proteins were found respectively within cells of three strains collected at middle and late lipid accumulation stages. Significantly up-regulation or down-regulation of proteins were experienced among comparison. Essential proteins correlated to lipid synthesis and regulation were detected. Our approach provides valuable indication and better understanding for lipid accumulation mechanism from proteomics level and would further contribute to genetic engineering of oleaginous yeasts. PMID:24386479

  2. Development of quantitative plasma N-glycoproteomics using label-free 2-D LC-MALDI MS and its applicability for biomarker discovery in hepatocellular carcinoma.

    PubMed

    Ishihara, Takeshi; Fukuda, Isao; Morita, Atsushi; Takinami, Yoshihiko; Okamoto, Hiroyuki; Nishimura, Shin-Ichiro; Numata, Yoshito

    2011-09-01

    There has been rapid progress in the development of clinical proteomic methodologies with improvements in mass spectrometric technologies and bioinformatics, leading to many new methodologies for biomarker discovery from human plasma. However, it is not easy to find new biomarkers because of the wide dynamic range of plasma proteins and the need for their quantification. Here, we report a new methodology for relative quantitative proteomic analysis combining large-scale glycoproteomics with label-free 2-D LC-MALDI MS. In this method, enrichment of glycopeptides using hydrazide resin enables focusing on plasma proteins with lower abundance corresponding to the tissue leakage region. On quantitative analysis, signal intensities by 2-D LC-MALDI MS were normalized using a peptide internal control, and the values linked to LC data were treated with DeView™ software. Our proteomic method revealed that the quantitative dynamic ranged from 10² to 10⁶ pg/mL of plasma proteins with good reproducibility, and the limit of detection was of the order of a few ng/mL of proteins in biological samples. To evaluate the applicability of our method for biomarker discovery, we performed a feasibility study using plasma samples from patients with hepatocellular carcinoma, and identified biomarker candidates, including ceruloplasmin, alpha-1 antichymotrypsin, and multimerin-1. PMID:21704746

  3. [Comparative proteomics study of different processing technology for pilose antler using iTRAQ technology coupled with 2D LC-MS].

    PubMed

    Jin, Meng-ya; Dong, Ling; Luo, Yuan-ming; Yu, Li; Mo, Mei; Hou, Cheng-bo; Li, Zhi-yuan

    2015-12-01

    This study was designed to use iTRAQ technology coupled with 2D LC-MS/MS to study the comparative proteomics of different processing technology for pilose antler. 1015 proteins were identified with 2D LC combined with MOLDI TOF/TOF mass spectrometry. Comparative analysis with Protein Pilot (Version 4.5) revealed that 87 proteins were changed (P ≤ 0.05, the ratio of > 1.50 or < 0.60 as the threshold selection of difference proteins), of which 24 were up regulated and 33 were down regulated in the traditional frying process (TFP) compared with the fresh pilose antler (P ≤ 0.05). 7 significant different proteins (P ≤ 0.001), most of these significantly changed proteins were found to be involved in calcium ion binding and ATP binding associated with human healthy. Freeze drying with protective agent (FDP) (Trehalose) can improve the content of significantly different proteins (P ≤ 0.001) including Collagen alpha-1 (XII) chain (COL12A1) and Collagen alpha-1 (II) chain (COL2A1). The significant function involves in platelets activating, maintenance of spermatogonium, and disorder expression in tumor cells. The functional annotation by Hierarchical clustering and GO (gene ontology) showed that the main molecule functions of the proteins significantly changed in these processes were involved in binding (52.7%), catalytic (25.3%), structural molecule and transporter (6.6%). PMID:27169289

  4. Characterization of the isomeric configuration and impurities of (Z)-endoxifen by 2D NMR, high resolution LC⬜MS, and quantitative HPLC analysis.

    PubMed

    Elkins, Phyllis; Coleman, Donna; Burgess, Jason; Gardner, Michael; Hines, John; Scott, Brendan; Kroenke, Michelle; Larson, Jami; Lightner, Melissa; Turner, Gregory; White, Jonathan; Liu, Paul

    2014-01-01

    (Z)-Endoxifen (4-hydroxy-N-desmethyltamoxifen), an active metabolite generated via actions of CYP3A4/5 and CYP2D6, is a more potent selective estrogen receptor modulator (SERM) than tamoxifen. In the MCF-7 human mammary tumor xenograft model with female athymic mice, (Z)-endoxifen, at an oral dose of 4⬜8 mg/kg, significantly inhibits tumor growth. (Z)-Endoxifen's potential as an alternative therapeutic agent independent of CYP2D6 activities, which can vary widely in ER+ breast cancer patients, is being actively evaluated. This paper describes confirmation of the configuration of the active (Z)-isomer through 2D NMR experiments, including NOE (ROESY) to establish spatial proton⬜proton correlations, and identification of the major impurity as the (E)-isomer in endoxifen drug substance by HPLC/HRMS (HPLC/MS-TOF). Stability of NMR solutions was confirmed by HPLC/UV analysis. For pre-clinical studies, a reverse-phase HPLC⬜UV method, with methanol/water mobile phases containing 10 mM ammonium formate at pH 4.3, was developed and validated for the accurate quantitation and impurity profiling of drug substance and drug product. Validation included demonstration of linearity, method precision, accuracy, and specificity in the presence of impurities, excipients (for the drug product), and degradation products. Ruggedness and reproducibility of the method were confirmed by collaborative studies between two independent laboratories. The method is being applied for quality control of the API and oral drug product. Kinetic parameters of Z- to E-isomerization were also delineated in drug substance and in aqueous formulation, showing conversion at temperatures above 25 °C. PMID:24055701

  5. NMR profiling of biomolecules at natural abundance using 2D 1H-15N and 1H-13C multiplicity-separated (MS) HSQC spectra

    NASA Astrophysics Data System (ADS)

    Chen, Kang; Freedberg, Darón I.; Keire, David A.

    2015-02-01

    2D NMR 1H-X (X = 15N or 13C) HSQC spectra contain cross-peaks for all XHn moieties. Multiplicity-edited1H-13C HSQC pulse sequences generate opposite signs between peaks of CH2 and CH/CH3 at a cost of lower signal-to-noise due to the 13C T2 relaxation during an additional 1/1JCH period. Such CHn-editing experiments are useful in assignment of chemical shifts and have been successfully applied to small molecules and small proteins (e.g. ubiquitin) dissolved in deuterated solvents where, generally, peak overlap is minimal. By contrast, for larger biomolecules, peak overlap in 2D HSQC spectra is unavoidable and peaks with opposite phases cancel each other out in the edited spectra. However, there is an increasing need for using NMR to profile biomolecules at natural abundance dissolved in water (e.g., protein therapeutics) where NMR experiments beyond 2D are impractical. Therefore, the existing 2D multiplicity-edited HSQC methods must be improved to acquire data on nuclei other than 13C (i.e.15N), to resolve more peaks, to reduce T2 losses and to accommodate water suppression approaches. To meet these needs, a multiplicity-separated1H-X HSQC (MS-HSQC) experiment was developed and tested on 500 and 700 MHz NMR spectrometers equipped with room temperature probes using RNase A (14 kDa) and retroviral capsid (26 kDa) proteins dissolved in 95% H2O/5% D2O. In this pulse sequence, the 1/1JXH editing-period is incorporated into the semi-constant time (semi-CT) X resonance chemical shift evolution period, which increases sensitivity, and importantly, the sum and the difference of the interleaved 1JXH-active and the 1JXH-inactive HSQC experiments yield two separate spectra for XH2 and XH/XH3. Furthermore we demonstrate improved water suppression using triple xyz-gradients instead of the more widely used z-gradient only water-suppression approach.

  6. LC-MS/MS analysis of surface layer proteins as a useful method for the identification of lactobacilli from the Lactobacillus acidophilus group.

    PubMed

    Podlesny, Marcin; Jarocki, Piotr; Komon, Elwira; Glibowska, Agnieszka; Targonski, Zdzislaw

    2011-04-01

    For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/ MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels. PMID:21532327

  7. Moving pieces in a taxonomic puzzle: venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones).

    PubMed

    Nascimento, Danielle G; Rates, Breno; Santos, Daniel M; Verano-Braga, Thiago; Barbosa-Silva, Adriano; Dutra, Alexandre A A; Biondi, Ilka; Martin-Eauclaire, Marie France; De Lima, Maria Elena; Pimenta, Adriano M C

    2006-05-01

    The Buthidae is the most clinically important scorpion family, with over 500 species distributed worldwide. Taxonomical positions and phylogenetic relationships concerning the representative genera and species of this family have been mostly inferred based upon comparisons between morphological characters. Yet, some authors have performed such inferences by comparing some structural properties of a few selected molecules found in the venoms from these scorpions. Here, we propose a novel methodology pipeline designed to address these issues. We have analyzed the whole venoms from some species that exemplify peculiar cases in the Buthidae family (Tityus stigmurus, Tityus serrulatus, Tityus bahiensis, Leiurus quinquestriatus quinquestriatus and Leiurus quinquestriatus hebraeus), by means of a proteomic approach using a 2D-LC/MS technique. The molecules found in these venoms were clustered according to their physicochemical properties (molecular mass and hydrophobicity), by using the machine learning-based Weka software. The clusters assessment, along with the number of molecules found in a given cluster for each scorpion, which assigns for the venom and structural family complexities, respectively, was used to generate a phenetic correlation tree for positioning these species. Our results were in accordance with the classical taxonomy viewpoint, which places T. serrulatus and T. stigmurus as very close species, T. bahiensis as a less related species in the Tityus genus and L. q. quinquestriatus and L. q. hebraeus with small differences within the same species (L. quinquestriatus). Therefore, we believe that this is a well-suited method to determine venom complexities that reflect the scorpions' evolutionary history, which can be crucial to reconstruct their phylogeny through the molecular evolution of their venoms. PMID:16551474

  8. Absorption Mode FT-ICR Mass Spectrometry Imaging

    SciTech Connect

    Smith, Donald F.; Kilgour, David P.; Konijnenburg, Marco; O'Connor, Peter B.; Heeren, Ronald M.

    2013-12-03

    Fourier transform ion cyclotron resonance mass spectrometry offers the highest mass resolving power for molecular imaging experiments. This high mass resolving power ensures that closely spaced peaks at the same nominal mass are resolved for proper image generation. Typically higher magnetic fields are used to increase mass resolving power. However, a gain in mass resolving power can also be realized by phase correction of the data for absorption mode display. In addition to mass resolving power, absorption mode offers higher mass accuracy and signal-to-noise ratio over the conventional magnitude mode. Here we present the first use of absorption mode for Fourier transform ion cyclotron resonance mass spectrometry imaging. The Autophaser algorithm is used to phase correct each spectrum (pixel) in the image and then these parameters are used by the Chameleon work-flow based data processing software to generate absorption mode ?Datacubes? for image and spectral viewing. Absorption mode reveals new mass and spatial features that are not resolved in magnitude mode and results in improved selected ion image contrast.

  9. Determination of optimal protein quantity required to identify abundant and less abundant soybean seed proteins by 2D-PAGE and MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optimizing the amounts of proteins required to separate and characterize both abundant and less abundant proteins by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is critical for conducting proteomic research. In this study, we tested five different levels of soybean seed proteins (7...

  10. 2D-DIGE and MALDI TOF/TOF MS analysis reveal that small GTPase signaling pathways may play an important role in cadmium-induced colon cell malignant transformation.

    PubMed

    Lu, Jian; Zhou, Zhongping; Zheng, Jianzhou; Zhang, Zhuyi; Lu, Rongzhu; Liu, Hanqing; Shi, Haifeng; Tu, Zhigang

    2015-10-01

    Cadmium is a toxic heavy metal present in the environment and in industrial materials. Cadmium has demonstrated carcinogenic activity that induces cell transformation, but how this occurs is unclear. We used 2D-DIGE and MALDI TOF/TOF MS combined with bioinformatics and immunoblotting to investigate the molecular mechanism of cadmium transformation. We found that small GTPases were critical for transformation. Additionally, proteins involved in mitochondrial transcription, DNA repair, and translation also had altered expression patterns in cadmium treated cells. Collectively, our results suggest that activation of small GTPases contributes to cadmium-induced transformation of colon cells. PMID:26220685

  11. Identification of Differential Protein Expression in Hepatocellular Carcinoma Induced Wistar Albino Rats by 2D Electrophoresis and MALDI-TOF-MS Analysis.

    PubMed

    Vedarethinam, Vadanasundari; Dhanaraj, Karthik; Soundherrajan, Ilavenil; Sivanesan, Ravikumar

    2016-04-01

    Hepato cellular carcinoma (HCC) is a type of malignant tumor. To investigate the proteins in cancer molecular mechanism and its role in HCC, we have used proteomic tools such as 2DE and MALDI-TOF-MS. Our investigation ravels that, plasma α-fetoprotein and carcinoembryonic antigen levels were elevated in DEN induced rats and gradually decreased after the treatment with 1,3BPMU. 2DE and MALDI-TOF-MS tool offers to identify the up and down regulation of proteins in HCC. Proteomic study reveals that, five differentially expressed proteins were identified in DEN induced rats and 1,3BPMU treated rats i.e. three up regulated protein such as T kininogen, NDPKB, PRMT1 (DEN induced rats), RGS19 and PAF (1,3BPMU treated rats) in 3BPMU treated rats, activation of transcription of a single gene from multiple promoters provides flexibility in the controlled gene expression. The regulations of hepatocyte stimulating factor were slow down the proliferation of hepatic cell and uncontrolled hepatic cell growth and also molecular signals strongly argue for a patho-physiological role in liver metastasis to control the cell aggression. This indicates that, anti cancer property of 1,3BPMU can be used as potent anti cancer agent. The present study also shows the proteomic approach helps to elucidate the tumor maker as well as regulatory marker proteins in HCC. PMID:27069327

  12. Qualitative and quantitative analysis of the unsaponifiable fraction of vegetable oils by using comprehensive 2D GC with dual MS/FID detection.

    PubMed

    Tranchida, Peter Q; Salivo, Simona; Franchina, Flavio A; Bonaccorsi, Ivana; Dugo, Paola; Mondello, Luigi

    2013-05-01

    The present investigation is focused on the development of a comprehensive two-dimensional GC (GC × GC) method, with dual MS/FID detection, for the qualitative and quantitative analysis of the entire unsaponifiable fraction of vegetable oils. The unsaponifiable fraction forms a minor, highly specific part of a vegetable oil, and can be used as an indicator of genuineness. The column set used consisted of a low-polarity first dimension, and a medium-polarity secondary one, both characterized by a high thermal stability. The use of dual detection enabled the attainment of both mass spectral information and relative % FID data. The complexity of the fingerprint, generated by the unsaponifiable fraction, fully justified the employment of the two-dimensional GC technology. Furthermore, two other GC × GC benefits contributed greatly to the attainment of promising results, namely sensitivity enhancement and the formation of group-type patterns. The method herein proposed could potentially open a new opportunity for the more in-depth knowledge of the unsaponifiable fraction of vegetable oils. PMID:23334257

  13. On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrene-divinylbenzene) columns for ultrasensitive proteomic analysis.

    PubMed

    Luo, Quanzhou; Yue, Guihua; Valaskovic, Gary A; Gu, Ye; Wu, Shiaw-Lin; Karger, Barry L

    2007-08-15

    Following on our recent work, on-line one-dimensional (1D) and two-dimensional (2D) porous layer open tubular/liquid chromatography-electrospray ionization-mass spectrometry (PLOT/LC-ESI-MS) platforms using 3.2 mx10 microm i.d. poly(styrene-divinylbenzene) (PS-DVB) PLOT columns have been developed to provide robust, high-performance, and ultrasensitive proteomic analysis. With the use of a PicoClear tee, the dead volume connection between a 50 microm i.d. PS-DVB monolithic micro-SPE column and the PLOT column was minimized. The micro-SPE/PLOT column assembly provided a separation performance similar to that obtained with direct injection onto the PLOT column at a mobile phase flow rate of 20 nL/min. The trace analysis potential of the platform was evaluated using an in-gel tryptic digest sample of a gel fraction (15-40 kDa) of a cervical cancer (SiHa) cell line. As an example of the sensitivity of the system, approximately 2.5 ng of protein in 2 microL of solution, an amount corresponding to 20 SiHa cells, was subjected to on-line micro-SPE-PLOT/LC-ESI-MS/MS analysis using a linear ion trap MS. A total of 237 peptides associated with 163 unique proteins were identified from a single analysis when using stringent criteria associated with a false positive rate of less than 1%. The number of identified peptides and proteins increased to 638 and 343, respectively, as the injection amount was raised to approximately 45 ng of protein, an amount corresponding to 350 SiHa cells. In comparison, only 338 peptides and 231 unique proteins were identified (false positive rate again less than 1%) from 750 ng of protein from the identical gel fraction, an amount corresponding to 6000 SiHa cells, using a typical 15 cmx75 microm i.d. packed capillary column. The greater sensitivity, higher recovery, and higher resolving power of the PLOT column resulted in the increased number of identifications from only approximately 5% of the injected sample amount. The resolving power of the

  14. A 430 mW 16 b 170 MS/s CMOS pipelined ADC with 77.2 dB SNR and 97.6 dB SFDR

    NASA Astrophysics Data System (ADS)

    Hui, Zhang; Dan, Li; Lei, Wan; Hui, Zhang; Haijun, Wang; Yuan, Gao; Feili, Zhu; Ziqi, Wang; Xuexin, Ding

    2016-03-01

    A 16-bit 170 MS/s pipelined ADC implemented in 0.18 μm CMOS process is presented in this paper. An improved digital calibration method and a linearized sampling front-end are employed to achieve a high SFDR. The enlarged full scale range makes it possible to obtain a high SNR with smaller sampling capacitors, thus achieving higher speed and low power. This ADC attains an SNR of 77.2 dBFS, an SFDR of 97.6 dBc for a 10 MHz input signal, while preserving an SFDR > 80 dBc up to 300 MHz input frequency. The ADC consumes 430 mW from a 1.8 V supply and occupies a 17 mm2 active area. Project supported by the National Science and Technology Major Project (No. 2009ZX01034-002-001-016).

  15. Chemical profile of mango (Mangifera indica L.) using electrospray ionisation mass spectrometry (ESI-MS).

    PubMed

    Oliveira, Bruno G; Costa, Helber B; Ventura, José A; Kondratyuk, Tamara P; Barroso, Maria E S; Correia, Radigya M; Pimentel, Elisângela F; Pinto, Fernanda E; Endringer, Denise C; Romão, Wanderson

    2016-08-01

    Mangifera indica L., mango fruit, is consumed as a dietary supplement with purported health benefits; it is widely used in the food industry. Herein, the chemical profile of the Ubá mango at four distinct maturation stages was evaluated during the process of growth and maturity using negative-ion mode electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI(-)FT-ICR MS) and physicochemical characterisation analysis (total titratable acidity (TA), total soluble solids (TSS), TSS/TA ratio, and total polyphenolic content). Primary (organic acids and sugars) and secondary metabolites (polyphenolic compounds) were mostly identified in the third maturation stage, thus indicating the best stage for harvesting and consuming the fruit. In addition, the potential cancer chemoprevention of the secondary metabolites (phenolic extracts obtained from mango samples) was evaluated using the induction of quinone reductase activity, concluding that fruit polyphenols have the potential for cancer chemoprevention. PMID:26988473

  16. Characterization of ANFO explosive by high accuracy ESI(±)-FTMS with forensic identification on real samples by EASI(-)-MS.

    PubMed

    Hernandes, Vinicius Veri; Franco, Marcos Fernado; Santos, Jandyson Machado; Melendez-Perez, Jose J; de Morais, Damila Rodrigues; Rocha, Werickson Fortunato de Carvalho; Borges, Rodrigo; de Souza, Wanderley; Zacca, Jorge Jardim; Logrado, Lucio Paulo Lima; Eberlin, Marcos Nogueira; Correa, Deleon Nascimento

    2015-04-01

    Ammonium nitrate fuel oil (ANFO) is an explosive used in many civil applications. In Brazil, ANFO has unfortunately also been used in criminal attacks, mainly in automated teller machine (ATM) explosions. In this paper, we describe a detailed characterization of the ANFO composition and its two main constituents (diesel and a nitrate explosive) using high resolution and accuracy mass spectrometry performed on an FT-ICR-mass spectrometer with electrospray ionization (ESI(±)-FTMS) in both the positive and negative ion modes. Via ESI(-)-MS, an ion marker for ANFO was characterized. Using a direct and simple ambient desorption/ionization technique, i.e., easy ambient sonic-spray ionization mass spectrometry (EASI-MS), in a simpler, lower accuracy but robust single quadrupole mass spectrometer, the ANFO ion marker was directly detected from the surface of banknotes collected from ATM explosion theft. PMID:25700111

  17. Cross Gradient Based Joint Inversion of 2D Wide Angle Seismic Reflection/Refraction and Gravity Data Along the Profile Through the 2010 Ms 7.1 Yushu Earthquake, China

    NASA Astrophysics Data System (ADS)

    Xiang, S.; Zhang, H.

    2015-12-01

    2D wide-angle seismic reflection/refraction survey has been widely used to investigate crustal structure and Moho topography. Similarly gravity survey is also very important in the study of local and regional earth features. Seismic survey is sensitive to the seismic velocity parameters and interface variations. For gravity survey, it is sensitive to density parameters of the medium but the resolution along the vertical direction is relatively poor. In this study, we have developed a strategy to jointly invert for seismic velocity model, density model and interface positions using the gravity observations and seismic arrival times from different phases. For the joint inversion of seismic and gravity data, it often relies on the empirical relationship between seismic velocity and density. In comparison, our joint inversion strategy also includes the cross-gradient based structure constraint for seismic velocity and density models in addition to the empirical relationship between them. The objective function for the joint inversion includes data misfit terms for seismic travel times and gravity observations, the cross-gradient constraint, the smoothness terms for two models, and the data misfit term between predicted gravity data based on density model converted from velocity model using the empirical relationship. Each term has its respective weight. We have applied the new joint inversion method to the Riwoqe-Yushu-Maduo profile in northwest China. The profile crosses through the Qiangtang block and Bayan Har block from southwest to northeast, respectively. The 2010 Ms 7.1 Yushu earthquake is located on the profile, around the Ganzi-Yushu fault zone. The joint inversion produces the velocity and density models that are similar in structure and at the same time fit their respective data sets well. Compared to separate seismic inversion using seismic travel times, the joint inversion with gravity data gives a velocity model that better delineates the fault zones. Low

  18. Efficient Readout of Post-translational Codes on the 50-Residue Tail of Histone H3 by High-Resolution MS/MS

    PubMed Central

    Siuti, Nertila; Kelleher, Neil L.

    2009-01-01

    Histone modifications are highly linked to DNA methylation and together they exert epigenetic control over many activities in the cell including gene transcription. Using a streamlined mass spectrometric approach to determine changes in modification states in the first 50 residues of histone H3, we found a decrease in the global methylation states of H3.1 at Lys 9, Lys 14 and Lys 27 after inhibition of DNA methyltransferases by 5-aza-2′-deoxycytidine. Collisional ion dissociation methods proved adequate to determine site-specific H3 PTMs because ample backbone bonds are cleaved between each modification site and PTMs were stable to MS/MS using threshold fragmentation in a linear ion trap (LTQ). Our assay allows for a quick profiling and site-specific interrogation of modification states on the first 50 residues of H3 and is directly applicable to H3.1, H3.2 or H3.3 using most OrbiTrap, FT ICR, or TOF mass spectrometers. PMID:19761750

  19. Aniso2D

    2005-07-01

    Aniso2d is a two-dimensional seismic forward modeling code. The earth is parameterized by an X-Z plane in which the seismic properties Can have monoclinic with x-z plane symmetry. The program uses a user define time-domain wavelet to produce synthetic seismograms anrwhere within the two-dimensional media.

  20. Mesh2d

    SciTech Connect

    Greg Flach, Frank Smith

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.

  1. Mesh2d

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assignsmore » an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.« less

  2. A broad-band FT-ICR Penning trap system for KATRIN

    NASA Astrophysics Data System (ADS)

    Ubieto-Díaz, M.; Rodríguez, D.; Lukic, S.; Nagy, Sz; Stahl, S.; Blaum, K.

    2009-12-01

    The KArlsruhe TRItium Neutrino experiment KATRIN aims at improving the upper limit of the mass of the electron antineutrino to about 0.2 eV (90% c.l.) by investigating the -decay of tritium gas molecules . The experiment is currently under construction to start first data taking in 2012. One source of systematic uncertainties in the KATRIN experiment is the formation of ion clusters when tritium decays and decay products interact with residual tritium molecules. It is essential to monitor the abundances of these clusters since they have different final state energies than tritium ions. For this purpose, a prototype of a cylindrical Penning trap has been constructed and tested at the Max-Planck-Institute for Nuclear Physics in Heidelberg, which will be installed in the KATRIN beam line. This system employs the technique of Fourier-Transform Ion-Cyclotron-Resonance in order to measure the abundances of the different stored ion species.

  3. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

    Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.

  4. High divergent 2D grating

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Ma, Jianyong; Zhou, Changhe

    2014-11-01

    A 3×3 high divergent 2D-grating with period of 3.842μm at wavelength of 850nm under normal incidence is designed and fabricated in this paper. This high divergent 2D-grating is designed by the vector theory. The Rigorous Coupled Wave Analysis (RCWA) in association with the simulated annealing (SA) is adopted to calculate and optimize this 2D-grating.The properties of this grating are also investigated by the RCWA. The diffraction angles are more than 10 degrees in the whole wavelength band, which are bigger than the traditional 2D-grating. In addition, the small period of grating increases the difficulties of fabrication. So we fabricate the 2D-gratings by direct laser writing (DLW) instead of traditional manufacturing method. Then the method of ICP etching is used to obtain the high divergent 2D-grating.

  5. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

    Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

  6. Novel Cysteine Tags for the Sequencing of Non-Tryptic Disulfide Peptides of Anurans: ESI-MS Study of Fragmentation Efficiency

    NASA Astrophysics Data System (ADS)

    Samgina, Tatyana Y.; Vorontsov, Egor A.; Gorshkov, Vladimir A.; Artemenko, Konstantin A.; Nifant'ev, Ilya E.; Kanawati, Basem; Schmitt-Kopplin, Philippe; Zubarev, Roman A.; Lebedev, Albert T.

    2011-12-01

    Mass spectrometry faces considerable difficulties in de novo sequencing of long non-tryptic peptides with S-S bonds. Long disulfide-containing peptides brevinins 1E and 2Ec from frog Rana ridibunda were reduced and alkylated with nine novel and three known derivatizing agents. Eight of the novel reagents are maleimide derivatives. Modified samples were subjected to MS/MS studies on FT-ICR and Orbitrap mass spectrometers using CAD/HCD or ECD/ETD techniques. Procedures, fragmentation patterns, and sequence coverage for two peptides modified with 12 tags are described. ECD/ETD and CAD fragmentation revealed complementary sequence information. Higher-energy collisionally activated dissociation (HCD) sufficiently enhanced y-ions formation for brevinin 1E, but not for brevinin 2Ec. Some novel tags [ N-benzylmaleimide, N-(2,6-dimethylphenyl)maleimide] along with known N-phenylmaleimide and iodoacetic acid showed high total sequence coverage taking into account combined ETD and HCD fragmentation. Moreover, modification of long (34 residues) brevinin 2Ec with N-benzylmaleimide or N-(2,6-dimethylphenyl)maleimide yielded high sequence coverage and full C-terminal sequence determination with ECD alone.

  7. AnisWave 2D

    2004-08-01

    AnisWave2D is a 2D finite-difference code for a simulating seismic wave propagation in fully anisotropic materials. The code is implemented to run in parallel over multiple processors and is fully portable. A mesh refinement algorithm has been utilized to allow the grid-spacing to be tailored to the velocity model, avoiding the over-sampling of high-velocity materials that usually occurs in fixed-grid schemes.

  8. Pediatric MS

    MedlinePlus

    ... of the oral medications in the pediatric population. Network of Pediatric MS Centers The National MS Society ... MS Study Group (2004) and established a nationwide network of six Pediatric MS Centers of Excellence (2006) ...

  9. CD4+NKG2D+ T Cells Exhibit Enhanced Migratory and Encephalitogenic Properties in Neuroinflammation

    PubMed Central

    Ruck, Tobias; Bittner, Stefan; Gross, Catharina C.; Breuer, Johanna; Albrecht, Stefanie; Korr, Sabrina; Göbel, Kerstin; Pankratz, Susann; Henschel, Christian M.; Schwab, Nicholas; Staszewski, Ori; Prinz, Marco; Kuhlmann, Tanja

    2013-01-01

    Migration of encephalitogenic CD4+ T lymphocytes across the blood-brain barrier is an essential step in the pathogenesis of multiple sclerosis (MS). We here demonstrate that expression of the co-stimulatory receptor NKG2D defines a subpopulation of CD4+ T cells with elevated levels of markers for migration, activation, and cytolytic capacity especially when derived from MS patients. Furthermore, CD4+NKG2D+ cells produce high levels of proinflammatory IFN-γ and IL-17 upon stimulation. NKG2D promotes the capacity of CD4+NKG2D+ cells to migrate across endothelial cells in an in vitro model of the blood-brain barrier. CD4+NKG2D+ T cells are enriched in the cerebrospinal fluid of MS patients, and a significant number of CD4+ T cells in MS lesions coexpress NKG2D. We further elucidated the role of CD4+NKG2D+ T cells in the mouse system. NKG2D blockade restricted central nervous system migration of T lymphocytes in vivo, leading to a significant decrease in the clinical and pathologic severity of experimental autoimmune encephalomyelitis, an animal model of MS. Blockade of NKG2D reduced killing of cultivated mouse oligodendrocytes by activated CD4+ T cells. Taken together, we identify CD4+NKG2D+ cells as a subpopulation of T helper cells with enhanced migratory, encephalitogenic and cytotoxic properties involved in inflammatory CNS lesion development. PMID:24282598

  10. Conductive carbon tape used for support and mounting of both whole animal and fragile heat-treated tissue sections for MALDI MS imaging and quantitation.

    PubMed

    Goodwin, Richard J A; Nilsson, Anna; Borg, Daniel; Langridge-Smith, Pat R R; Harrison, David J; Mackay, C Logan; Iverson, Suzanne L; Andrén, Per E

    2012-08-30

    Analysis of whole animal tissue sections by MALDI MS imaging (MSI) requires effective sample collection and transfer methods to allow the highest quality of in situ analysis of small or hard to dissect tissues. We report on the use of double-sided adhesive conductive carbon tape during whole adult rat tissue sectioning of carboxymethyl cellulose (CMC) embedded animals, with samples mounted onto large format conductive glass and conductive plastic MALDI targets, enabling MSI analysis to be performed on both TOF and FT-ICR MALDI mass spectrometers. We show that mounting does not unduly affect small molecule MSI detection by analyzing tiotropium abundance and distribution in rat lung tissues, with direct on-tissue quantitation achieved. Significantly, we use the adhesive tape to provide support to embedded delicate heat-stabilized tissues, enabling sectioning and mounting to be performed that maintained tissue integrity on samples that had previously been impossible to adequately prepare section for MSI analysis. The mapping of larger peptidomic molecules was not hindered by tape mounting samples and we demonstrate this by mapping the distribution of PEP-19 in both native and heat-stabilized rat brains. Furthermore, we show that without heat stabilization PEP-19 degradation fragments can detected and identified directly by MALDI MSI analysis. PMID:22796569

  11. Stacking up 2D materials

    NASA Astrophysics Data System (ADS)

    Mayor, Louise

    2016-05-01

    Graphene might be the most famous example, but there are other 2D materials and compounds too. Louise Mayor explains how these atomically thin sheets can be layered together to create flexible “van der Waals heterostructures”, which could lead to a range of novel applications.

  12. MOSS2D V1

    2001-01-31

    This software reduces the data from two-dimensional kSA MOS program, k-Space Associates, Ann Arbor, MI. Initial MOS data is recorded without headers in 38 columns, with one row of data per acquisition per lase beam tracked. The final MOSS 2d data file is reduced, graphed, and saved in a tab-delimited column format with headers that can be plotted in any graphing software.

  13. Nanoimprint lithography: 2D or not 2D? A review

    NASA Astrophysics Data System (ADS)

    Schift, Helmut

    2015-11-01

    Nanoimprint lithography (NIL) is more than a planar high-end technology for the patterning of wafer-like substrates. It is essentially a 3D process, because it replicates various stamp topographies by 3D displacement of material and takes advantage of the bending of stamps while the mold cavities are filled. But at the same time, it keeps all assets of a 2D technique being able to pattern thin masking layers like in photon- and electron-based traditional lithography. This review reports about 20 years of development of replication techniques at Paul Scherrer Institut, with a focus on 3D aspects of molding, which enable NIL to stay 2D, but at the same time enable 3D applications which are "more than Moore." As an example, the manufacturing of a demonstrator for backlighting applications based on thermally activated selective topography equilibration will be presented. This technique allows generating almost arbitrary sloped, convex and concave profiles in the same polymer film with dimensions in micro- and nanometer scale.

  14. Impact of different ionization methods on the molecular assignments of asphaltenes by FT-ICR mass spectrometry.

    PubMed

    Gaspar, Andras; Zellermann, Elio; Lababidi, Sami; Reece, Jennifer; Schrader, Wolfgang

    2012-06-19

    Over the years, ultrahigh resolution mass spectrometry has successfully illustrated the extreme complexity of crude oil and related solubility or polarity based fractions on a molecular level. However, the applied ionization technique greatly influences the outcome and may provide misleading information. In this work, we investigate the atmospheric pressure laser ionization (APLI) technique coupled with Fourier transform ion cyclotron resonance mass spectrometer to analyze the asphaltene fraction of a crude oil. These results were compared to data obtained by using other existing atmospheric pressure ionization methods. Furthermore elemental analysis and solid state NMR were used to obtain the bulk characteristics of the asphaltene sample. The results of the different ionization techniques were compared with the bulk properties in order to describe the potential discrimination effects of the ionization techniques that were observed. The results showed that APLI expands the range of the assigned molecules, while retaining information already observed with the generally used ion sources. PMID:22607608

  15. High-field FT-ICR mass spectrometry and NMR spectroscopy to characterize DOM removal through a nanofiltration pilot plant.

    PubMed

    Cortés-Francisco, Nuria; Harir, Mourad; Lucio, Marianna; Ribera, Gemma; Martínez-Lladó, Xavier; Rovira, Miquel; Schmitt-Kopplin, Philipe; Hertkorn, Norbert; Caixach, Josep

    2014-12-15

    Ultrahigh resolution Fourier transform ion cyclotron mass spectrometry and nuclear magnetic resonance spectroscopy were combined to evaluate the molecular changes of dissolved organic matter (DOM) through an ultrafiltration-nanofiltration (UF-NF) pilot plant, using two dissimilar NF membranes tested in parallel. The sampling was performed on seven key locations within the pilot plant: pretreated water, UF effluent, UF effluent after addition of reagents, permeate NF 1, permeate NF 2, brine NF 1 and brine NF 2, during two sampling campaigns. The study showed that there is no significant change in the nature of DOM at molecular level, when the water was treated with UF and/or with the addition of sodium metabisulfite and antiscaling agents. However, enormous decrease of DOM concentration was observed when the water was treated on the NF membranes. The NF process preferentially removed compounds with higher oxygen and nitrogen content (more hydrophilic compounds), whereas molecules with longer pure aliphatic chains and less content of oxygen were the ones capable of passing through the membranes. Moreover, slight molecular selectivity between the two NF membranes was also observed. PMID:25269107

  16. Improved mass analysis of oligoribonucleotides by 13C, 15N double depletion and electrospray ionization FT-ICR mass spectrometry.

    PubMed

    Xiong, Ying; Schroeder, Kersten; Greenbaum, Nancy L; Hendrickson, Christopher L; Marshall, Alan G

    2004-03-15

    13C, 15N doubly depleted 32-ribonucleotide was synthesized enzymatically by in vitro transcription from nucleoside triphosphates isolated from E. coli grown in a minimal medium containing 12C, 14N-enriched glucose and ammonium sulfate. Following purification and desalting by reversed-phase HPLC, buffer exchange with Microcon YM-3, and ethanol precipitation, electrospray ionization Fourier transform ion cyclotron resonance mass spectra revealed greatly enhanced abundance of monoisotopic ions (by a factor of approximately 100) and a narrower isotopic distribution with higher signal-to-noise ratio. The abrupt onset and high magnitude of the monoisotopic species promise to facilitate accurate mass measurement of RNA's. PMID:15018587

  17. LC-MS analysis in the aquatic environment and in water treatment technology--a critical review. Part II: Applications for emerging contaminants and related pollutants, microorganisms and humic acids.

    PubMed

    Zwiener, Christian; Frimmel, Fritz H

    2004-02-01

    substances have been made possible by FT-ICR-MS due to its ultrahigh mass resolution. Finally, exciting possibilities for rapid detection and identification of microorganisms have been made possible by MALDI and LC-MS methods. PMID:14673565

  18. A novel improved method for analysis of 2D diffusion relaxation data—2D PARAFAC-Laplace decomposition

    NASA Astrophysics Data System (ADS)

    Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.

    2007-09-01

    This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it

  19. Surface-Induced Dissociation of Ions Produced by Matrix-Assisted Laser Desorption Ionization in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

    SciTech Connect

    Laskin, Julia; Beck, Kenneth M.; Hache, John J.; Futrell, Jean H.

    2004-01-15

    Intermediate pressure matrix assisted laser ionization (MALDI) source was constructed and interfaced with a 6T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for surface-induced dissociation (SID) studies.

  20. A regional study of the seasonal variation in the molecular composition of rainwater

    NASA Astrophysics Data System (ADS)

    Cottrell, Barbara A.; Gonsior, Michael; Isabelle, Lorne M.; Luo, W.; Perraud, Véronique; McIntire, Theresa M.; Pankow, James F.; Schmitt-Kopplin, Philippe; Cooper, William J.; Simpson, André J.

    2013-10-01

    Rainwater is not only a critical source of drinking and agricultural water but it plays a key role in the fate and transport of contaminants through their removal by wet deposition. Rainwater is a complex mixture of organic compounds yet despite its importance its spatial and temporal variability are not well understood and less than 50% of the organic matter has been characterized. In-depth analytical approaches were used in this study to characterize the seasonal variation in rainwater composition. Rainwater samples were collected over a one-year period in Scarborough, Ontario, Canada. The seasonal variation of atmospheric organic carbon (AOC) in rainwater was analyzed by excitation-emission matrix spectroscopy (EEMs), 1D and 2D NMR with compound identification by spectral database matching, GC-MS, FT-ICR-MS, and GC × GC-TOFMS. This combination of techniques provided four complementary datasets, with less than 10% overlap, of anthropogenic and biogenic AOC. NMR with database matching identified over 100 compounds, primarily carboxylic acids, carbohydrates, and nitrogen-containing compounds. GC × GC-TOFMS analysis identified 344 compounds in two rain events with 33% of the compounds common to both events. FT-ICR-MS generated a seasonally dependent profile of 1226-1575 molecular ions of CHO, CHOS, and CHON elemental composition. FT-ICR-MS and GC × GC-TOFMS datasets were compared using van Krevelen diagrams (H/C vs. O/C), the H/C ratio vs. mass/charge (m/z), and the carbon oxidation state/carbon number matrix. Fluorescence patterns were correlated with NMR results resulting in the identification one seasonally-dependent component of chromophoric dissolved organic matter (CDOM). This study demonstrated the importance of using of an integrated analytical approach to monitor the compositional variation of AOC.

  1. NKG2D ligands as therapeutic targets

    PubMed Central

    Spear, Paul; Wu, Ming-Ru; Sentman, Marie-Louise; Sentman, Charles L.

    2013-01-01

    The Natural Killer Group 2D (NKG2D) receptor plays an important role in protecting the host from infections and cancer. By recognizing ligands induced on infected or tumor cells, NKG2D modulates lymphocyte activation and promotes immunity to eliminate ligand-expressing cells. Because these ligands are not widely expressed on healthy adult tissue, NKG2D ligands may present a useful target for immunotherapeutic approaches in cancer. Novel therapies targeting NKG2D ligands for the treatment of cancer have shown preclinical success and are poised to enter into clinical trials. In this review, the NKG2D receptor and its ligands are discussed in the context of cancer, infection, and autoimmunity. In addition, therapies targeting NKG2D ligands in cancer are also reviewed. PMID:23833565

  2. Perspectives for spintronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Han, Wei

    2016-03-01

    The past decade has been especially creative for spintronics since the (re)discovery of various two dimensional (2D) materials. Due to the unusual physical characteristics, 2D materials have provided new platforms to probe the spin interaction with other degrees of freedom for electrons, as well as to be used for novel spintronics applications. This review briefly presents the most important recent and ongoing research for spintronics in 2D materials.

  3. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  4. Staring 2-D hadamard transform spectral imager

    DOEpatents

    Gentry, Stephen M.; Wehlburg, Christine M.; Wehlburg, Joseph C.; Smith, Mark W.; Smith, Jody L.

    2006-02-07

    A staring imaging system inputs a 2D spatial image containing multi-frequency spectral information. This image is encoded in one dimension of the image with a cyclic Hadamarid S-matrix. The resulting image is detecting with a spatial 2D detector; and a computer applies a Hadamard transform to recover the encoded image.

  5. Light field morphing using 2D features.

    PubMed

    Wang, Lifeng; Lin, Stephen; Lee, Seungyong; Guo, Baining; Shum, Heung-Yeung

    2005-01-01

    We present a 2D feature-based technique for morphing 3D objects represented by light fields. Existing light field morphing methods require the user to specify corresponding 3D feature elements to guide morph computation. Since slight errors in 3D specification can lead to significant morphing artifacts, we propose a scheme based on 2D feature elements that is less sensitive to imprecise marking of features. First, 2D features are specified by the user in a number of key views in the source and target light fields. Then the two light fields are warped view by view as guided by the corresponding 2D features. Finally, the two warped light fields are blended together to yield the desired light field morph. Two key issues in light field morphing are feature specification and warping of light field rays. For feature specification, we introduce a user interface for delineating 2D features in key views of a light field, which are automatically interpolated to other views. For ray warping, we describe a 2D technique that accounts for visibility changes and present a comparison to the ideal morphing of light fields. Light field morphing based on 2D features makes it simple to incorporate previous image morphing techniques such as nonuniform blending, as well as to morph between an image and a light field. PMID:15631126

  6. 2D materials for nanophotonic devices

    NASA Astrophysics Data System (ADS)

    Xu, Renjing; Yang, Jiong; Zhang, Shuang; Pei, Jiajie; Lu, Yuerui

    2015-12-01

    Two-dimensional (2D) materials have become very important building blocks for electronic, photonic, and phononic devices. The 2D material family has four key members, including the metallic graphene, transition metal dichalcogenide (TMD) layered semiconductors, semiconducting black phosphorous, and the insulating h-BN. Owing to the strong quantum confinements and defect-free surfaces, these atomically thin layers have offered us perfect platforms to investigate the interactions among photons, electrons and phonons. The unique interactions in these 2D materials are very important for both scientific research and application engineering. In this talk, I would like to briefly summarize and highlight the key findings, opportunities and challenges in this field. Next, I will introduce/highlight our recent achievements. We demonstrated atomically thin micro-lens and gratings using 2D MoS2, which is the thinnest optical component around the world. These devices are based on our discovery that the elastic light-matter interactions in highindex 2D materials is very strong. Also, I would like to introduce a new two-dimensional material phosphorene. Phosphorene has strongly anisotropic optical response, which creates 1D excitons in a 2D system. The strong confinement in phosphorene also enables the ultra-high trion (charged exciton) binding energies, which have been successfully measured in our experiments. Finally, I will briefly talk about the potential applications of 2D materials in energy harvesting.

  7. Inertial solvation in femtosecond 2D spectra

    NASA Astrophysics Data System (ADS)

    Hybl, John; Albrecht Ferro, Allison; Farrow, Darcie; Jonas, David

    2001-03-01

    We have used 2D Fourier transform spectroscopy to investigate polar solvation. 2D spectroscopy can reveal molecular lineshapes beneath ensemble averaged spectra and freeze molecular motions to give an undistorted picture of the microscopic dynamics of polar solvation. The transition from "inhomogeneous" to "homogeneous" 2D spectra is governed by both vibrational relaxation and solvent motion. Therefore, the time dependence of the 2D spectrum directly reflects the total response of the solvent-solute system. IR144, a cyanine dye with a dipole moment change upon electronic excitation, was used to probe inertial solvation in methanol and propylene carbonate. Since the static Stokes' shift of IR144 in each of these solvents is similar, differences in the 2D spectra result from solvation dynamics. Initial results indicate that the larger propylene carbonate responds more slowly than methanol, but appear to be inconsistent with rotational estimates of the inertial response. To disentangle intra-molecular vibrations from solvent motion, the 2D spectra of IR144 will be compared to the time-dependent 2D spectra of the structurally related nonpolar cyanine dye HDITCP.

  8. Internal Photoemission Spectroscopy of 2-D Materials

    NASA Astrophysics Data System (ADS)

    Nguyen, Nhan; Li, Mingda; Vishwanath, Suresh; Yan, Rusen; Xiao, Shudong; Xing, Huili; Cheng, Guangjun; Hight Walker, Angela; Zhang, Qin

    Recent research has shown the great benefits of using 2-D materials in the tunnel field-effect transistor (TFET), which is considered a promising candidate for the beyond-CMOS technology. The on-state current of TFET can be enhanced by engineering the band alignment of different 2D-2D or 2D-3D heterostructures. Here we present the internal photoemission spectroscopy (IPE) approach to determine the band alignments of various 2-D materials, in particular SnSe2 and WSe2, which have been proposed for new TFET designs. The metal-oxide-2-D semiconductor test structures are fabricated and characterized by IPE, where the band offsets from the 2-D semiconductor to the oxide conduction band minimum are determined by the threshold of the cube root of IPE yields as a function of photon energy. In particular, we find that SnSe2 has a larger electron affinity than most semiconductors and can be combined with other semiconductors to form near broken-gap heterojunctions with low barrier heights which can produce a higher on-state current. The details of data analysis of IPE and the results from Raman spectroscopy and spectroscopic ellipsometry measurements will also be presented and discussed.

  9. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

    DYNA2D is an explicit Lagrangian finite element code used to model dynamic events where stress wave interactions influence the overall response of the system. DYNA2D is often used to model penetration problems involving ductile-to-ductile impacts; however, with the advent of the use of ceramics in the armor-anti-armor community and the need to model damage to laser optics components, good brittle damage models are now needed in DYNA2D. This report will detail the implementation of four brittle damage models in DYNA2D, three scalar damage models and one tensor damage model. These new brittle damage models are then used to predict experimental results from three distinctly different glass damage problems.

  10. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  11. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  12. 2D electronic materials for army applications

    NASA Astrophysics Data System (ADS)

    O'Regan, Terrance; Perconti, Philip

    2015-05-01

    The record electronic properties achieved in monolayer graphene and related 2D materials such as molybdenum disulfide and hexagonal boron nitride show promise for revolutionary high-speed and low-power electronic devices. Heterogeneous 2D-stacked materials may create enabling technology for future communication and computation applications to meet soldier requirements. For instance, transparent, flexible and even wearable systems may become feasible. With soldier and squad level electronic power demands increasing, the Army is committed to developing and harnessing graphene-like 2D materials for compact low size-weight-and-power-cost (SWAP-C) systems. This paper will review developments in 2D electronic materials at the Army Research Laboratory over the last five years and discuss directions for future army applications.

  13. 2-d Finite Element Code Postprocessor

    1996-07-15

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forcesmore » along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.« less

  14. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

    Chemistry plays an ever-increasing role in the production, functionalization, processing and applications of graphene and other 2D materials. This special issue highlights a selection of enlightening chemical approaches to 2D materials, which nicely reflect the breadth of the field and convey the excitement of the individuals involved in it, who are trying to translate graphene and related materials from the laboratory into a real, high-impact technology. PMID:27478083

  15. Extended 2D generalized dilaton gravity theories

    NASA Astrophysics Data System (ADS)

    de Mello, R. O.

    2008-09-01

    We show that an anomaly-free description of matter in (1+1) dimensions requires a deformation of the 2D relativity principle, which introduces a non-trivial centre in the 2D Poincaré algebra. Then we work out the reduced phase space of the anomaly-free 2D relativistic particle, in order to show that it lives in a noncommutative 2D Minkowski space. Moreover, we build a Gaussian wave packet to show that a Planck length is well defined in two dimensions. In order to provide a gravitational interpretation for this noncommutativity, we propose to extend the usual 2D generalized dilaton gravity models by a specific Maxwell component, which guages the extra symmetry associated with the centre of the 2D Poincaré algebra. In addition, we show that this extension is a high energy correction to the unextended dilaton theories that can affect the topology of spacetime. Further, we couple a test particle to the general extended dilaton models with the purpose of showing that they predict a noncommutativity in curved spacetime, which is locally described by a Moyal star product in the low energy limit. We also conjecture a probable generalization of this result, which provides strong evidence that the noncommutativity is described by a certain star product which is not of the Moyal type at high energies. Finally, we prove that the extended dilaton theories can be formulated as Poisson Sigma models based on a nonlinear deformation of the extended Poincaré algebra.

  16. MS Detectors

    SciTech Connect

    Koppenaal, David W.; Barinaga, Charles J.; Denton, M Bonner B.; Sperline, Roger P.; Hieftje, Gary M.; Schilling, G. D.; Andrade, Francisco J.; Barnes IV., James H.

    2005-11-01

    Good eyesight is often taken for granted, a situation that everyone appreciates once vision begins to fade with age. New eyeglasses or contact lenses are traditional ways to improve vision, but recent new technology, i.e. LASIK laser eye surgery, provides a new and exciting means for marked vision restoration and improvement. In mass spectrometry, detectors are the 'eyes' of the MS instrument. These 'eyes' have also been taken for granted. New detectors and new technologies are likewise needed to correct, improve, and extend ion detection and hence, our 'chemical vision'. The purpose of this report is to review and assess current MS detector technology and to provide a glimpse towards future detector technologies. It is hoped that the report will also serve to motivate interest, prompt ideas, and inspire new visions for ion detection research.

  17. Optical modulators with 2D layered materials

    NASA Astrophysics Data System (ADS)

    Sun, Zhipei; Martinez, Amos; Wang, Feng

    2016-04-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that 2D layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this Review, we cover the state of the art of optical modulators based on 2D materials, including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as 2D heterostructures, plasmonic structures, and silicon and fibre integrated structures. We also take a look at the future perspectives and discuss the potential of yet relatively unexplored mechanisms, such as magneto-optic and acousto-optic modulation.

  18. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

    Transition metal dichalcogenides (TMDs) have generated significant interest for numerous applications including sensors, flexible electronics, heterostructures and optoelectronics due to their interesting, thickness-dependent properties. Despite recent progress, the synthesis of high-quality and highly uniform TMDs on a large scale is still a challenge. In this talk, synthesis routes for WSe2 and MoS2 that achieve monolayer thickness uniformity across large area substrates with electrical properties equivalent to geological crystals will be described. Controlled doping of 2D semiconductors is also critically required. However, methods established for conventional semiconductors, such as ion implantation, are not easily applicable to 2D materials because of their atomically thin structure. Redox-active molecular dopants will be demonstrated which provide large changes in carrier density and workfunction through the choice of dopant, treatment time, and the solution concentration. Finally, several applications of these large-area, uniform 2D materials will be described including heterostructures, biosensors and strain sensors.

  19. 2D microwave imaging reflectometer electronics

    SciTech Connect

    Spear, A. G.; Domier, C. W. Hu, X.; Muscatello, C. M.; Ren, X.; Luhmann, N. C.; Tobias, B. J.

    2014-11-15

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  20. 2D microwave imaging reflectometer electronics

    NASA Astrophysics Data System (ADS)

    Spear, A. G.; Domier, C. W.; Hu, X.; Muscatello, C. M.; Ren, X.; Tobias, B. J.; Luhmann, N. C.

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  1. 2D microwave imaging reflectometer electronics.

    PubMed

    Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program. PMID:25430247

  2. 2D-Crystal-Based Functional Inks.

    PubMed

    Bonaccorso, Francesco; Bartolotta, Antonino; Coleman, Jonathan N; Backes, Claudia

    2016-08-01

    The possibility to produce and process graphene, related 2D crystals, and heterostructures in the liquid phase makes them promising materials for an ever-growing class of applications as composite materials, sensors, in flexible optoelectronics, and energy storage and conversion. In particular, the ability to formulate functional inks with on-demand rheological and morphological properties, i.e., lateral size and thickness of the dispersed 2D crystals, is a step forward toward the development of industrial-scale, reliable, inexpensive printing/coating processes, a boost for the full exploitation of such nanomaterials. Here, the exfoliation strategies of graphite and other layered crystals are reviewed, along with the advances in the sorting of lateral size and thickness of the exfoliated sheets together with the formulation of functional inks and the current development of printing/coating processes of interest for the realization of 2D-crystal-based devices. PMID:27273554

  3. The 2D lingual appliance system.

    PubMed

    Cacciafesta, Vittorio

    2013-09-01

    The two-dimensional (2D) lingual bracket system represents a valuable treatment option for adult patients seeking a completely invisible orthodontic appliance. The ease of direct or simplified indirect bonding of 2D lingual brackets in combination with low friction mechanics makes it possible to achieve a good functional and aesthetic occlusion, even in the presence of a severe malocclusion. The use of a self-ligating bracket significantly reduces chair-side time for the orthodontist, and the low-profile bracket design greatly improves patient comfort. PMID:24005953

  4. Inkjet printing of 2D layered materials.

    PubMed

    Li, Jiantong; Lemme, Max C; Östling, Mikael

    2014-11-10

    Inkjet printing of 2D layered materials, such as graphene and MoS2, has attracted great interests for emerging electronics. However, incompatible rheology, low concentration, severe aggregation and toxicity of solvents constitute critical challenges which hamper the manufacturing efficiency and product quality. Here, we introduce a simple and general technology concept (distillation-assisted solvent exchange) to efficiently overcome these challenges. By implementing the concept, we have demonstrated excellent jetting performance, ideal printing patterns and a variety of promising applications for inkjet printing of 2D layered materials. PMID:25169938

  5. Measurement of 2D birefringence distribution

    NASA Astrophysics Data System (ADS)

    Noguchi, Masato; Ishikawa, Tsuyoshi; Ohno, Masahiro; Tachihara, Satoru

    1992-10-01

    A new measuring method of 2-D birefringence distribution has been developed. It has not been an easy job to get a birefringence distribution in an optical element with conventional ellipsometry because of its lack of scanning means. Finding an analogy between the rotating analyzer method in ellipsometry and the phase-shifting method in recently developed digital interferometry, we have applied the phase-shifting algorithm to ellipsometry, and have developed a new method that makes the measurement of 2-D birefringence distribution easy and possible. The system contains few moving parts, assuring reliability, and measures a large area of a sample at one time, making the measuring time very short.

  6. Highly resolved measurements of atmospheric turbulence with the new 2d-Atmospheric Laser Cantilever Anemometer

    NASA Astrophysics Data System (ADS)

    Jeromin, A.; Schaffarczyk, A. P.; Puczylowski, J.; Peinke, J.; Hölling, M.

    2014-12-01

    For the investigation of atmospheric turbulent flows on small scales a new anemometer was developed, the so-called 2d-Atmospheric Laser Cantilever Anemometer (2d-ALCA). It performs highly resolved measurements with a spatial resolution in millimeter range and temporal resolution in kHz range, thus detecting very small turbulent structures. The anemometer is a redesign of the successfully operating 2d-LCA for laboratory application. The new device was designed to withstand hostile operating environments (rain and saline, humid air). In February 2012, the 2d-ALCA was used for the first time in a test field. The device was mounted in about 53 m above ground level on a lattice tower near the German North Sea coast. Wind speed was measured by the 2d-ALCA at 10 kHz sampling rate and by cup anemometers at 1 Hz. The instantaneous wind speed ranged from 8 m/s to 19 m/s at an average turbulence level of about 7 %. Wind field characteristics were analyzed based on cup anemometer as well as 2d-ALCA. The combination of both devices allowed the study of atmospheric turbulence over several magnitudes in turbulent scales.

  7. Parallel stitching of 2D materials

    DOE PAGESBeta

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; et al

    2016-01-27

    Diverse parallel stitched 2D heterostructures, including metal–semiconductor, semiconductor–semiconductor, and insulator–semiconductor, are synthesized directly through selective “sowing” of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. Lastly, the methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  8. Parallel Stitching of 2D Materials.

    PubMed

    Ling, Xi; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; Hsu, Allen L; Bie, Yaqing; Lee, Yi-Hsien; Zhu, Yimei; Wu, Lijun; Li, Ju; Jarillo-Herrero, Pablo; Dresselhaus, Mildred; Palacios, Tomás; Kong, Jing

    2016-03-01

    Diverse parallel stitched 2D heterostructures, including metal-semiconductor, semiconductor-semiconductor, and insulator-semiconductor, are synthesized directly through selective "sowing" of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. The methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits. PMID:26813882

  9. Baby universes in 2d quantum gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, Jan; Jain, Sanjay; Thorleifsson, Gudmar

    1993-06-01

    We investigate the fractal structure of 2d quantum gravity, both for pure gravity and for gravity coupled to multiple gaussian fields and for gravity coupled to Ising spins. The roughness of the surfaces is described in terms of baby universes and using numerical simulations we measure their distribution which is related to the string susceptibility exponent γstring.

  10. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology

    PubMed Central

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct “beyond graphene” domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  11. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology.

    PubMed

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct "beyond graphene" domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  12. Static & Dynamic Response of 2D Solids

    1996-07-15

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surfacemore » contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.« less

  13. Stochastic Inversion of 2D Magnetotelluric Data

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function ismore » explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows« less

  14. Stochastic Inversion of 2D Magnetotelluric Data

    SciTech Connect

    Chen, Jinsong

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function is explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows

  15. Explicit 2-D Hydrodynamic FEM Program

    1996-08-07

    DYNA2D* is a vectorized, explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. DYNA2D* contains 13 material models and 9 equations of state (EOS) to cover a wide range of material behavior. The material models implemented in all machine versions are: elastic, orthotropic elastic, kinematic/isotropic elastic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, rubber, high explosive burn, isotropic elastic-plastic, temperature-dependent elastic-plastic. Themore » isotropic and temperature-dependent elastic-plastic models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state including linear polynomial, JWL high explosive, Sack Tuesday high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, and tabulated.« less

  16. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

    Sahoo, Nanda Gopal; Esteves, Richard J.; Punetha, Vinay Deep; Pestov, Dmitry; Arachchige, Indika U.; McLeskey, James T.

    2016-07-01

    We report on the fabrication and characterization of a Schottky diode made using 2D germanane (hydrogenated germanene). When compared to germanium, the 2D structure has higher electron mobility, an optimal band-gap, and exceptional stability making germanane an outstanding candidate for a variety of opto-electronic devices. One-atom-thick sheets of hydrogenated puckered germanium atoms have been synthesized from a CaGe2 framework via intercalation and characterized by XRD, Raman, and FTIR techniques. The material was then used to fabricate Schottky diodes by suspending the germanane in benzonitrile and drop-casting it onto interdigitated metal electrodes. The devices demonstrate significant rectifying behavior and the outstanding potential of this material.

  17. Layer Engineering of 2D Semiconductor Junctions.

    PubMed

    He, Yongmin; Sobhani, Ali; Lei, Sidong; Zhang, Zhuhua; Gong, Yongji; Jin, Zehua; Zhou, Wu; Yang, Yingchao; Zhang, Yuan; Wang, Xifan; Yakobson, Boris; Vajtai, Robert; Halas, Naomi J; Li, Bo; Xie, Erqing; Ajayan, Pulickel

    2016-07-01

    A new concept for junction fabrication by connecting multiple regions with varying layer thicknesses, based on the thickness dependence, is demonstrated. This type of junction is only possible in super-thin-layered 2D materials, and exhibits similar characteristics as p-n junctions. Rectification and photovoltaic effects are observed in chemically homogeneous MoSe2 junctions between domains of different thicknesses. PMID:27136275

  18. 2dF mechanical engineering

    NASA Astrophysics Data System (ADS)

    Smith, Greg; Lankshear, Allan

    1998-07-01

    2dF is a multi-object instrument mounted at prime focus at the AAT capable of spectroscopic analysis of 400 objects in a single 2 degree field. It also prepares a second 2 degree 400 object field while the first field is being observed. At its heart is a high precision robotic positioner that places individual fiber end magnetic buttons on one of two field plates. The button gripper is carried on orthogonal gantries powered by linear synchronous motors and contains a TV camera which precisely locates backlit buttons to allow placement in user defined locations to 10 (mu) accuracy. Fiducial points on both plates can also be observed by the camera to allow repeated checks on positioning accuracy. Field plates rotate to follow apparent sky rotation. The spectrographs both analyze light from the 200 observing fibers each and back- illuminate the 400 fibers being re-positioned during the observing run. The 2dF fiber position and spectrograph system is a large and complex instrument located at the prime focus of the Anglo Australian Telescope. The mechanical design has departed somewhat from the earlier concepts of Gray et al, but still reflects the audacity of those first ideas. The positioner is capable of positioning 400 fibers on a field plate while another 400 fibers on another plate are observing at the focus of the telescope and feeding the twin spectrographs. When first proposed it must have seemed like ingenuity unfettered by caution. Yet now it works, and works wonderfully well. 2dF is a system which functions as the result of the combined and coordinated efforts of the astronomers, the mechanical designers and tradespeople, the electronic designers, the programmers, the support staff at the telescope, and the manufacturing subcontractors. The mechanical design of the 2dF positioner and spectrographs was carried out by the mechanical engineering staff of the AAO and the majority of the manufacture was carried out in the AAO workshops.

  19. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Vračko, Marjan; Zupan, Jure; Novič, Marjana

    2003-05-01

    We present a novel 2-D graphical representation for DNA sequences which has an important advantage over the existing graphical representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the 'worm' curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.

  20. 2D materials: Graphene and others

    NASA Astrophysics Data System (ADS)

    Bansal, Suneev Anil; Singh, Amrinder Pal; Kumar, Suresh

    2016-05-01

    Present report reviews the recent advancements in new atomically thick 2D materials. Materials covered in this review are Graphene, Silicene, Germanene, Boron Nitride (BN) and Transition metal chalcogenides (TMC). These materials show extraordinary mechanical, electronic and optical properties which make them suitable candidates for future applications. Apart from unique properties, tune-ability of highly desirable properties of these materials is also an important area to be emphasized on.

  1. TACO (2D AND 3D). Taco

    SciTech Connect

    Mason, W.E.

    1983-03-01

    A set of finite element codes for the solution of nonlinear, two-dimensional (TACO2D) and three-dimensional (TACO3D) heat transfer problems. Performs linear and nonlinear analyses of both transient and steady state heat transfer problems. Has the capability to handle time or temperature dependent material properties. Materials may be either isotropic or orthotropic. A variety of time and temperature dependent boundary conditions and loadings are available including temperature, flux, convection, radiation, and internal heat generation.

  2. Tomosynthesis imaging with 2D scanning trajectories

    NASA Astrophysics Data System (ADS)

    Khare, Kedar; Claus, Bernhard E. H.; Eberhard, Jeffrey W.

    2011-03-01

    Tomosynthesis imaging in chest radiography provides volumetric information with the potential for improved diagnostic value when compared to the standard AP or LAT projections. In this paper we explore the image quality benefits of 2D scanning trajectories when coupled with advanced image reconstruction approaches. It is intuitively clear that 2D trajectories provide projection data that is more complete in terms of Radon space filling, when compared with conventional tomosynthesis using a linearly scanned source. Incorporating this additional information for obtaining improved image quality is, however, not a straightforward problem. The typical tomosynthesis reconstruction algorithms are based on direct inversion methods e.g. Filtered Backprojection (FBP) or iterative algorithms that are variants of the Algebraic Reconstruction Technique (ART). The FBP approach is fast and provides high frequency details in the image but at the same time introduces streaking artifacts degrading the image quality. The iterative methods can reduce the image artifacts by using image priors but suffer from a slow convergence rate, thereby producing images lacking high frequency details. In this paper we propose using a fast converging optimal gradient iterative scheme that has advantages of both the FBP and iterative methods in that it produces images with high frequency details while reducing the image artifacts. We show that using favorable 2D scanning trajectories along with the proposed reconstruction method has the advantage of providing improved depth information for structures such as the spine and potentially producing images with more isotropic resolution.

  3. MAGNUM-2D computer code: user's guide

    SciTech Connect

    England, R.L.; Kline, N.W.; Ekblad, K.J.; Baca, R.G.

    1985-01-01

    Information relevant to the general use of the MAGNUM-2D computer code is presented. This computer code was developed for the purpose of modeling (i.e., simulating) the thermal and hydraulic conditions in the vicinity of a waste package emplaced in a deep geologic repository. The MAGNUM-2D computer computes (1) the temperature field surrounding the waste package as a function of the heat generation rate of the nuclear waste and thermal properties of the basalt and (2) the hydraulic head distribution and associated groundwater flow fields as a function of the temperature gradients and hydraulic properties of the basalt. MAGNUM-2D is a two-dimensional numerical model for transient or steady-state analysis of coupled heat transfer and groundwater flow in a fractured porous medium. The governing equations consist of a set of coupled, quasi-linear partial differential equations that are solved using a Galerkin finite-element technique. A Newton-Raphson algorithm is embedded in the Galerkin functional to formulate the problem in terms of the incremental changes in the dependent variables. Both triangular and quadrilateral finite elements are used to represent the continuum portions of the spatial domain. Line elements may be used to represent discrete conduits. 18 refs., 4 figs., 1 tab.

  4. Engineering light outcoupling in 2D materials.

    PubMed

    Lien, Der-Hsien; Kang, Jeong Seuk; Amani, Matin; Chen, Kevin; Tosun, Mahmut; Wang, Hsin-Ping; Roy, Tania; Eggleston, Michael S; Wu, Ming C; Dubey, Madan; Lee, Si-Chen; He, Jr-Hau; Javey, Ali

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells. PMID:25602462

  5. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

    2D superconductivity is attracting a renewed interest due to the discoveries of new highly crystalline 2D superconductors in the past decade. Superconductivity at the oxide interfaces triggered by LaAlO3/SrTiO3 has become one of the promising routes for creation of new 2D superconductors. Also, the MBE grown metallic monolayers including FeSe are also offering a new platform of 2D superconductors. In the last two years, there appear a variety of monolayer/bilayer superconductors fabricated by CVD or mechanical exfoliation. Among these, electric field induced superconductivity by electric double layer transistor (EDLT) is a unique platform of 2D superconductivity, because of its ability of high density charge accumulation, and also because of the versatility in terms of materials, stemming from oxides to organics and layered chalcogenides. In this presentation, the following issues of electric filed induced superconductivity will be addressed; (1) Tunable carrier density, (2) Weak pinning, (3) Absence of inversion symmetry. (1) Since the sheet carrier density is quasi-continuously tunable from 0 to the order of 1014 cm-2, one is able to establish an electronic phase diagram of superconductivity, which will be compared with that of bulk superconductors. (2) The thickness of superconductivity can be estimated as 2 - 10 nm, dependent on materials, and is much smaller than the in-plane coherence length. Such a thin but low resistance at normal state results in extremely weak pinning beyond the dirty Boson model in the amorphous metallic films. (3) Due to the electric filed, the inversion symmetry is inherently broken in EDLT. This feature appears in the enhancement of Pauli limit of the upper critical field for the in-plane magnetic fields. In transition metal dichalcogenide with a substantial spin-orbit interactions, we were able to confirm the stabilization of Cooper pair due to its spin-valley locking. This work has been supported by Grant-in-Aid for Specially

  6. GBL-2D Version 1.0: a 2D geometry boolean library.

    SciTech Connect

    McBride, Cory L. (Elemental Technologies, American Fort, UT); Schmidt, Rodney Cannon; Yarberry, Victor R.; Meyers, Ray J.

    2006-11-01

    This report describes version 1.0 of GBL-2D, a geometric Boolean library for 2D objects. The library is written in C++ and consists of a set of classes and routines. The classes primarily represent geometric data and relationships. Classes are provided for 2D points, lines, arcs, edge uses, loops, surfaces and mask sets. The routines contain algorithms for geometric Boolean operations and utility functions. Routines are provided that incorporate the Boolean operations: Union(OR), XOR, Intersection and Difference. A variety of additional analytical geometry routines and routines for importing and exporting the data in various file formats are also provided. The GBL-2D library was originally developed as a geometric modeling engine for use with a separate software tool, called SummitView [1], that manipulates the 2D mask sets created by designers of Micro-Electro-Mechanical Systems (MEMS). However, many other practical applications for this type of software can be envisioned because the need to perform 2D Boolean operations can arise in many contexts.

  7. 2D Seismic Reflection Data across Central Illinois

    SciTech Connect

    Smith, Valerie; Leetaru, Hannes

    2014-09-30

    In a continuing collaboration with the Midwest Geologic Sequestration Consortium (MGSC) on the Evaluation of the Carbon Sequestration Potential of the Cambro-Ordovician Strata of the Illinois and Michigan Basins project, Schlumberger Carbon Services and WesternGeco acquired two-dimensional (2D) seismic data in the Illinois Basin. This work included the design, acquisition and processing of approximately 125 miles of (2D) seismic reflection surveys running west to east in the central Illinois Basin. Schlumberger Carbon Services and WesternGeco oversaw the management of the field operations (including a pre-shoot planning, mobilization, acquisition and de-mobilization of the field personnel and equipment), procurement of the necessary permits to conduct the survey, post-shoot closure, processing of the raw data, and provided expert consultation as needed in the interpretation of the delivered product. Three 2D seismic lines were acquired across central Illinois during November and December 2010 and January 2011. Traversing the Illinois Basin, this 2D seismic survey was designed to image the stratigraphy of the Cambro-Ordovician sections and also to discern the basement topography. Prior to this survey, there were no regionally extensive 2D seismic data spanning this section of the Illinois Basin. Between the NW side of Morgan County and northwestern border of Douglas County, these seismic lines ran through very rural portions of the state. Starting in Morgan County, Line 101 was the longest at 93 miles in length and ended NE of Decatur, Illinois. Line 501 ran W-E from the Illinois Basin – Decatur Project (IBDP) site to northwestern Douglas County and was 25 miles in length. Line 601 was the shortest and ran N-S past the IBDP site and connected lines 101 and 501. All three lines are correlated to well logs at the IBDP site. Originally processed in 2011, the 2D seismic profiles exhibited a degradation of signal quality below ~400 millisecond (ms) which made

  8. Interparticle Attraction in 2D Complex Plasmas

    NASA Astrophysics Data System (ADS)

    Kompaneets, Roman; Morfill, Gregor E.; Ivlev, Alexei V.

    2016-03-01

    Complex (dusty) plasmas allow experimental studies of various physical processes occurring in classical liquids and solids by directly observing individual microparticles. A major problem is that the interaction between microparticles is generally not molecularlike. In this Letter, we propose how to achieve a molecularlike interaction potential in laboratory 2D complex plasmas. We argue that this principal aim can be achieved by using relatively small microparticles and properly adjusting discharge parameters. If experimentally confirmed, this will make it possible to employ complex plasmas as a model system with an interaction potential resembling that of conventional liquids.

  9. Periodically sheared 2D Yukawa systems

    SciTech Connect

    Kovács, Anikó Zsuzsa; Hartmann, Peter; Donkó, Zoltán

    2015-10-15

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates.

  10. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

    The equilibrium states of 2D non-coarsening fluid foams, which consist of bubbles with fixed areas, correspond to local minima of the total perimeter. (1) The authors find an approximate value of the global minimum, and determine directly from an image how far a foam is from its ground state. (2) For (small) area disorder, small bubbles tend to sort inwards and large bubbles outwards. (3) Topological charges of the same sign repel while charges of opposite sign attract. (4) They discuss boundary conditions and the uniqueness of the pattern for fixed topology.

  11. A scalable 2-D parallel sparse solver

    SciTech Connect

    Kothari, S.C.; Mitra, S.

    1995-12-01

    Scalability beyond a small number of processors, typically 32 or less, is known to be a problem for existing parallel general sparse (PGS) direct solvers. This paper presents a parallel general sparse PGS direct solver for general sparse linear systems on distributed memory machines. The algorithm is based on the well-known sequential sparse algorithm Y12M. To achieve efficient parallelization, a 2-D scattered decomposition of the sparse matrix is used. The proposed algorithm is more scalable than existing parallel sparse direct solvers. Its scalability is evaluated on a 256 processor nCUBE2s machine using Boeing/Harwell benchmark matrices.

  12. 2D stepping drive for hyperspectral systems

    NASA Astrophysics Data System (ADS)

    Endrödy, Csaba; Mehner, Hannes; Grewe, Adrian; Sinzinger, Stefan; Hoffmann, Martin

    2015-07-01

    We present the design, fabrication and characterization of a compact 2D stepping microdrive for pinhole array positioning. The miniaturized solution enables a highly integrated compact hyperspectral imaging system. Based on the geometry of the pinhole array, an inch-worm drive with electrostatic actuators was designed resulting in a compact (1 cm2) positioning system featuring a step size of about 15 µm in a 170 µm displacement range. The high payload (20 mg) as required for the pinhole array and the compact system design exceed the known electrostatic inch-worm-based microdrives.

  13. The application of 2-D dual nanoscale liquid chromatography and triple quadrupole-linear ion trap system for the identification of proteins.

    PubMed

    Tschäppät, Viviane; Varesio, Emmanuel; Signor, Luca; Hopfgartner, Gérard

    2005-09-01

    2-D nanoscale LC combined with a triple quadrupole-linear ion trap mass spectrometer was applied to the analysis of a complex peptide mixture. A 2-D dual nanoscale LC-MS/MS system was compared to a conventional one. Peptides were separated with a strong cation exchange (SCX) microcolumn in the first dimension and two C18 nanocolumns were used as second dimension. MS experiments were performed using information-dependent data acquisition, where two precursor ions were selected from an enhanced MS (EMS) or an enhanced multicharged ion (EMC) as survey scan. The major benefit of EMC instead of EMS was a two-fold reduction of the data file and a 15% increase of characterized proteins. The advantage of the 2-D dual nanoscale LC-MS/MS system versus the conventional 2-D nanoscale LC-MS/MS system was reflected in the significant increase of peptides which were successfully identified within the same time frame. The first factor contributing to this increase was that the mass spectrometer was collecting twice the number of relevant MS/MS data. The second factor is the use of twice the number of SCX salt fractions in the first dimension, allowing a better sample fractionation, thereby reducing the number of peptides transferred to the second chromatographic dimension per salt fraction. PMID:16224964

  14. Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics.

    PubMed

    Lohnes, Karen; Quebbemann, Neil R; Liu, Kate; Kobzeff, Fred; Loo, Joseph A; Ogorzalek Loo, Rachel R

    2016-07-15

    The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics. PMID:26826592

  15. WFR-2D: an analytical model for PWAS-generated 2D ultrasonic guided wave propagation

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Giurgiutiu, Victor

    2014-03-01

    This paper presents WaveFormRevealer 2-D (WFR-2D), an analytical predictive tool for the simulation of 2-D ultrasonic guided wave propagation and interaction with damage. The design of structural health monitoring (SHM) systems and self-aware smart structures requires the exploration of a wide range of parameters to achieve best detection and quantification of certain types of damage. Such need for parameter exploration on sensor dimension, location, guided wave characteristics (mode type, frequency, wavelength, etc.) can be best satisfied with analytical models which are fast and efficient. The analytical model was constructed based on the exact 2-D Lamb wave solution using Bessel and Hankel functions. Damage effects were inserted in the model by considering the damage as a secondary wave source with complex-valued directivity scattering coefficients containing both amplitude and phase information from wave-damage interaction. The analytical procedure was coded with MATLAB, and a predictive simulation tool called WaveFormRevealer 2-D was developed. The wave-damage interaction coefficients (WDICs) were extracted from harmonic analysis of local finite element model (FEM) with artificial non-reflective boundaries (NRB). The WFR-2D analytical simulation results were compared and verified with full scale multiphysics finite element models and experiments with scanning laser vibrometer. First, Lamb wave propagation in a pristine aluminum plate was simulated with WFR-2D, compared with finite element results, and verified by experiments. Then, an inhomogeneity was machined into the plate to represent damage. Analytical modeling was carried out, and verified by finite element simulation and experiments. This paper finishes with conclusions and suggestions for future work.

  16. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

    Two-dimensional materials have emerged as extremely important materials with applications ranging from energy and environmental science to electronics and biology. Here we report our discovery of a universal, ultrafast, green, solvo-thermal technology for producing excellent-quality, few-layered nanosheets in liquid phase from well-known 2D materials such as such hexagonal boron nitride (h-BN), graphite, and MoS2. We start by mixing the uniform bulk-layered material with a common organic solvent that matches its surface energy to reduce the van der Waals attractive interactions between the layers; next, the solutions are heated in a commercial microwave oven to overcome the energy barrier between bulk and few-layers states. We discovered the minutes-long rapid exfoliation process is highly temperature dependent, which requires precise thermal management to obtain high-quality inks. We hypothesize a possible mechanism of this proposed solvo-thermal process; our theory confirms the basis of this novel technique for exfoliation of high-quality, layered 2D materials by using an as yet unknown role of the solvent.

  17. Photocurrent spectroscopy of 2D materials

    NASA Astrophysics Data System (ADS)

    Cobden, David

    Confocal photocurrent measurements provide a powerful means of studying many aspects of the optoelectronic and electrical properties of a 2D device or material. At a diffraction-limited point they can provide a detailed absorption spectrum, and they can probe local symmetry, ultrafast relaxation rates and processes, electron-electron interaction strengths, and transport coefficients. We illustrate this with several examples, once being the photo-Nernst effect. In gapless 2D materials, such as graphene, in a perpendicular magnetic field a photocurrent antisymmetric in the field is generated near to the free edges, with opposite sign at opposite edges. Its origin is the transverse thermoelectric current associated with the laser-induced electron temperature gradient. This effect provides an unambiguous demonstration of the Shockley-Ramo nature of long-range photocurrent generation in gapless materials. It also provides a means of investigating quasiparticle properties. For example, in the case of graphene on hBN, it can be used to probe the Lifshitz transition that occurs due to the minibands formed by the Moire superlattice. We also observe and discuss photocurrent generated in other semimetallic (WTe2) and semiconducting (WSe2) monolayers. Work supported by DoE BES and NSF EFRI grants.

  18. Multienzyme Inkjet Printed 2D Arrays.

    PubMed

    Gdor, Efrat; Shemesh, Shay; Magdassi, Shlomo; Mandler, Daniel

    2015-08-19

    The use of printing to produce 2D arrays is well established, and should be relatively facile to adapt for the purpose of printing biomaterials; however, very few studies have been published using enzyme solutions as inks. Among the printing technologies, inkjet printing is highly suitable for printing biomaterials and specifically enzymes, as it offers many advantages. Formulation of the inkjet inks is relatively simple and can be adjusted to a variety of biomaterials, while providing nonharmful environment to the enzymes. Here we demonstrate the applicability of inkjet printing for patterning multiple enzymes in a predefined array in a very straightforward, noncontact method. Specifically, various arrays of the enzymes glucose oxidase (GOx), invertase (INV) and horseradish peroxidase (HP) were printed on aminated glass surfaces, followed by immobilization using glutardialdehyde after printing. Scanning electrochemical microscopy (SECM) was used for imaging the printed patterns and to ascertain the enzyme activity. The successful formation of 2D arrays consisting of enzymes was explored as a means of developing the first surface confined enzyme based logic gates. Principally, XOR and AND gates, each consisting of two enzymes as the Boolean operators, were assembled, and their operation was studied by SECM. PMID:26214072

  19. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

  20. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

    PubMed Central

    Ghaste, Manoj; Mistrik, Robert; Shulaev, Vladimir

    2016-01-01

    Metabolomics, along with other “omics” approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data. PMID:27231903

  1. Identification of Potential Glycoprotein Biomarkers in Estrogen Receptor Positive (ER+) and Negative (ER-) Human Breast Cancer Tissues by LC-LTQ/FT-ICR Mass Spectrometry

    PubMed Central

    Semaan, Suzan M.; Wang, Xu; Marshall, Alan G.; Sang, Qing-Xiang Amy

    2012-01-01

    Breast cancer is the second most fatal cancer in American women. To increase the life expectancy of patients with breast cancer new diagnostic and prognostic biomarkers and drug targets must be identified. A change in the glycosylation on a glycoprotein often causes a change in the function of that glycoprotein; such a phenomenon is correlated with cancerous transformation. Thus, glycoproteins in human breast cancer estrogen receptor positive (ER+) tissues and those in the more advanced stage of breast cancer, estrogen receptor negative (ER-) tissues, were compared. Glycoproteins showing differences in glycosylation were examined by 2-dimensional gel electrophoresis with double staining (glyco- and total protein staining) and identified by reversed-phase nano-liquid chromatography coupled with a hybrid linear quadrupole ion trap/ Fourier transform ion cyclotron resonance mass spectrometer. Among the identified glycosylated proteins are alpha 1 acid glycoprotein, alpha-1-antitrypsin, calmodulin, and superoxide dismutase mitochondrial precursor that were further verified by Western blotting for both ER+ and ER- human breast tissues. Results show the presence of a possible glycosylation difference in alpha-1-antitrypsin, a potential tumor-derived biomarker for breast cancer progression, which was expressed highest in the ER- samples. PMID:22773931

  2. Oligomers Formed Through In-cloud Metylglyoxal Reactions: Chemical Composition, Properties, and Mechanisms Investigated by Ultra-high Resolution FT-ICR Mass Spectrometry

    EPA Science Inventory

    Secondary organic aerosol (SOA) is a substantial component of total atmospheric organic particulate matter, but little is known about the composition of SOA formed through cloud processing. We conducted aqueous phase photooxidation experiments of methylglyoxal and hydroxyl radica...

  3. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics.

    PubMed

    Ghaste, Manoj; Mistrik, Robert; Shulaev, Vladimir

    2016-01-01

    Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data. PMID:27231903

  4. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

    A ground state is defined as the positive radial solution of the multidimensional nonlinear problem \\varepsilon propto k_ bot 1 - ξ with the function f being either f(u) =a|u|p-1u or f(u) =a|u|pu+b|u|2pu. The numerical evaluation of ground states is based on the shooting method applied to an equivalent dynamical system. A combination of fourth order Runge-Kutta method and Hermite extrapolation formula is applied to solving the resulting initial value problem. The efficiency of this procedure is demonstrated in the 1D case, where the maximal difference between the exact and numerical solution is ≈ 10-11 for a discretization step 0:00025. As a major application, we evaluate numerically the critical energy constant. This constant is defined as a functional of the ground state and is used in the study of the 2D Boussinesq equations.

  5. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

    Child, R. D.; Henderson, W. P.

    1978-01-01

    A closely-coupled canard fighter with vectorable two-dimensional nozzle was designed for enhanced transonic maneuvering. The HiMAT maneuver goal of a sustained 8g turn at a free-stream Mach number of 0.9 and 30,000 feet was the primary design consideration. The aerodynamic design process was initiated with a linear theory optimization minimizing the zero percent suction drag including jet effects and refined with three-dimensional nonlinear potential flow techniques. Allowances were made for mutual interference and viscous effects. The design process to arrive at the resultant configuration is described, and the design of a powered 2-D nozzle model to be tested in the LRC 16-foot Propulsion Wind Tunnel is shown.

  6. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Jones, Justin S.; Kelly, Daniel P.; Zheng, Yun; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    An electrostatically actuated microshutter array consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutter arrays demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  7. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Kelly, Daniel P.; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    Electrostatically actuated microshutter arrays consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutters demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  8. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  9. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  10. The mouse ruby-eye 2(d) (ru2(d) /Hps5(ru2-d) ) allele inhibits eumelanin but not pheomelanin synthesis.

    PubMed

    Hirobe, Tomohisa; Ito, Shosuke; Wakamatsu, Kazumasa

    2013-09-01

    The novel mutation named ru2(d) /Hps5(ru2-d) , characterized by light-colored coats and ruby-eyes, prohibits differentiation of melanocytes by inhibiting tyrosinase (Tyr) activity, expression of Tyr, Tyr-related protein 1 (Tyrp1), Tyrp2, and Kit. However, it is not known whether the ru2(d) allele affects pheomelanin synthesis in recessive yellow (e/Mc1r(e) ) or in pheomelanic stage in agouti (A) mice. In this study, effects of the ru2(d) allele on pheomelanin synthesis were investigated by chemical analysis of melanin present in dorsal hairs of 5-week-old mice from F2 generation between C57BL/10JHir (B10)-co-isogenic ruby-eye 2(d) and B10-congenic recessive yellow or agouti. Eumelanin content was decreased in ruby-eye 2(d) and ruby-eye 2(d) agouti mice, whereas pheomelanin content in ruby-eye 2(d) recessive yellow and ruby-eye 2(d) agouti mice did not differ from the corresponding Ru2(d) /- mice, suggesting that the ru2(d) allele inhibits eumelanin but not pheomelanin synthesis. PMID:23672590

  11. A new inversion method for (T2, D) 2D NMR logging and fluid typing

    NASA Astrophysics Data System (ADS)

    Tan, Maojin; Zou, Youlong; Zhou, Cancan

    2013-02-01

    One-dimensional nuclear magnetic resonance (1D NMR) logging technology has some significant limitations in fluid typing. However, not only can two-dimensional nuclear magnetic resonance (2D NMR) provide some accurate porosity parameters, but it can also identify fluids more accurately than 1D NMR. In this paper, based on the relaxation mechanism of (T2, D) 2D NMR in a gradient magnetic field, a hybrid inversion method that combines least-squares-based QR decomposition (LSQR) and truncated singular value decomposition (TSVD) is examined in the 2D NMR inversion of various fluid models. The forward modeling and inversion tests are performed in detail with different acquisition parameters, such as magnetic field gradients (G) and echo spacing (TE) groups. The simulated results are discussed and described in detail, the influence of the above-mentioned observation parameters on the inversion accuracy is investigated and analyzed, and the observation parameters in multi-TE activation are optimized. Furthermore, the hybrid inversion can be applied to quantitatively determine the fluid saturation. To study the effects of noise level on the hybrid method and inversion results, the numerical simulation experiments are performed using different signal-to-noise-ratios (SNRs), and the effect of different SNRs on fluid typing using three fluid models are discussed and analyzed in detail.

  12. Radiofrequency Spectroscopy and Thermodynamics of Fermi Gases in the 2D to Quasi-2D Dimensional Crossover

    NASA Astrophysics Data System (ADS)

    Cheng, Chingyun; Kangara, Jayampathi; Arakelyan, Ilya; Thomas, John

    2016-05-01

    We tune the dimensionality of a strongly interacting degenerate 6 Li Fermi gas from 2D to quasi-2D, by adjusting the radial confinement of pancake-shaped clouds to control the radial chemical potential. In the 2D regime with weak radial confinement, the measured pair binding energies are in agreement with 2D-BCS mean field theory, which predicts dimer pairing energies in the many-body regime. In the qausi-2D regime obtained with increased radial confinement, the measured pairing energy deviates significantly from 2D-BCS theory. In contrast to the pairing energy, the measured radii of the cloud profiles are not fit by 2D-BCS theory in either the 2D or quasi-2D regimes, but are fit in both regimes by a beyond mean field polaron-model of the free energy. Supported by DOE, ARO, NSF, and AFOSR.

  13. Competing coexisting phases in 2D water

    PubMed Central

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  14. 2D Radiative Processes Near Cloud Edges

    NASA Technical Reports Server (NTRS)

    Varnai, T.

    2012-01-01

    Because of the importance and complexity of dynamical, microphysical, and radiative processes taking place near cloud edges, the transition zone between clouds and cloud free air has been the subject of intense research both in the ASR program and in the wider community. One challenge in this research is that the one-dimensional (1D) radiative models widely used in both remote sensing and dynamical simulations become less accurate near cloud edges: The large horizontal gradients in particle concentrations imply that accurate radiative calculations need to consider multi-dimensional radiative interactions among areas that have widely different optical properties. This study examines the way the importance of multidimensional shortwave radiative interactions changes as we approach cloud edges. For this, the study relies on radiative simulations performed for a multiyear dataset of clouds observed over the NSA, SGP, and TWP sites. This dataset is based on Microbase cloud profiles as well as wind measurements and ARM cloud classification products. The study analyzes the way the difference between 1D and 2D simulation results increases near cloud edges. It considers both monochromatic radiances and broadband radiative heating, and it also examines the influence of factors such as cloud type and height, and solar elevation. The results provide insights into the workings of radiative processes and may help better interpret radiance measurements and better estimate the radiative impacts of this critical region.

  15. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse. PMID:26988702

  16. Phase Engineering of 2D Tin Sulfides.

    PubMed

    Mutlu, Zafer; Wu, Ryan J; Wickramaratne, Darshana; Shahrezaei, Sina; Liu, Chueh; Temiz, Selcuk; Patalano, Andrew; Ozkan, Mihrimah; Lake, Roger K; Mkhoyan, K A; Ozkan, Cengiz S

    2016-06-01

    Tin sulfides can exist in a variety of phases and polytypes due to the different oxidation states of Sn. A subset of these phases and polytypes take the form of layered 2D structures that give rise to a wide host of electronic and optical properties. Hence, achieving control over the phase, polytype, and thickness of tin sulfides is necessary to utilize this wide range of properties exhibited by the compound. This study reports on phase-selective growth of both hexagonal tin (IV) sulfide SnS2 and orthorhombic tin (II) sulfide SnS crystals with diameters of over tens of microns on SiO2 substrates through atmospheric pressure vapor-phase method in a conventional horizontal quartz tube furnace with SnO2 and S powders as the source materials. Detailed characterization of each phase of tin sulfide crystals is performed using various microscopy and spectroscopy methods, and the results are corroborated by ab initio density functional theory calculations. PMID:27099950

  17. Ion Transport in 2-D Graphene Nanochannels

    NASA Astrophysics Data System (ADS)

    Xie, Quan; Foo, Elbert; Duan, Chuanhua

    2015-11-01

    Graphene membranes have recently attracted wide attention due to its great potential in water desalination and selective molecular sieving. Further developments of these membranes, including enhancing their mass transport rate and/or molecular selectivity, rely on the understanding of fundamental transport mechanisms through graphene membranes, which has not been studied experimentally before due to fabrication and measurement difficulties. Herein we report the fabrication of the basic constituent of graphene membranes, i.e. 2-D single graphene nanochannels (GNCs) and the study of ion transport in these channels. A modified bonding technique was developed to form GNCs with well-defined geometry and uniform channel height. Ion transport in such GNCs was studied using DC conductance measurement. Our preliminary results showed that the ion transport in GNCs is still governed by surface charge at low concentrations (10-6M to 10-4M). However, GNCs exhibits much higher ionic conductances than silica nanochannels with the same geometries in the surface-charge-governed regime. This conductance enhancement can be attributed to the pre-accumulation of charges on graphene surfaces. The work is supported by the Faculty Startup Fund (Boston University, USA).

  18. Parallel map analysis on 2-D grids

    SciTech Connect

    Berry, M.; Comiskey, J.; Minser, K.

    1993-12-31

    In landscape ecology, computer modeling is used to assess habitat fragmentation and its ecological iMPLications. Specifically, maps (2-D grids) of habitat clusters must be analyzed to determine number, sizes and geometry of clusters. Models prior to this study relied upon sequential Fortran-77 programs which limited the sizes of maps and densities of clusters which could be analyzed. In this paper, we present more efficient computer models which can exploit recursion or parallelism. Significant improvements over the original Fortran-77 programs have been achieved using both recursive and nonrecursive C implementations on a variety of workstations such as the Sun Sparc 2, IBM RS/6000-350, and HP 9000-750. Parallel implementations on a 4096-processor MasPar MP-1 and a 32-processor CM-5 are also studied. Preliminary experiments suggest that speed improvements for the parallel model on the MasPar MP-1 (written in MPL) and on the CM-5 (written in C using CMMD) can be as much as 39 and 34 times faster, respectively, than the most efficient sequential C program on a Sun Sparc 2 for a 512 map. An important goal in this research effort is to produce a scalable map analysis algorithm for the identification and characterization of clusters for relatively large maps on massively-parallel computers.

  19. 2D Turbulence with Complicated Boundaries

    NASA Astrophysics Data System (ADS)

    Roullet, G.; McWilliams, J. C.

    2014-12-01

    We examine the consequences of lateral viscous boundary layers on the 2D turbulence that arises in domains with complicated boundaries (headlands, bays etc). The study is carried out numerically with LES. The numerics are carefully designed to ensure all global conservation laws, proper boundary conditions and a minimal range of dissipation scales. The turbulence dramatically differs from the classical bi-periodic case. Boundary layer separations lead to creation of many small vortices and act as a continuing energy source exciting the inverse cascade of energy throughout the domain. The detachments are very intermittent in time. In free decay, the final state depends on the effective numerical resolution: laminar with a single dominant vortex for low Re and turbulent with many vortices for large enough Re. After very long time, the turbulent end-state exhibits a striking tendency for the emergence of shielded vortices which then interact almost elastically. In the forced case, the boundary layers allow the turbulence to reach a statistical steady state without any artificial hypo-viscosity or other large-scale dissipation. Implications are discussed for the oceanic mesoscale and submesoscale turbulence.

  20. Competing coexisting phases in 2D water

    NASA Astrophysics Data System (ADS)

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-05-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules.

  1. Competing coexisting phases in 2D water.

    PubMed

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  2. 2-D wavelet with position controlled resolution

    NASA Astrophysics Data System (ADS)

    Walczak, Andrzej; Puzio, Leszek

    2005-09-01

    Wavelet transformation localizes all irregularities in the scene. It is most effective in the case when intensities in the scene have no sharp details. It is the case often present in a medical imaging. To identify the shape one has to extract it from the scene as typical irregularity. When the scene does not contain sharp changes then common differential filters are not efficient tool for a shape extraction. The new 2-D wavelet for such task has been proposed. Described wavelet transform is axially symmetric and has varied scale in dependence on the distance from the centre of the wavelet symmetry. The analytical form of the wavelet has been presented as well as its application for details extraction in the scene. Most important feature of the wavelet transform is that it gives a multi-scale transformation, and if zoom is on the wavelet selectivity varies proportionally to the zoom step. As a result, the extracted shape does not change during zoom operation. What is more the wavelet selectivity can be fit to the local intensity gradient properly to obtain best extraction of the irregularities.

  3. Real-time 2D separation by LC × differential ion mobility hyphenated to mass spectrometry.

    PubMed

    Varesio, Emmanuel; Le Blanc, J C Yves; Hopfgartner, Gérard

    2012-03-01

    The liquid chromatography-mass spectrometry (LC-MS) analysis of complex samples such as biological fluid extracts is widespread when searching for new biomarkers as in metabolomics. The success of this hyphenation resides in the orthogonality of both separation techniques. However, there are frequent cases where compounds are co-eluting and the resolving power of mass spectrometry (MS) is not sufficient (e.g., isobaric compounds and interfering isotopic clusters). Different strategies are discussed to solve these cases and a mixture of eight compounds (i.e., bromazepam, chlorprothixene, clonapzepam, fendiline, flusilazol, oxfendazole, oxycodone, and pamaquine) with identical nominal mass (i.e., m/z 316) is taken to illustrate them. Among the different approaches, high-resolution mass spectrometry or liquid chromatography (i.e., UHPLC) can easily separate these compounds. Another technique, mostly used with low resolving power MS analyzers, is differential ion mobility spectrometry (DMS), where analytes are gas-phase separated according to their size-to-charge ratio. Detailed investigations of the addition of different polar modifiers (i.e., methanol, ethanol, and isopropanol) into the transport gas (nitrogen) to enhance the peak capacity of the technique were carried out. Finally, a complex urine sample fortified with 36 compounds of various chemical properties was analyzed by real-time 2D separation LC×DMS-MS(/MS). The addition of this orthogonal gas-phase separation technique in the LC-MS(/MS) hyphenation greatly improved data quality by resolving composite MS/MS spectra, which is mandatory in metabolomics when performing database generation and search. PMID:22006241

  4. 2-D Animation's Not Just for Mickey Mouse.

    ERIC Educational Resources Information Center

    Weinman, Lynda

    1995-01-01

    Discusses characteristics of two-dimensional (2-D) animation; highlights include character animation, painting issues, and motion graphics. Sidebars present Silicon Graphics animations tools and 2-D animation programs for the desktop computer. (DGM)

  5. Quantitative Analysis of Long Chain Fatty Acids Present in a Type I Kerogen Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: Compared with BF3/MeOH Methylation/GC-FID

    NASA Astrophysics Data System (ADS)

    Kamga, Albert W.; Behar, Fancoise; Hatcher, Patrick G.

    2014-05-01

    Long chain fatty acids (LCFAs) are present in various natural samples and are easily detectable using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) in negative ion mode. The capability of the ESI-FT-ICR-MS for quantifying LCFAs was evaluated by performing a standard addition followed by an internal standard methodology to several kerogen extracts using n-C20 fatty acid as standard. As the concentration of the standard increased, the magnitude of its peak ( m/z 311.29525) increased linearly but with two separate slopes, leaving the entire mass spectra relatively unchanged, which shows evidence of reproducibility. Response factors of other LCFAs are obtained using a standard addition approach. We employed five LCFA standards ( n-C15, n-C19, n-C24, n-C26, and n-C30) with different carbon numbers. This allowed us to determine the response factor of all fatty acids (with carbon number between 15 and 30) by plotting the slope of each standard versus its carbon number. With the observed response factors and use of the internal standard, the concentrations of LCFAs in four kerogen extracts were measured by ESI-FT-ICR-MS and compared with those from GC-FID. The carbon number distribution obtained by ESI-FT-ICR-MS matched well the GC-FID distribution (5%-50%) with the exception of C16 and C18, considering that ESI-FT-ICR-MS does not differentiate between normal and branched LCFAs, whereas GC-FID does. This allows one to quantitatively compare samples with a relatively similar matrix for specific compounds such as LCFAs with no need of time-consuming derivatization procedures. Moreover, the calibration can be extended to higher carbon numbers with ESI-FT-ICR-MS, beyond the capabilities of GC/MS.

  6. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  7. On 2D graphical representation of DNA sequence of nondegeneracy

    NASA Astrophysics Data System (ADS)

    Zhang, Yusen; Liao, Bo; Ding, Kequan

    2005-08-01

    Some two-dimensional (2D) graphical representations of DNA sequences have been given by Gates, Nandy, Leong and Mogenthaler, Randić, and Liao et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a nondegeneracy 2D graphical representation of DNA sequence, which is different from Randić's novel 2D representation and Liao's 2D representation. We also present the nondegeneracy forms corresponding to the representations of Gates, Nandy, Leong and Mogenthaler.

  8. Generates 2D Input for DYNA NIKE & TOPAZ

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  9. 2d PDE Linear Symmetric Matrix Solver

    1983-10-01

    ICCG2 (Incomplete Cholesky factorized Conjugate Gradient algorithm for 2d symmetric problems) was developed to solve a linear symmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as resistive MHD, spatial diffusive transport, and phase space transport (Fokker-Planck equation) problems. These problems share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized withmore » finite-difference or finite-element methods,the resulting matrix system is frequently of block-tridiagonal form. To use ICCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. The incomplete Cholesky conjugate gradient algorithm is used to solve the linear symmetric matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For matrices lacking symmetry, ILUCG2 should be used. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  10. 2d PDE Linear Asymmetric Matrix Solver

    1983-10-01

    ILUCG2 (Incomplete LU factorized Conjugate Gradient algorithm for 2d problems) was developed to solve a linear asymmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as plasma diffusion, equilibria, and phase space transport (Fokker-Planck equation) problems. These equations share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized with finite-difference or finite-elementmore » methods, the resulting matrix system is frequently of block-tridiagonal form. To use ILUCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. A generalization of the incomplete Cholesky conjugate gradient algorithm is used to solve the matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For problems having a symmetric matrix ICCG2 should be used since it runs up to four times faster and uses approximately 30% less storage. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source, containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  11. Ultrasonic 2D matrix PVDF transducer

    NASA Astrophysics Data System (ADS)

    Ptchelintsev, A.; Maev, R. Gr.

    2000-05-01

    During the past decade a substantial amount of work has been done in the area of ultrasonic imaging technology using 2D arrays. The main problems arising for the two-dimensional matrix transducers at megahertz frequencies are small size and huge count of the elements, high electrical impedance, low sensitivity, bad SNR and slower data acquisition rate. The major technological difficulty remains the high density of the interconnect. To solve these problems numerous approaches have been suggested. In the present work, a 24×24 elements (24 transmit+24 receive) matrix and a switching board were developed. The transducer consists of two 52 μm PVDF layers each representing a linear array of 24 elements placed one on the top of the other. Electrodes in these two layers are perpendicular and form the grid of 0.5×0.5 mm pitch. The layers are bonded together with the ground electrode being monolithic and located between the layers. The matrix is backed from the rear surface with an epoxy composition. During the emission, a linear element from the emitting layer generates a longitudinal wave pulse propagating inside the test object. Reflected pulses are picked-up by the receiving layer. During one transmit-receive cycle one transmit element and one receive element are selected by corresponding multiplexers. These crossed elements emulate a small element formed by their intersection. The present design presents the following advantages: minimizes number of active channels and density of the interconnect; reduces the electrical impedance of the element improving electrical matching; enables the transmit-receive mode; due to the efficient backing provides bandwidth and good time resolution; and, significantly reduces the electronics complexity. The matrix can not be used for the beam steering and focusing. Owing to this impossibility of focusing, the penetration depth is limited as well by the diffraction phenomena.

  12. A Planar Quantum Transistor Based on 2D-2D Tunneling in Double Quantum Well Heterostructures

    SciTech Connect

    Baca, W.E.; Blount, M.A.; Hafich, M.J.; Lyo, S.K.; Moon, J.S.; Reno, J.L.; Simmons, J.A.; Wendt, J.R.

    1998-12-14

    We report on our work on the double electron layer tunneling transistor (DELTT), based on the gate-control of two-dimensional -- two-dimensional (2D-2D) tunneling in a double quantum well heterostructure. While previous quantum transistors have typically required tiny laterally-defined features, by contrast the DELTT is entirely planar and can be reliably fabricated in large numbers. We use a novel epoxy-bond-and-stop-etch (EBASE) flip-chip process, whereby submicron gating on opposite sides of semiconductor epitaxial layers as thin as 0.24 microns can be achieved. Because both electron layers in the DELTT are 2D, the resonant tunneling features are unusually sharp, and can be easily modulated with one or more surface gates. We demonstrate DELTTs with peak-to-valley ratios in the source-drain I-V curve of order 20:1 below 1 K. Both the height and position of the resonant current peak can be controlled by gate voltage over a wide range. DELTTs with larger subband energy offsets ({approximately} 21 meV) exhibit characteristics that are nearly as good at 77 K, in good agreement with our theoretical calculations. Using these devices, we also demonstrate bistable memories operating at 77 K. Finally, we briefly discuss the prospects for room temperature operation, increases in gain, and high-speed.

  13. Correlated Electron Phenomena in 2D Materials

    NASA Astrophysics Data System (ADS)

    Lambert, Joseph G.

    In this thesis, I present experimental results on coherent electron phenomena in layered two-dimensional materials: single layer graphene and van der Waals coupled 2D TiSe2. Graphene is a two-dimensional single-atom thick sheet of carbon atoms first derived from bulk graphite by the mechanical exfoliation technique in 2004. Low-energy charge carriers in graphene behave like massless Dirac fermions, and their density can be easily tuned between electron-rich and hole-rich quasiparticles with electrostatic gating techniques. The sharp interfaces between regions of different carrier densities form barriers with selective transmission, making them behave as partially reflecting mirrors. When two of these interfaces are set at a separation distance within the phase coherence length of the carriers, they form an electronic version of a Fabry-Perot cavity. I present measurements and analysis of multiple Fabry-Perot modes in graphene with parallel electrodes spaced a few hundred nanometers apart. Transition metal dichalcogenide (TMD) TiSe2 is part of the family of materials that coined the term "materials beyond graphene". It contains van der Waals coupled trilayer stacks of Se-Ti-Se. Many TMD materials exhibit a host of interesting correlated electronic phases. In particular, TiSe2 exhibits chiral charge density waves (CDW) below TCDW ˜ 200 K. Upon doping with copper, the CDW state gets suppressed with Cu concentration, and CuxTiSe2 becomes superconducting with critical temperature of T c = 4.15 K. There is still much debate over the mechanisms governing the coexistence of the two correlated electronic phases---CDW and superconductivity. I will present some of the first conductance spectroscopy measurements of proximity coupled superconductor-CDW systems. Measurements reveal a proximity-induced critical current at the Nb-TiSe2 interfaces, suggesting pair correlations in the pure TiSe2. The results indicate that superconducting order is present concurrently with CDW in

  14. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  15. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  16. Development of a 2D precision cryogenic chopper for METIS

    NASA Astrophysics Data System (ADS)

    Paalvast, Sander L.; Janssen, Huub; Teuwen, Maurice; Huisman, Robert; Brandl, Bernhard; Molster, Frank; Venema, Lars

    2012-09-01

    The Mid-infrared E-ELT Imager and Spectrograph, or METIS, is foreseen as the third instrument for the European Extremely Large Telescope (E-ELT). A key part of METIS is the Cold Chopper (MCC) which switches the optical beam between the target and a nearby reference sky during observation for elimination of the fluctuating IR background signal in post-processing. This paper discusses the development of the MCC demonstrator. The chopper mirror (Ø64mm) has to tip/tilt in 2D with a combined angle of up to 13.6mrad with 1.7μrad stability and repeatability within 5ms (95% duty cycle at 5Hz) at 80K. As these requirements cannot be met in the presence of friction or backlash, the mirror is guided by a monolithically integrated flexure mechanism. The angular position is actuated by three linear actuators and measured by three linear position sensors, resulting in a fast tip, tilt, and focus mirror. Using the third actuator to introduce symmetry, homogeneity in forces and heat flux is obtained. Both the actuators and the sensors are key components. A voice coil actuator had to be custom designed, to achieve the required acceleration force within the specified 1W heat load. The requirements for the displacement measurement can be met with a commercially available, fiber interferometry system. For integration of this system, stray light elimination is a critical design aspect and retro-reflectors have been used to reflect sufficient power into the fiber at large tip/tilt angles.

  17. Steroid Constituents from the Soft Coral Sinularia nanolobata.

    PubMed

    Ngoc, Ninh Thi; Huong, Pham Thi Mai; Thanh, Nguyen Van; Cuong, Nguyen Xuan; Nam, Nguyen Hoai; Thung, Do Cong; Kiem, Phan Van; Minh, Chau Van

    2016-09-01

    Six steroids (1-6), including the two new compounds 3β,4α-dihydroxyergosta-5,24(28)-diene (1) and 24(S),28-epoxyergost-5-ene-3β,4α-diol (2), were isolated from the methanol extract of the Vietnamese soft coral Sinularia nanolobata. Their structures were elucidated by spectroscopic methods including one and two dimensional (1D- and 2D)-NMR, Fourier transform ion cyclotron resonance (FT-ICR)-MS, and circular dichroism (CD). Compound 2 exhibited moderate cytotoxicity against the acute leukemia (HL-60) cell line with IC50 value of 33.53±4.25 µM and weak effect on the hepatoma cancer (HepG2) and colon adenocarcinoma (SW480) cell lines with IC50 values of 64.35±7.00 and 71.02±4.00 µM, respectively. PMID:27321426

  18. New pyrano-pyrone from Goniothalamus tamirensis enhances the proliferation and differentiation of osteoblastic MC3T3-E1 cells.

    PubMed

    Tai, Bui Huu; Huyen, Vu Thi; Huong, Tran Thu; Nhiem, Nguyen Xuan; Choi, Eun-Mi; Kim, Jeong Ah; Long, Pham Quoc; Cuong, Nguyen Manh; Kim, Young Ho

    2010-04-01

    The new pyrano-pyrone, (+)-8-epi-9-deoxygoniopypyrone (1) and (+)-9-deoxygoniopypyrone (2) were isolated from a chloroform extract of Goniothalamus tamirensis leaves. Their absolute stereostructures were discussed and confirmed by using infrared (IR), Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), one (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) spectra, Mosher's method, and comparison with the known compounds leiocapin A (3), deoxygoniopypyrone A (4), and (-)-8-epi-9-deoxygoniopypyrone (5). At concentrations of 2.67 microM, compounds 1 and 2 significantly increased the growth of osteoblastic MC3T3-E1 cells and caused a significant elevation of collagen content, alkaline phosphatase activity, and nodule mineralization in the cells (p<0.05). Our data suggest that the enhancement of osteoblast function by 1 and 2 may result in the prevention of osteoporosis. PMID:20410636

  19. Differential CYP 2D6 Metabolism Alters Primaquine Pharmacokinetics

    PubMed Central

    Potter, Brittney M. J.; Xie, Lisa H.; Vuong, Chau; Zhang, Jing; Zhang, Ping; Duan, Dehui; Luong, Thu-Lan T.; Bandara Herath, H. M. T.; Dhammika Nanayakkara, N. P.; Tekwani, Babu L.; Walker, Larry A.; Nolan, Christina K.; Sciotti, Richard J.; Zottig, Victor E.; Smith, Philip L.; Paris, Robert M.; Read, Lisa T.; Li, Qigui; Pybus, Brandon S.; Sousa, Jason C.; Reichard, Gregory A.

    2015-01-01

    Primaquine (PQ) metabolism by the cytochrome P450 (CYP) 2D family of enzymes is required for antimalarial activity in both humans (2D6) and mice (2D). Human CYP 2D6 is highly polymorphic, and decreased CYP 2D6 enzyme activity has been linked to decreased PQ antimalarial activity. Despite the importance of CYP 2D metabolism in PQ efficacy, the exact role that these enzymes play in PQ metabolism and pharmacokinetics has not been extensively studied in vivo. In this study, a series of PQ pharmacokinetic experiments were conducted in mice with differential CYP 2D metabolism characteristics, including wild-type (WT), CYP 2D knockout (KO), and humanized CYP 2D6 (KO/knock-in [KO/KI]) mice. Plasma and liver pharmacokinetic profiles from a single PQ dose (20 mg/kg of body weight) differed significantly among the strains for PQ and carboxy-PQ. Additionally, due to the suspected role of phenolic metabolites in PQ efficacy, these were probed using reference standards. Levels of phenolic metabolites were highest in mice capable of metabolizing CYP 2D6 substrates (WT and KO/KI 2D6 mice). PQ phenolic metabolites were present in different quantities in the two strains, illustrating species-specific differences in PQ metabolism between the human and mouse enzymes. Taking the data together, this report furthers understanding of PQ pharmacokinetics in the context of differential CYP 2D metabolism and has important implications for PQ administration in humans with different levels of CYP 2D6 enzyme activity. PMID:25645856

  20. 2D to 3D to 2D Dimensionality Crossovers in Thin BSCCO Films

    NASA Astrophysics Data System (ADS)

    Williams, Gary A.

    2003-03-01

    With increasing temperature the superfluid fraction in very thin BSCCO films undergoes a series of dimensionality crossovers. At low temperatures the strong anisotropy causes the thermal excitations to be 2D pancake-antipancake pairs in uncoupled layers. At higher temperatures where the c-axis correlation length becomes larger than a layer there is a crossover to 3D vortex loops. These are initially elliptical, but as the 3D Tc is approached they become more circular as the anisotropy scales away, as modeled by Shenoy and Chattopadhyay [1]. Close to Tc when the correlation length becomes comparable to the film thickness there is a further crossover to a 2D Kosterlitz-Thouless transition, with a drop of the superfluid fraction to zero at T_KT which can be of the order of 1 K below T_c. Good agreement with this model is found for experiments on thin BSCCO 2212 films [2]. 1. S. R. Shenoy and B. Chattopadhyay, Phys. Rev. B 51, 9129 (1995). 2. K. Osborn et al., cond-mat/0204417.

  1. Mechanical characterization of 2D, 2D stitched, and 3D braided/RTM materials

    NASA Technical Reports Server (NTRS)

    Deaton, Jerry W.; Kullerd, Susan M.; Portanova, Marc A.

    1993-01-01

    Braided composite materials have potential for application in aircraft structures. Fuselage frames, floor beams, wing spars, and stiffeners are examples where braided composites could find application if cost effective processing and damage tolerance requirements are met. Another important consideration for braided composites relates to their mechanical properties and how they compare to the properties of composites produced by other textile composite processes being proposed for these applications. Unfortunately, mechanical property data for braided composites do not appear extensively in the literature. Data are presented in this paper on the mechanical characterization of 2D triaxial braid, 2D triaxial braid plus stitching, and 3D (through-the-thickness) braid composite materials. The braided preforms all had the same graphite tow size and the same nominal braid architectures, (+/- 30 deg/0 deg), and were resin transfer molded (RTM) using the same mold for each of two different resin systems. Static data are presented for notched and unnotched tension, notched and unnotched compression, and compression after impact strengths at room temperature. In addition, some static results, after environmental conditioning, are included. Baseline tension and compression fatigue results are also presented, but only for the 3D braided composite material with one of the resin systems.

  2. Polymer architectures via mass spectrometry and hyphenated techniques: A review.

    PubMed

    Crotty, Sarah; Gerişlioğlu, Selim; Endres, Kevin J; Wesdemiotis, Chrys; Schubert, Ulrich S

    2016-08-17

    This review covers the application of mass spectrometry (MS) and its hyphenated techniques to synthetic polymers of varying architectural complexities. The synthetic polymers are discussed as according to their architectural complexity from linear homopolymers and copolymers to stars, dendrimers, cyclic copolymers and other polymers. MS and tandem MS (MS/MS) has been extensively used for the analysis of synthetic polymers. However, the increase in structural or architectural complexity can result in analytical challenges that MS or MS/MS cannot overcome alone. Hyphenation to MS with different chromatographic techniques (2D × LC, SEC, HPLC etc.), utilization of other ionization methods (APCI, DESI etc.) and various mass analyzers (FT-ICR, quadrupole, time-of-flight, ion trap etc.) are applied to overcome these challenges and achieve more detailed structural characterizations of complex polymeric systems. In addition, computational methods (software: MassChrom2D, COCONUT, 2D maps etc.) have also reached polymer science to facilitate and accelerate data interpretation. Developments in technology and the comprehension of different polymer classes with diverse architectures have significantly improved, which allow for smart polymer designs to be examined and advanced. We present specific examples covering diverse analytical aspects as well as forthcoming prospects in polymer science. PMID:27286765

  3. Development and validation of sensitive LC-MS/MS assays for quantification of HP-β-CD in human plasma and CSF

    PubMed Central

    Jiang, Hui; Sidhu, Rohini; Fujiwara, Hideji; De Meulder, Marc; de Vries, Ronald; Gong, Yong; Kao, Mark; Porter, Forbes D.; Yanjanin, Nicole M.; Carillo-Carasco, Nuria; Xu, Xin; Ottinger, Elizabeth; Woolery, Myra; Ory, Daniel S.; Jiang, Xuntian

    2014-01-01

    2-Hydroxypropyl-β-cyclodextrin (HP-β-CD), a widely used excipient for drug formulation, has emerged as an investigational new drug for the treatment of Niemann-Pick type C1 (NPC1) disease, a neurodegenerative cholesterol storage disorder. Development of a sensitive quantitative LC-MS/MS assay to monitor the pharmacokinetics (PKs) of HP-β-CD required for clinical trials has been challenging owing to the dispersity of the HP-β-CD. To support a phase 1 clinical trial for ICV delivery of HP-β-CD in NPC1 patients, novel methods for quantification of HP-β-CD in human plasma and cerebrospinal fluid (CSF) using LC-MS/MS were developed and validated: a 2D-LC-in-source fragmentation-MS/MS (2D-LC-IF-MS/MS) assay and a reversed phase ultra performance LC-MS/MS (RP-UPLC-MS/MS) assay. In both assays, protein precipitation and “dilute and shoot” procedures were used to process plasma and CSF, respectively. The assays were fully validated and in close agreement, and allowed determination of PK parameters for HP-β-CD. The LC-MS/MS methods are ∼100-fold more sensitive than the current HPLC assay, and were successfully employed to analyze HP-β-CD in human plasma and CSF samples to support the phase 1 clinical trial of HP-β-CD in NPC1 patients. PMID:24868096

  4. Characterization of zebrafish cardiac proteome using online pH gradient SCX-RP HPLC-MS/MS platform.

    PubMed

    Zhang, Jiang; Lanham, Kevin A; Heideman, Warren; Peterson, Richard E; Li, Lingjun

    2013-01-01

    Two-dimensional HPLC coupled with tandem MS (MS/MS) has become a mainstream technique in the shotgun proteomics for large-scale identification of proteins from biological samples. This powerful technology provides speed, sensitivity, and dynamic range which are essential to probe complex peptide mixtures from proteomic samples. Herein we present a pH gradient SCX-RP 2D HPLC-MS/MS method designed to improve the peptide resolution and protein identification from complex proteomic samples. The comparison between the pH gradient SCX-RP 2D HPLC method and traditional salt gradient SCX-RP method was presented. A two-step sample prefractionation method utilizing microwave-assisted tryptic digestion to improve the identification of insoluble proteins was also introduced. This novel 2D HPLC-MS/MS method was applied to the heart proteomic sample of the zebrafish, Danio rerio, to provide comprehensive cardiac proteomic profiling of this important model organism for cardiovascular and environmental toxicology studies. PMID:23606253

  5. Depth-dependent variations of sedimentary dissolved organic matter composition in a eutrophic lake: Implications for lake restoration.

    PubMed

    Xu, Huacheng; Guo, Laodong; Jiang, Helong

    2016-02-01

    Dissolved organic matter (DOM) plays a significant role in regulating nutrients and carbon cycling and the reactivity of trace metals and other contaminants in the environment. However, the environmental/ecological role of sedimentary DOM is highly dependent on organic composition. In this study, fluorescence excitation emission matrix-parallel factor (EEM-PARAFAC) analysis, two dimensional correlation spectroscopy (2D-COS), and ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) were applied to investigate the depth-dependent variations of sediment-leached DOM components in a eutrophic lake. Results of EEM-PARAFAC and 2D-COS showed that fluorescent humic-like component was preferentially degraded microbially over fulvic-like component at greater sediment depths, and the relative abundance of non-fluorescent components decreased with increasing depth, leaving the removal rate of carbohydrates > lignins. The predominant sedimentary DOM components derived from FT-ICR-MS were lipids (>50%), followed by lignins (∼15%) and proteins (∼15%). The relative abundance of carbohydrates, lignins, and condensed aromatics decreased significantly at greater depths, whereas that of lipids increased in general with depth. There existed a significant negative correlation between the short-range ordered (SRO) minerals and the total dissolved organic carbon concentration or the relative contents of lignins and condensed aromatics (p < 0.05), suggesting that SRO mineral sorption plays a significant role in controlling the composition heterogeneity and releasing of DOM in lake sediments. Higher metal binding potential observed for DOM at deeper sediment depth (e.g., 25-30 cm) supported the ecological safety of sediment dredging technique from the viewpoint of heavy metal de-toxicity. PMID:26706464

  6. Differential Cytochrome P450 2D Metabolism Alters Tafenoquine Pharmacokinetics

    PubMed Central

    Vuong, Chau; Xie, Lisa H.; Potter, Brittney M. J.; Zhang, Jing; Zhang, Ping; Duan, Dehui; Nolan, Christina K.; Sciotti, Richard J.; Zottig, Victor E.; Nanayakkara, N. P. Dhammika; Tekwani, Babu L.; Walker, Larry A.; Smith, Philip L.; Paris, Robert M.; Read, Lisa T.; Li, Qigui; Pybus, Brandon S.; Sousa, Jason C.; Reichard, Gregory A.; Smith, Bryan

    2015-01-01

    Cytochrome P450 (CYP) 2D metabolism is required for the liver-stage antimalarial efficacy of the 8-aminoquinoline molecule tafenoquine in mice. This could be problematic for Plasmodium vivax radical cure, as the human CYP 2D ortholog (2D6) is highly polymorphic. Diminished CYP 2D6 enzyme activity, as in the poor-metabolizer phenotype, could compromise radical curative efficacy in humans. Despite the importance of CYP 2D metabolism for tafenoquine liver-stage efficacy, the exact role that CYP 2D metabolism plays in the metabolism and pharmacokinetics of tafenoquine and other 8-aminoquinoline molecules has not been extensively studied. In this study, a series of tafenoquine pharmacokinetic experiments were conducted in mice with different CYP 2D metabolism statuses, including wild-type (WT) (reflecting extensive metabolizers for CYP 2D6 substrates) and CYPmouse 2D knockout (KO) (reflecting poor metabolizers for CYP 2D6 substrates) mice. Plasma and liver pharmacokinetic profiles from a single 20-mg/kg of body weight dose of tafenoquine differed between the strains; however, the differences were less striking than previous results obtained for primaquine in the same model. Additionally, the presence of a 5,6-ortho-quinone tafenoquine metabolite was examined in both mouse strains. The 5,6-ortho-quinone species of tafenoquine was observed, and concentrations of the metabolite were highest in the WT extensive-metabolizer phenotype. Altogether, this study indicates that CYP 2D metabolism in mice affects tafenoquine pharmacokinetics and could have implications for human tafenoquine pharmacokinetics in polymorphic CYP 2D6 human populations. PMID:25870069

  7. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry.

    PubMed

    Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna; Sharma, Bechan; Bhagyawant, Sameer S

    2016-01-01

    Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0-10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana. PMID:27144024

  8. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

    PubMed Central

    Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna

    2016-01-01

    Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana. PMID:27144024

  9. A Geometric Boolean Library for 2D Objects

    2006-01-05

    The 2D Boolean Library is a collection of C++ classes -- which primarily represent 2D geometric data and relationships, and routines -- which contain algorithms for 2D geometric Boolean operations and utility functions. Classes are provided for 2D points, lines, arcs, edgeuses, loops, surfaces and mask sets. Routines are provided that incorporate the Boolean operations Union(OR), XOR, Intersection and Difference. Various analytical geometry routines and routines for importing and exporting the data in various filemore » formats, are also provided in the library.« less

  10. A Geometric Boolean Library for 2D Objects

    SciTech Connect

    McBride, Corey L.; Yarberry, Victor; Jorgensen, Craig

    2006-01-05

    The 2D Boolean Library is a collection of C++ classes -- which primarily represent 2D geometric data and relationships, and routines -- which contain algorithms for 2D geometric Boolean operations and utility functions. Classes are provided for 2D points, lines, arcs, edgeuses, loops, surfaces and mask sets. Routines are provided that incorporate the Boolean operations Union(OR), XOR, Intersection and Difference. Various analytical geometry routines and routines for importing and exporting the data in various file formats, are also provided in the library.

  11. Computational and Experimental Studies On The Hydrolysis of Bryostatin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bryostatin is a marine natural product studied in over 30 clinical cancer therapy trials. Its large bryophan ring is held together by an ester bond. This study was conducted in three phases. The first phase is a compilation of experimental data obtained with TLC-MALDI-TOF-MS, FT-ICR and LC-MS techni...

  12. AnisWave2D: User's Guide to the 2d Anisotropic Finite-DifferenceCode

    SciTech Connect

    Toomey, Aoife

    2005-01-06

    This document describes a parallel finite-difference code for modeling wave propagation in 2D, fully anisotropic materials. The code utilizes a mesh refinement scheme to improve computational efficiency. Mesh refinement allows the grid spacing to be tailored to the velocity model, so that fine grid spacing can be used in low velocity zones where the seismic wavelength is short, and coarse grid spacing can be used in zones with higher material velocities. Over-sampling of the seismic wavefield in high velocity zones is therefore avoided. The code has been implemented to run in parallel over multiple processors and allows large-scale models and models with large velocity contrasts to be simulated with ease.

  13. Klassifikation von Standardebenen in der 2D-Echokardiographie mittels 2D-3D-Bildregistrierung

    NASA Astrophysics Data System (ADS)

    Bergmeir, Christoph; Subramanian, Navneeth

    Zum Zweck der Entwicklung eines Systems, das einen unerfahrenen Anwender von Ultraschall (US) zur Aufnahme relevanter anatomischer Strukturen leitet, untersuchen wir die Machbarkeit von 2D-US zu 3D-CT Registrierung. Wir verwenden US-Aufnahmen von Standardebenen des Herzens, welche zu einem 3D-CT-Modell registriert werden. Unser Algorithmus unterzieht sowohl die US-Bilder als auch den CT-Datensatz Vorverarbeitungsschritten, welche die Daten durch Segmentierung auf wesentliche Informationen in Form von Labein für Muskel und Blut reduzieren. Anschließend werden diese Label zur Registrierung mittels der Match-Cardinality-Metrik genutzt. Durch mehrmaliges Registrieren mit verschiedenen Initialisierungen ermitteln wir die im US-Bild sichtbare Standardebene. Wir evaluierten die Methode auf sieben US-Bildern von Standardebenen. Fünf davon wurden korrekt zugeordnet.

  14. Depth-selective 2D-ACAR studies on low- k dielectric thin films

    NASA Astrophysics Data System (ADS)

    Eijt, S. W. H.; van Veen, A.; Falub, C. V.; Galindo, R. Escobar; Schut, H.; Mijnarends, P. E.; de Theije, F. K.; Balkenende, A. R.

    2003-10-01

    Depth-selective 2D-ACAR investigations on ordered mesoporous silica thin films provide direct evidence that para-positronium ( p-Ps) created deep in the films can escape through a network of interconnected pores. The depth dependence of the escape fraction and of the average kinetic energy of non-thermally excited p-Ps is in quantitative agreement with Monte Carlo modeling, assuming classical collisions of p-Ps with the pore walls. The model provides insight in the shape of the angular correlation distributions and their sensitivity to, e.g., the effective wall mass Ms and pore dimensions.

  15. Functional characterization of CYP2D6 enhancer polymorphisms

    PubMed Central

    Wang, Danxin; Papp, Audrey C.; Sun, Xiaochun

    2015-01-01

    CYP2D6 metabolizes nearly 25% of clinically used drugs. Genetic polymorphisms cause large inter-individual variability in CYP2D6 enzyme activity and are currently used as biomarker to predict CYP2D6 metabolizer phenotype. Previously, we had identified a region 115 kb downstream of CYP2D6 as enhancer for CYP2D6, containing two completely linked single nucleotide polymorphisms (SNPs), rs133333 and rs5758550, associated with enhanced transcription. However, the enhancer effect on CYP2D6 expression, and the causative variant, remained to be ascertained. To characterize the CYP2D6 enhancer element, we applied chromatin conformation capture combined with the next-generation sequencing (4C assays) and chromatin immunoprecipitation with P300 antibody, in HepG2 and human primary culture hepatocytes. The results confirmed the role of the previously identified enhancer region in CYP2D6 expression, expanding the number of candidate variants to three highly linked SNPs (rs133333, rs5758550 and rs4822082). Among these, only rs5758550 demonstrated regulating enhancer activity in a reporter gene assay. Use of clustered regularly interspaced short palindromic repeats mediated genome editing in HepG2 cells targeting suspected enhancer regions decreased CYP2D6 mRNA expression by 70%, only upon deletion of the rs5758550 region. These results demonstrate robust effects of both the enhancer element and SNP rs5758550 on CYP2D6 expression, supporting consideration of rs5758550 for CYP2D6 genotyping panels to yield more accurate phenotype prediction. PMID:25381333

  16. An Incompressible 2D Didactic Model with Singularity and Explicit Solutions of the 2D Boussinesq Equations

    NASA Astrophysics Data System (ADS)

    Chae, Dongho; Constantin, Peter; Wu, Jiahong

    2014-09-01

    We give an example of a well posed, finite energy, 2D incompressible active scalar equation with the same scaling as the surface quasi-geostrophic equation and prove that it can produce finite time singularities. In spite of its simplicity, this seems to be the first such example. Further, we construct explicit solutions of the 2D Boussinesq equations whose gradients grow exponentially in time for all time. In addition, we introduce a variant of the 2D Boussinesq equations which is perhaps a more faithful companion of the 3D axisymmetric Euler equations than the usual 2D Boussinesq equations.

  17. Nested data independent MS/MS acquisition.

    PubMed

    Kaufmann, Anton; Walker, Stephan

    2016-07-01

    Data independent acquisition (DIA) attempts to provide comprehensive MS/MS data while providing a cycle time that is capable of following the elution profile of chromatographic peaks. Currently available MS technology is not yet fully capable of fulfilling these expectations. This paper suggests a new multiplex-based approach to more closely achieve this objective. Customized scans have been programmed for a Q Orbitrap instrument. Multiple nonadjacent mass range segments are sequentially collected (cut out) by the quadrupole. These combined mass ranges undergo fragmentation, and the resulting product ions are analyzed as a whole by the Orbitrap analyzer. The systematical variation of the mass range segments (nested design) permits the mathematical assignment of the observed product ions within a narrow precursor mass range. The proposed approach allows the use of mass windows that are narrower than those in conventional DIA (SWATH). A unique aspect of the proposed approach is the fact that halving the mass window width requires the addition of only a single multiplexed scan. This is different from conventional DIA, which requires the number of mass windows to be doubled in order to achieve the same objective. This paper shows that for a given cycle time, the proposed nested DIA technique produces significantly less chimeric product ion spectra than conventional DIA. However, further improvements from the programming, and most likely the hardware side, are still required in order to achieve the aim of comprehensive MS/MS. Graphical Abstract Schematic of nested design. PMID:27188447

  18. Efficient Visible Quasi-2D Perovskite Light-Emitting Diodes.

    PubMed

    Byun, Jinwoo; Cho, Himchan; Wolf, Christoph; Jang, Mi; Sadhanala, Aditya; Friend, Richard H; Yang, Hoichang; Lee, Tae-Woo

    2016-09-01

    Efficient quasi-2D-structure perovskite light-emitting diodes (4.90 cd A(-1) ) are demonstrated by mixing a 3D-structured perovskite material (methyl ammonium lead bromide) and a 2D-structured perovskite material (phenylethyl ammonium lead bromide), which can be ascribed to better film uniformity, enhanced exciton confinement, and reduced trap density. PMID:27334788

  19. Integrating Mobile Multimedia into Textbooks: 2D Barcodes

    ERIC Educational Resources Information Center

    Uluyol, Celebi; Agca, R. Kagan

    2012-01-01

    The major goal of this study was to empirically compare text-plus-mobile phone learning using an integrated 2D barcode tag in a printed text with three other conditions described in multimedia learning theory. The method examined in the study involved modifications of the instructional material such that: a 2D barcode was used near the text, the…

  20. Van der Waals stacked 2D layered materials for optoelectronics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjing; Wang, Qixing; Chen, Yu; Wang, Zhuo; Wee, Andrew T. S.

    2016-06-01

    The band gaps of many atomically thin 2D layered materials such as graphene, black phosphorus, monolayer semiconducting transition metal dichalcogenides and hBN range from 0 to 6 eV. These isolated atomic planes can be reassembled into hybrid heterostructures made layer by layer in a precisely chosen sequence. Thus, the electronic properties of 2D materials can be engineered by van der Waals stacking, and the interlayer coupling can be tuned, which opens up avenues for creating new material systems with rich functionalities and novel physical properties. Early studies suggest that van der Waals stacked 2D materials work exceptionally well, dramatically enriching the optoelectronics applications of 2D materials. Here we review recent progress in van der Waals stacked 2D materials, and discuss their potential applications in optoelectronics.

  1. Unitary quantum lattice gas representation of 2D quantum turbulence

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Vahala, George; Vahala, Linda; Soe, Min

    2011-05-01

    Quantum vortex structures and energy cascades are examined for two dimensional quantum turbulence (2D QT) using a special unitary evolution algorithm. The qubit lattice gas (QLG) algorithm, is employed to simulate the weakly-coupled Bose-Einstein condensate (BEC) governed by the Gross-Pitaevskii (GP) equation. A parameter regime is uncovered in which, as in 3D QT, there is a very short Poincare recurrence time. This short recurrence time is destroyed as the nonlinear interaction energy is increased. Energy cascades for 2D QT are considered to examine whether 2D QT exhibits the inverse cascades of 2D classical turbulence. In the parameter regime considered, the spectra analysis reveals no such dual cascades---dual cascades being a hallmark of 2D classical turbulence.

  2. CYP2D6 polymorphism in patients with eating disorders.

    PubMed

    Peñas-Lledó, E M; Dorado, P; Agüera, Z; Gratacós, M; Estivill, X; Fernández-Aranda, F; Llerena, A

    2012-04-01

    CYP2D6 polymorphism is associated with variability in drug response, endogenous metabolism (that is, serotonin), personality, neurocognition and psychopathology. The relationship between CYP2D6 genetic polymorphism and the risk of eating disorders (ED) was analyzed in 267 patients with ED and in 285 controls. A difference in the CYP2D6 active allele distribution was found between these groups. Women carrying more than two active genes (ultrarapid metabolizers) (7.5 vs 4.6%) or two (67 vs 58.9%) active genes were more frequent among patients with ED, whereas those with one (20.6 vs 30.2%) or zero active genes (4.9 vs 6.3%) were more frequent among controls (P<0.05). Although further research is needed, present findings suggest an association between CYP2D6 and ED. CYP2D6 allele distribution in patients with ED seems related to increased enzyme activity. PMID:20877302

  3. 2D materials and van der Waals heterostructures.

    PubMed

    Novoselov, K S; Mishchenko, A; Carvalho, A; Castro Neto, A H

    2016-07-29

    The physics of two-dimensional (2D) materials and heterostructures based on such crystals has been developing extremely fast. With these new materials, truly 2D physics has begun to appear (for instance, the absence of long-range order, 2D excitons, commensurate-incommensurate transition, etc.). Novel heterostructure devices--such as tunneling transistors, resonant tunneling diodes, and light-emitting diodes--are also starting to emerge. Composed from individual 2D crystals, such devices use the properties of those materials to create functionalities that are not accessible in other heterostructures. Here we review the properties of novel 2D crystals and examine how their properties are used in new heterostructure devices. PMID:27471306

  4. Primary-Progressive MS (PPMS)

    MedlinePlus

    ... MS? Types of MS Primary progressive MS (PPMS) Primary progressive MS (PPMS) Share Smaller Text Larger Text Print In this article Overview PPMS is characterized by worsening neurologic function ( ...

  5. Sensitivity of GC-EI/MS, GC-EI/MS/MS, LC-ESI/MS/MS, LC-Ag(+) CIS/MS/MS, and GC-ESI/MS/MS for analysis of anabolic steroids in doping control.

    PubMed

    Cha, Eunju; Kim, Sohee; Kim, Ho Jun; Lee, Kang Mi; Kim, Ki Hun; Kwon, Oh-Seung; Lee, Jaeick

    2015-01-01

    This study compared the sensitivity of various separation and ionization methods, including gas chromatography with an electron ionization source (GC-EI), liquid chromatography with an electrospray ionization source (LC-ESI), and liquid chromatography with a silver ion coordination ion spray source (LC-Ag(+) CIS), coupled to a mass spectrometer (MS) for steroid analysis. Chromatographic conditions, mass spectrometric transitions, and ion source parameters were optimized. The majority of steroids in GC-EI/MS/MS and LC-Ag(+) CIS/MS/MS analysis showed higher sensitivities than those obtained with other analytical methods. The limits of detection (LODs) of 65 steroids by GC-EI/MS/MS, 68 steroids by LC-Ag(+) CIS/MS/MS, 56 steroids by GC-EI/MS, 54 steroids by LC-ESI/MS/MS, and 27 steroids by GC-ESI/MS/MS were below cut-off value of 2.0 ng/mL. LODs of steroids that formed protonated ions in LC-ESI/MS/MS analysis were all lower than the cut-off value. Several steroids such as unconjugated C3-hydroxyl with C17-hydroxyl structure showed higher sensitivities in GC-EI/MS/MS analysis relative to those obtained using the LC-based methods. The steroids containing 4, 9, 11-triene structures showed relatively poor sensitivities in GC-EI/MS and GC-ESI/MS/MS analysis. The results of this study provide information that may be useful for selecting suitable analytical methods for confirmatory analysis of steroids. PMID:26489966

  6. Targeted fluorescence imaging enhanced by 2D materials: a comparison between 2D MoS2 and graphene oxide.

    PubMed

    Xie, Donghao; Ji, Ding-Kun; Zhang, Yue; Cao, Jun; Zheng, Hu; Liu, Lin; Zang, Yi; Li, Jia; Chen, Guo-Rong; James, Tony D; He, Xiao-Peng

    2016-08-01

    Here we demonstrate that 2D MoS2 can enhance the receptor-targeting and imaging ability of a fluorophore-labelled ligand. The 2D MoS2 has an enhanced working concentration range when compared with graphene oxide, resulting in the improved imaging of both cell and tissue samples. PMID:27378648

  7. CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation

    PubMed Central

    Mougou-Zerelli, Soumaya; Thomas, Sophie; Szenker, Emmanuelle; Audollent, Sophie; Elkhartoufi, Nadia; Babarit, Candice; Romano, Stéphane; Salomon, Rémi; Amiel, Jeanne; Esculpavit, Chantal; Gonzales, Marie; Escudier, Estelle; Leheup, Bruno; Loget, Philippe; Odent, Sylvie; Roume, Joëlle; Gérard, Marion; Delezoide, Anne-Lise; Khung, Suonavy; Patrier, Sophie; Cordier, Marie-Pierre; Bouvier, Raymonde; Martinovic, Jéléna; Gubler, Marie-Claire; Boddaert, Nathalie; Munnich, Arnold; Encha-Razavi, Férechté; Valente, Enza Maria; Saad, Ali; Saunier, Sophie; Vekemans, Michel; Attié-Bitach, Tania

    2009-01-01

    The Meckel syndrome (MKS) is a lethal fetal disorder characterized by diffuse renal cystic dysplasia, polydactyly, a brain malformation that is usually occipital encephalocele and/or vermian agenesis, with intrahepatic biliary duct proliferation. Joubert syndrome (JBS) is a viable neurological disorder with a characteristic “molar tooth sign” (MTS) on axial images reflecting cerebellar vermian hypoplasia/dysplasia. Both conditions are classified as ciliopathies with an autosomal recessive mode of inheritance. Allelism of MS and JBS has been reported for TMEM67/MKS3, CEP290/MKS4, and RPGRIP1L/MKS5. Recently, one homozygous splice mutation with a founder effect was reported in the CC2D2A gene in Finnish fetuses with MKS, defining the 6th locus for MKS. Shortly thereafter, CC2D2A mutations were reported in JBS also. The analysis of the CC2D2A gene in our series of MKS fetuses, identified 14 novel truncating mutations in 11 cases. These results confirm the involvement of CC2D2A in MKS and reveal a major contribution of CC2D2A to the disease. We also identified three missense CC2D2A mutations in two JBS cases. Therefore and in accordance with the data reported regarding RPGRIP1L, our results indicate phenotype-genotype correlations, as missense and presumably hypomorphic mutations lead to JBS while all null alleles lead to MKS. PMID:19777577

  8. Polycyclic aromatic hydrocarbons (PAHs) in ambient aerosols from Beijing: characterization of low volatile PAHs by positive-ion atmospheric pressure photoionization (APPI) coupled with Fourier transform ion cyclotron resonance.

    PubMed

    Jiang, Bin; Liang, Yongmei; Xu, Chunming; Zhang, Jingyi; Hu, Miao; Shi, Quan

    2014-05-01

    Aromatic fractions derived from aerosol samples were characterized by gas chromatography and mass spectrometry (GC-MS), high temperature simulated distillation (SIMDIS), and positive-ion atmospheric pressure photoionization (APPI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), respectively. It was found that about 27 wt % compounds in aromatic fractions could not be eluted from a GC column and some large molecule PAHs were neglected in GC-MS analysis. APPI FT-ICR MS was proven to be a powerful approach for characterizing the molecular composition of aromatics, especially for the large molecular species. An aromatic sample from Beijing urban aerosol was successfully characterized by APPI FT-ICR MS. Results showed that most abundant aromatic compounds in PM2.5 (particles with aerodynamic diameter ≤ 2.5 μm) were highly condensed hydrocarbons with 4-8 aromatic rings and their homologues with very short alkyl chains. Furthermore, heteroatom-containing hydrocarbons were found as the significant components of the aromatic fractions: O1, O2, N1, and S1 class species with 10-28 DBEs (double bond equivalents) and 14-38 carbon numbers were identified by APPI FT-ICR MS. The heteroatom PAHs had similar DBEs and carbon number distribution as regular PAHs. PMID:24702199

  9. 2D vs. 3D mammography observer study

    NASA Astrophysics Data System (ADS)

    Fernandez, James Reza F.; Hovanessian-Larsen, Linda; Liu, Brent

    2011-03-01

    Breast cancer is the most common type of non-skin cancer in women. 2D mammography is a screening tool to aid in the early detection of breast cancer, but has diagnostic limitations of overlapping tissues, especially in dense breasts. 3D mammography has the potential to improve detection outcomes by increasing specificity, and a new 3D screening tool with a 3D display for mammography aims to improve performance and efficiency as compared to 2D mammography. An observer study using a mammography phantom was performed to compare traditional 2D mammography with this ne 3D mammography technique. In comparing 3D and 2D mammography there was no difference in calcification detection, and mass detection was better in 2D as compared to 3D. There was a significant decrease in reading time for masses, calcifications, and normals in 3D compared to 2D, however, as well as more favorable confidence levels in reading normal cases. Given the limitations of the mammography phantom used, however, a clearer picture in comparing 3D and 2D mammography may be better acquired with the incorporation of human studies in the future.

  10. Efficient 2D MRI relaxometry using compressed sensing

    NASA Astrophysics Data System (ADS)

    Bai, Ruiliang; Cloninger, Alexander; Czaja, Wojciech; Basser, Peter J.

    2015-06-01

    Potential applications of 2D relaxation spectrum NMR and MRI to characterize complex water dynamics (e.g., compartmental exchange) in biology and other disciplines have increased in recent years. However, the large amount of data and long MR acquisition times required for conventional 2D MR relaxometry limits its applicability for in vivo preclinical and clinical MRI. We present a new MR pipeline for 2D relaxometry that incorporates compressed sensing (CS) as a means to vastly reduce the amount of 2D relaxation data needed for material and tissue characterization without compromising data quality. Unlike the conventional CS reconstruction in the Fourier space (k-space), the proposed CS algorithm is directly applied onto the Laplace space (the joint 2D relaxation data) without compressing k-space to reduce the amount of data required for 2D relaxation spectra. This framework is validated using synthetic data, with NMR data acquired in a well-characterized urea/water phantom, and on fixed porcine spinal cord tissue. The quality of the CS-reconstructed spectra was comparable to that of the conventional 2D relaxation spectra, as assessed using global correlation, local contrast between peaks, peak amplitude and relaxation parameters, etc. This result brings this important type of contrast closer to being realized in preclinical, clinical, and other applications.

  11. NKG2D receptor and its ligands in host defense

    PubMed Central

    Lanier, Lewis L.

    2015-01-01

    NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8+ T cells, and subsets of CD4+ T cells, iNKT cells, and γδ T cells. In humans NKG2D transmits signals by its association with the DAP10 adapter subunit and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least 8 genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and post-translation. In general healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyper-proliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves a mechanism for the immune system to detect and eliminate cells that have undergone “stress”. Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases. PMID:26041808

  12. 2D constant-loss taper for mode conversion

    NASA Astrophysics Data System (ADS)

    Horth, Alexandre; Kashyap, Raman; Quitoriano, Nathaniel J.

    2015-03-01

    Proposed in this manuscript is a novel taper geometry, the constant-loss taper (CLT). This geometry is derived with 1D slabs of silicon embedded in silicon dioxide using coupled-mode theory (CMT). The efficiency of the CLT is compared to both linear and parabolic tapers using CMT and 2D finite-difference time-domain simulations. It is shown that over a short 2D, 4.45 μm long taper the CLT's mode conversion efficiency is ~90% which is 10% and 18% more efficient than a 2D parabolic or linear taper, respectively.

  13. Recent advances in 2D materials for photocatalysis

    NASA Astrophysics Data System (ADS)

    Luo, Bin; Liu, Gang; Wang, Lianzhou

    2016-03-01

    Two-dimensional (2D) materials have attracted increasing attention for photocatalytic applications because of their unique thickness dependent physical and chemical properties. This review gives a brief overview of the recent developments concerning the chemical synthesis and structural design of 2D materials at the nanoscale and their applications in photocatalytic areas. In particular, recent progress on the emerging strategies for tailoring 2D material-based photocatalysts to improve their photo-activity including elemental doping, heterostructure design and functional architecture assembly is discussed.

  14. Comparison of 2D and 3D gamma analyses

    SciTech Connect

    Pulliam, Kiley B.; Huang, Jessie Y.; Howell, Rebecca M.; Followill, David; Kry, Stephen F.; Bosca, Ryan; O’Daniel, Jennifer

    2014-02-15

    Purpose: As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans. Methods: Fifty IMRT plans were selected from the authors’ clinical database, and recalculated using Monte Carlo. Treatment planning system-calculated (“evaluated dose distributions”) and Monte Carlo-recalculated (“reference dose distributions”) dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1%) and distance-to-agreement (5, 3, 2, and 1 mm) acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma. Results: The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D). Conclusions: The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must

  15. Materials for Flexible, Stretchable Electronics: Graphene and 2D Materials

    NASA Astrophysics Data System (ADS)

    Kim, Sang Jin; Choi, Kyoungjun; Lee, Bora; Kim, Yuna; Hong, Byung Hee

    2015-07-01

    Recently, 2D materials have been intensively studied as emerging materials for future electronics, including flexible electronics, photonics, and electrochemical energy storage devices. Among representative 2D materials (such as graphene, boron nitride, and transition metal dichalcogenides) that exhibit extraordinary properties, graphene stands out in the flexible electronics field due to its combination of high electron mobility, high thermal conductivity, high specific surface area, high optical transparency, excellent mechanical flexibility, and environmental stability. This review covers the synthesis, transfer, and characterization methods of graphene and 2D materials and graphene's application to flexible devices as well as comparison with other competing materials.

  16. Ms. Mentor Unmasked

    ERIC Educational Resources Information Center

    Krebs, Paula

    2008-01-01

    This article presents an interview with Emily Toth, who writes the monthly "Ms. Mentor" academic advice column in the "Chronicle of Higher Education" and teaches in the English department at Louisiana State University, in Baton Rouge. She is the author of "Ms. Mentor's Impeccable Advice for Women in Academia" (1997), "Inside Peyton Place: The Life…

  17. Recent developments in 2D layered inorganic nanomaterials for sensing

    NASA Astrophysics Data System (ADS)

    Kannan, Padmanathan Karthick; Late, Dattatray J.; Morgan, Hywel; Rout, Chandra Sekhar

    2015-08-01

    Two dimensional layered inorganic nanomaterials (2D-LINs) have recently attracted huge interest because of their unique thickness dependent physical and chemical properties and potential technological applications. The properties of these layered materials can be tuned via both physical and chemical processes. Some 2D layered inorganic nanomaterials like MoS2, WS2 and SnS2 have been recently developed and employed in various applications, including new sensors because of their layer-dependent electrical properties. This article presents a comprehensive overview of recent developments in the application of 2D layered inorganic nanomaterials as sensors. Some of the salient features of 2D materials for different sensing applications are discussed, including gas sensing, electrochemical sensing, SERS and biosensing, SERS sensing and photodetection. The working principles of the sensors are also discussed together with examples.

  18. 2. D Street facade and rear (east) blank wall of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. D Street facade and rear (east) blank wall of parking garage. Farther east is 408 8th Street (National Art And Frame Company). - PMI Parking Garage, 403-407 Ninth Street, Northwest, Washington, District of Columbia, DC

  19. Collective excitations in 2D hard-disc fluid.

    PubMed

    Huerta, Adrian; Bryk, Taras; Trokhymchuk, Andrij

    2015-07-01

    Collective dynamics of a two-dimensional (2D) hard-disc fluid was studied by molecular dynamics simulations in the range of packing fractions that covers states up to the freezing. Some striking features concerning collective excitations in this system were observed. In particular, the short-wavelength shear waves while being absent at low packing fractions were observed in the range of high packing fractions, just before the freezing transition in a 2D hard-disc fluid. In contrast, the so-called "positive sound dispersion" typically observed in dense Lennard-Jones-like fluids, was not detected for the 2D hard-disc fluid. The ratio of specific heats in the 2D hard-disc fluid shows a monotonic increase with density approaching the freezing, resembling in this way the similar behavior in the vicinity of the Widom line in the case of supercritical fluids. PMID:25595625

  20. Alloyed 2D Metal-Semiconductor Atomic Layer Junctions.

    PubMed

    Kim, Ah Ra; Kim, Yonghun; Nam, Jaewook; Chung, Hee-Suk; Kim, Dong Jae; Kwon, Jung-Dae; Park, Sang Won; Park, Jucheol; Choi, Sun Young; Lee, Byoung Hun; Park, Ji Hyeon; Lee, Kyu Hwan; Kim, Dong-Ho; Choi, Sung Mook; Ajayan, Pulickel M; Hahm, Myung Gwan; Cho, Byungjin

    2016-03-01

    Heterostructures of compositionally and electronically variant two-dimensional (2D) atomic layers are viable building blocks for ultrathin optoelectronic devices. We show that the composition of interfacial transition region between semiconducting WSe2 atomic layer channels and metallic NbSe2 contact layers can be engineered through interfacial doping with Nb atoms. WxNb1-xSe2 interfacial regions considerably lower the potential barrier height of the junction, significantly improving the performance of the corresponding WSe2-based field-effect transistor devices. The creation of such alloyed 2D junctions between dissimilar atomic layer domains could be the most important factor in controlling the electronic properties of 2D junctions and the design and fabrication of 2D atomic layer devices. PMID:26839956

  1. Technical Review of the UNET2D Hydraulic Model

    SciTech Connect

    Perkins, William A.; Richmond, Marshall C.

    2009-05-18

    The Kansas City District of the US Army Corps of Engineers is engaged in a broad range of river management projects that require knowledge of spatially-varied hydraulic conditions such as velocities and water surface elevations. This information is needed to design new structures, improve existing operations, and assess aquatic habitat. Two-dimensional (2D) depth-averaged numerical hydraulic models are a common tool that can be used to provide velocity and depth information. Kansas City District is currently using a specific 2D model, UNET2D, that has been developed to meet the needs of their river engineering applications. This report documents a tech- nical review of UNET2D.

  2. From weakly to strongly interacting 2D Fermi gases

    NASA Astrophysics Data System (ADS)

    Dyke, Paul; Fenech, Kristian; Lingham, Marcus; Peppler, Tyson; Hoinka, Sascha; Vale, Chris

    2014-05-01

    We study ultracold 2D Fermi gases of 6Li formed in a highly oblate trapping potential. The potential is generated by a cylindrically focused, blue detuned TEM01 mode laser beam. Weak magnetic field curvature provides highly harmonic confinement in the radial direction and we can readily produce single clouds with an aspect ratio of 230. Our experiments investigate the dimensional crossover from 3D to 2D for a two component Fermi gas in the Bose-Einstein Condensate to Bardeen Cooper Schrieffer crossover. Observation of an elbow in measurements of the cloud width vs. atom number is consistent with populating only the lowest transverse harmonic oscillator state for weak attractive interactions. This measurement is extended to the strongly interacting region using the broad Feshbach resonance at 832 G. We also report our progress towards measurement of the 2D equation of state for an interacting 2D Fermi gas via in-situ absorption imaging.

  3. Chemical vapour deposition: Transition metal carbides go 2D

    NASA Astrophysics Data System (ADS)

    Gogotsi, Yury

    2015-11-01

    The unique properties of 2D materials, such as graphene or transition metal dichalcogenides, have been attracting much attention in the past decade. Now, metallically conductive and even superconducting transition metal carbides are entering the game.

  4. Dominant 2D magnetic turbulence in the solar wind

    NASA Technical Reports Server (NTRS)

    Bieber, John W.; Wanner, Wolfgang; Matthaeus, William H.

    1995-01-01

    There have been recent suggestions that solar wind magnetic turbulence may be a composite of slab geometry (wavevector aligned with the mean magnetic field) and 2D geometry (wavevectors perpendicular to the mean field). We report results of two new tests of this hypothesis using Helios measurements of inertial ranged magnetic spectra in the solar wind. The first test is based upon a characteristic difference between perpendicular and parallel reduced power spectra which is expected for the 2D component but not for the slab component. The second test examines the dependence of power spectrum density upon the magnetic field angle (i.e., the angle between the mean magnetic field and the radial direction), a relationship which is expected to be in opposite directions for the slab and 2D components. Both tests support the presence of a dominant (approximately 85 percent by energy) 2D component in solar wind magnetic turbulence.

  5. Dominant 2D magnetic turbulence in the solar wind

    SciTech Connect

    Bieber, John W.; Wanner, Wolfgang; Matthaeus, William H.

    1996-07-20

    There have been recent suggestions that solar wind magnetic turbulence may be a composite of slab geometry (wavevectors aligned with the mean magnetic field) and 2D geometry (wavevectors perpendicular to the mean field). We report results of two new tests of this hypothesis using Helios measurements of mid-inertial range magnetic spectra in the solar wind. The first test is based upon a characteristic difference between reduced magnetic power spectra in the two different directions perpendicular to the mean field. Such a difference is expected for 2D geometry but not for slab geometry. The second test examines the dependence of power spectrum density upon the magnetic field angle (i.e., the angle between the mean magnetic field and the radial direction), a relationship which is expected to be in opposite directions for the slab and 2D components. Both tests support the presence of a dominant ({approx}85% by energy) 2D component in solar wind magnetic turbulence.

  6. Efficient framework for deformable 2D-3D registration

    NASA Astrophysics Data System (ADS)

    Fluck, Oliver; Aharon, Shmuel; Khamene, Ali

    2008-03-01

    Using 2D-3D registration it is possible to extract the body transformation between the coordinate systems of X-ray and volumetric CT images. Our initial motivation is the improvement of accuracy of external beam radiation therapy, an effective method for treating cancer, where CT data play a central role in radiation treatment planning. Rigid body transformation is used to compute the correct patient setup. The drawback of such approaches is that the rigidity assumption on the imaged object is not valid for most of the patient cases, mainly due to respiratory motion. In the present work, we address this limitation by proposing a flexible framework for deformable 2D-3D registration consisting of a learning phase incorporating 4D CT data sets and hardware accelerated free form DRR generation, 2D motion computation, and 2D-3D back projection.

  7. GPU accelerated generation of digitally reconstructed radiographs for 2-D/3-D image registration.

    PubMed

    Dorgham, Osama M; Laycock, Stephen D; Fisher, Mark H

    2012-09-01

    Recent advances in programming languages for graphics processing units (GPUs) provide developers with a convenient way of implementing applications which can be executed on the CPU and GPU interchangeably. GPUs are becoming relatively cheap, powerful, and widely available hardware components, which can be used to perform intensive calculations. The last decade of hardware performance developments shows that GPU-based computation is progressing significantly faster than CPU-based computation, particularly if one considers the execution of highly parallelisable algorithms. Future predictions illustrate that this trend is likely to continue. In this paper, we introduce a way of accelerating 2-D/3-D image registration by developing a hybrid system which executes on the CPU and utilizes the GPU for parallelizing the generation of digitally reconstructed radiographs (DRRs). Based on the advancements of the GPU over the CPU, it is timely to exploit the benefits of many-core GPU technology by developing algorithms for DRR generation. Although some previous work has investigated the rendering of DRRs using the GPU, this paper investigates approximations which reduce the computational overhead while still maintaining a quality consistent with that needed for 2-D/3-D registration with sufficient accuracy to be clinically acceptable in certain applications of radiation oncology. Furthermore, by comparing implementations of 2-D/3-D registration on the CPU and GPU, we investigate current performance and propose an optimal framework for PC implementations addressing the rigid registration problem. Using this framework, we are able to render DRR images from a 256×256×133 CT volume in ~24 ms using an NVidia GeForce 8800 GTX and in ~2 ms using NVidia GeForce GTX 580. In addition to applications requiring fast automatic patient setup, these levels of performance suggest image-guided radiation therapy at video frame rates is technically feasible using relatively low cost PC

  8. Computational Design of 2D materials for Energy Applications

    NASA Astrophysics Data System (ADS)

    Sun, Qiang

    2015-03-01

    Since the successful synthesis of graphene, tremendous efforts have been devoted to two-dimensional monolayers such as boron nitride (BN), silicene and MoS2. These 2D materials exhibit a large variety of physical and chemical properties with unprecedented applications. Here we report our recent studies of computational design of 2D materials for fuel cell applications which include hydrogen storage, CO2 capture, CO conversion and O2 reduction.

  9. Generating a 2D Representation of a Complex Data Structure

    NASA Technical Reports Server (NTRS)

    James, Mark

    2006-01-01

    A computer program, designed to assist in the development and debugging of other software, generates a two-dimensional (2D) representation of a possibly complex n-dimensional (where n is an integer >2) data structure or abstract rank-n object in that other software. The nature of the 2D representation is such that it can be displayed on a non-graphical output device and distributed by non-graphical means.

  10. Phylogenetic tree construction based on 2D graphical representation

    NASA Astrophysics Data System (ADS)

    Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

    2006-04-01

    A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

  11. MS/MS Automated Selected Ion Chromatograms

    2005-12-12

    This program can be used to read a LC-MS/MS data file from either a Finnigan ion trap mass spectrometer (.Raw file) or an Agilent Ion Trap mass spectrometer (.MGF and .CDF files) and create a selected ion chromatogram (SIC) for each of the parent ion masses chosen for fragmentation. The largest peak in each SIC is also identified, with reported statistics including peak elution time, height, area, and signal to noise ratio. It creates severalmore » output files, including a base peak intensity (BPI) chromatogram for the survey scan, a BPI for the fragmentation scans, an XML file containing the SIC data for each parent ion, and a "flat file" (ready for import into a database) containing summaries of the SIC data statistics.« less

  12. Simulating MEMS Chevron Actuator for Strain Engineering 2D Materials

    NASA Astrophysics Data System (ADS)

    Vutukuru, Mounika; Christopher, Jason; Bishop, David; Swan, Anna

    2D materials pose an exciting paradigm shift in the world of electronics. These crystalline materials have demonstrated high electric and thermal conductivities and tensile strength, showing great potential as the new building blocks of basic electronic circuits. However, strain engineering 2D materials for novel devices remains a difficult experimental feat. We propose the integration of 2D materials with MEMS devices to investigate the strain dependence on material properties such as electrical and thermal conductivity, refractive index, mechanical elasticity, and band gap. MEMS Chevron actuators, provides the most accessible framework to study strain in 2D materials due to their high output force displacements for low input power. Here, we simulate Chevron actuators on COMSOL to optimize actuator design parameters and accurately capture the behavior of the devices while under the external force of a 2D material. Through stationary state analysis, we analyze the response of the device through IV characteristics, displacement and temperature curves. We conclude that the simulation precisely models the real-world device through experimental confirmation, proving that the integration of 2D materials with MEMS is a viable option for constructing novel strain engineered devices. The authors acknowledge support from NSF DMR1411008.

  13. Development of a Sensitive LC/MS/MS Method for Vitamin D Metabolites: 1,25 Dihydroxyvitamin D2&3 Measurement Using a Novel Derivatization Agent

    PubMed Central

    Hedman, Curtis J.; Wiebe, Donald A.; Dey, Subhakar; Plath, Josh; Kemnitz, Joseph W.; Ziegler, Toni E.

    2014-01-01

    Active vitamin D metabolites 1,25-dihydroxyvitamin D2 [1,25-(OH)2-D2; derived from ergocalciferol] and D3 [1,25-(OH)2-D3; derived from cholecalciferol] are found in low levels in the circulation and require a very sensitive method for measurement. Radioimmunoassay (RIA) has been the method of choice, but it lacks the specificity needed to distinguish between 1,25-(OH)2-D2 and -D3whereas liquid chromatography-tandem mass spectrometry (LC/MS/MS) methods have the advantage of high specificity and sensitivity. Here, we compare a new derivative for ionizing 1,25-(OH)2-D to enhance the signal and provide the most sensitive assay for measuring vitamin D. We used the Amplifex diene method of derivatizing prior to LC/MS/MS and compared it to the standard RIA method and the 4-phenyl-1,2,4-triazole-3,5-dione (PTAD) method of derivatizing prior to LC/MS/MS. In the evaluation of 20 human serum samples, all methods correlated strongly across the upper levels of the standard 1,25-(OH)2-D2 and - D3 ranges (Amplifex and RIA, pc = 0.97; Amplifex and PTAD, pc = 0.96) but less strongly on the lower levels of the standard range (Amplifex and RIA, pc = 0.81; Amplifex and PTAD, pc = 0.65) suggesting differences in the sensitivities between the assays. The Amplifex method was determined to be more sensitive than the PTAD method, as peak areas were significantly higher for the Amplifex method and provided for a 10 fold higher signal-to-noise ratio than PTAD. Therefore, the Amplifex LC/MS/MS method is the most sensitive and specific method available for measuring 1,25-(OH)2-D2 and -D3 while using the smallest sample volume. PMID:24576767

  14. Assessment of local pulse wave velocity in arteries using 2D distension waveforms.

    PubMed

    Meinders, J M; Kornet, L; Brands, P J; Hoeks, A P

    2001-10-01

    The reciprocal of the arterial pulse wave velocity contains crucial information about the mechanical characteristics of the arterial wall but is difficult to assess noninvasively in vivo. In this paper, a new method to assess local pulse wave velocity (PWV) is presented. To this end, multiple adjacent distension waveforms are determined simultaneously along a short arterial segment, using a single 2D-vessel wall tracking system with a high frame rate (651 Hz). Each B-mode image consists of 16 echo lines spanning a total width of 15.86 mm. Dedicated software has been developed to extract the end-diastolic diameter from the B-mode image and the distension waveforms from the underlying radiofrequency (rf) information for each echo-line. The PWV is obtained by determining the ratio of the temporal and spatial gradient of adjacent distension velocity waveforms. The proposed method is verified in a phantom and in the common carotid artery (CCA) of humans. Phantom experiments show a high concordance between the PWV obtained from 2D distension velocity waveforms (4.21 +/- 0.02 m/s) and the PWV determined using two pressure catheters (4.26 +/- 0.02 m/s). Assuming linear spatial gradients, the PWV can also be obtained in vivo for CCA and averages to 5.5 +/- 1.5 m/s (intersubject variation, n = 23), which compares well to values found in literature. Furthermore, intrasubject PWV compares well with those calculated using the Bramwell-Hill equation. It can be concluded that the PWV can be obtained from the spatial and temporal gradient if the spatial gradient is linear over the observed length of the artery, i.e. the artery should be homogenous in diameter and distension and the influence of reflections must be small. PMID:12051275

  15. Managing Progressive MS

    MedlinePlus

    ... MS Society | 8 builders about renovations and home adaptations to support independence. OTs may also evaluate and ... Staying at home will mean making changes. Home adaptations do more than fight fatigue. They offer safety, ...

  16. Living with Advanced MS

    MedlinePlus

    ... Read More Read More Resource Edward M. Dowd Personal Advocate Program The Edward M. Dowd Personal Advocate ... Informed About the Society Vision Careers Leadership Cultural Values Financials News Press Room MS Prevalence Charitable Ratings ...

  17. Quantitative determination of vitamin D metabolites in plasma using UHPLC-MS/MS

    PubMed Central

    Ding, Shujing; Schoenmakers, Inez; Jones, Kerry; Koulman, Albert; Prentice, Ann

    2010-01-01

    Vitamin D is an important determinant of bone health at all ages. The plasma concentrations of 25-hydroxy vitamin D (25-OH D) and other metabolites are used as biomarkers for vitamin sufficiency and function. To allow for the simultaneous determination of five vitamin D metabolites, 25-OH D3, 25-OH D2, 24,25-(OH)2 D3, 1,25-(OH)2 D3, and 1,25-(OH)2 D2, in low volumes of human plasma, an assay using ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) was established. Plasma samples were spiked with isotope-labeled internal standards and pretreated using protein precipitation, solid-phase extraction (SPE) and a Diels–Alder derivatization step with 4-phenyl-1,2,4-triazoline-3,5-dione. The SPE recovery rates ranged from 55% to 85%, depending on the vitamin D metabolite; the total sample run time was <5 min. Mass spectrometry was conducted using positive ion electrospray ionization in the multiple reaction monitoring mode on a quadrupole–quadrupole-linear ion trap instrument after pre-column addition of methylamine to increase the ionization efficiency. The intra- and inter-day relative standard deviations were 1.6–4.1% and 3.7–6.8%, respectively. The limit of quantitation for these compounds was determined to be between 10 and 20 pg/mL. The 25-OH D results were compared with values obtained for reference materials (DEQAS). In addition, plasma samples were analyzed with two additional Diasorin antibody assays. All comparisons with conventional methods showed excellent correlations (r2 = 0.9738) for DEQAS samples, demonstrating the high degree of comparability of the new UHPLC-MS/MS technique to existing methods. PMID:20628873

  18. High resolution mass spectrometric alveolar proteomics: identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients.

    PubMed

    Bai, Yu; Galetskiy, Dmitry; Damoc, Eugen; Paschen, Christian; Liu, Zhiqiang; Griese, Mathias; Liu, Shuying; Przybylski, Michael

    2004-08-01

    In the present study, one- and two-dimensional gel electrophoresis combined with high resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) have been applied as powerful approaches for the proteome analysis of surfactant proteins SP-A and SP-D, including identification of structurally modified and truncation forms, in bronchoalveolar lavage fluid from patients with cystic fibrosis, chronic bronchitis and pulmonary alveolar proteinosis. Highly sensitive micropreparation techniques were developed for matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS analysis which provided the identification of surfactant proteins at very low levels. Owing to the high resolution, FT-ICR MS was found to provide substantial advantages for the structural identification of surfactant proteins from complex biological matrices with high mass determination accuracy. Several protein bands corresponding to SP-A and SP-D were identified by MALDI-FT-ICR MS after electrophoretic separation by one- and two-dimensional gel electrophoresis, and provided the identification of structural modifications (hydroxy-proline) and degradation products. The high resolution mass spectrometric proteome analysis should facilitate the unequivocal identification of subunits, aggregations, modifications and degradation products of surfactant proteins and hence contribute to the understanding of the mechanistic basis of lung disease pathogenesis. PMID:15274124

  19. Ion Trap with Narrow Aperture Detection Electrodes for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Nagornov, Konstantin O.; Kozhinov, Anton N.; Tsybin, Oleg Y.; Tsybin, Yury O.

    2015-05-01

    The current paradigm in ion trap (cell) design for Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the ion detection with wide aperture detection electrodes. Specifically, excitation and detection electrodes are typically 90° wide and positioned radially at a similar distance from the ICR cell axis. Here, we demonstrate that ion detection with narrow aperture detection electrodes (NADEL) positioned radially inward of the cell's axis is feasible and advantageous for FT-ICR MS. We describe design details and performance characteristics of a 10 T FT-ICR MS equipped with a NADEL ICR cell having a pair of narrow aperture (flat) detection electrodes and a pair of standard 90° excitation electrodes. Despite a smaller surface area of the detection electrodes, the sensitivity of the NADEL ICR cell is not reduced attributable to improved excite field distribution, reduced capacitance of the detection electrodes, and their closer positioning to the orbits of excited ions. The performance characteristics of the NADEL ICR cell are comparable with the state-of-the-art FT-ICR MS implementations for small molecule, peptide, protein, and petroleomics analyses. In addition, the NADEL ICR cell's design improves the flexibility of ICR cells and facilitates implementation of advanced capabilities (e.g., quadrupolar ion detection for improved mainstream applications). It also creates an intriguing opportunity for addressing the major bottleneck in FTMS—increasing its throughput via simultaneous acquisition of multiple transients or via generation of periodic non-sinusoidal transient signals.

  20. The coupling of direct analysis in real time ionization to Fourier transform ion cyclotron resonance mass spectrometry for ultrahigh-resolution mass analysis.

    PubMed

    Rummel, Julia L; McKenna, Amy M; Marshall, Alan G; Eyler, John R; Powell, David H

    2010-03-01

    Direct Analysis in Real Time (DART) is an ambient ionization technique for mass spectrometry that provides rapid and sensitive analyses with little or no sample preparation. DART has been reported primarily for mass analyzers of low to moderate resolving power such as quadrupole ion traps and time-of-flight (TOF) mass spectrometers. In the current work, a custom-built DART source has been successfully coupled to two different Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers for the first time. Comparison of spectra of the isobaric compounds, diisopropyl methylphosphonate and theophylline, acquired by 4.7 T FT-ICR MS and TOF MS, demonstrates that the TOF resolving power can be insufficient for compositionally complex samples. 9.4 T FT-ICR MS yielded the highest mass resolving power yet reported with DART ionization for 1,2-benzanthracene and 9,10-diphenylanthracene. Polycyclic aromatic hydrocarbons exhibit a spatial dependence in ionization mechanisms between the DART source and the mass spectrometer. The feasibility of analyzing a variety of samples was established with the introduction and analysis of food products and crude oil samples. DART FT-ICR MS provides complex sample analysis that is rapid, highly selective and information-rich, but limited to relatively low-mass analytes. PMID:20187081

  1. MS Based Metabonomics

    SciTech Connect

    Want, Elizabeth J.; Metz, Thomas O.

    2010-03-01

    Metabonomics is the latest and least mature of the systems biology triad, which also includes genomics and proteomics, and has its origins in the early orthomolecular medicine work pioneered by Linus Pauling and Arthur Robinson. It was defined by Nicholson and colleagues in 1999 as the quantitative measurement of perturbations in the metabolite complement of an integrated biological system in response to internal or external stimuli, and is often used today to describe many non-global types of metabolite analyses. Applications of metabonomics are extensive and include toxicology, nutrition, pharmaceutical research and development, physiological monitoring and disease diagnosis. For example, blood samples from millions of neonates are tested routinely by mass spectrometry (MS) as a diagnostic tool for inborn errors of metabolism. The metabonome encompasses a wide range of structurally diverse metabolites; therefore, no single analytical platform will be sufficient. Specialized sample preparation and detection techniques are required, and advances in NMR and MS technologies have led to enhanced metabonome coverage, which in turn demands improved data analysis approaches. The role of MS in metabonomics is still evolving as instrumentation and software becomes more sophisticated and as researchers realize the strengths and limitations of current technology. MS offers a wide dynamic range, high sensitivity, and reproducible, quantitative analysis. These attributes are essential for addressing the challenges of metabonomics, as the range of metabolite concentrations easily exceeds nine orders of magnitude in biofluids, and the diversity of molecular species ranges from simple amino and organic acids to lipids and complex carbohydrates. Additional challenges arise in generating a comprehensive metabolite profile, downstream data processing and analysis, and structural characterization of important metabolites. A typical workflow of MS-based metabonomics is shown in Figure

  2. IMS - MS Data Extractor

    2015-10-20

    An automated drift time extraction and computed associated collision cross section software tool for small molecule analysis with ion mobility spectrometry-mass spectrometry (IMS-MS). The software automatically extracts drift times and computes associated collision cross sections for small molecules analyzed using ion mobility spectrometry-mass spectrometry (IMS-MS) based on a target list of expected ions provided by the user.

  3. Growth and Characterization of Silicon at the 2D Limit

    NASA Astrophysics Data System (ADS)

    Mannix, Andrew; Kiraly, Brian; Hersam, Mark; Guisinger, Nathan

    2015-03-01

    Because bulk silicon has dominated the development of microelectronics over the past 50 years, the recent interest in two-dimensional (2D) materials (e.g., graphene, MoS2, phosphorene, etc.) naturally raises questions regarding the growth and properties of silicon at the 2D limit. Utilizing atomic-scale, ultra-high vacuum (UHV) scanning tunneling microscopy (STM), we have investigated the 2D limits of silicon growth on Ag(111). In agreement with previous reports of sp2-bonded silicene phases, we observe the temperature-dependent evolution of ordered 2D phases. However, we attribute these to apparent Ag-Si surface alloys. At sufficiently high silicon coverage, we observe the precipitation of crystalline, sp3-bonded Si(111) domains. These domains are capped with a √3 honeycomb phase that is indistinguishable from the silver-induced √3 honeycomb-chained-trimer reconstruction on bulk Si(111). Further ex-situcharacterization with Raman spectroscopy, atomic force microscopy, cross-sectional transmission electron microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy reveals that these sheets are ultrathin sheets of bulk-like, (111) oriented, sp3 silicon. Even at the 2D limit, scanning tunneling spectroscopy shows that these silicon nanosheets exhibit semiconducting electronic characteristics.

  4. 2D nanostructures for water purification: graphene and beyond.

    PubMed

    Dervin, Saoirse; Dionysiou, Dionysios D; Pillai, Suresh C

    2016-08-18

    Owing to their atomically thin structure, large surface area and mechanical strength, 2D nanoporous materials are considered to be suitable alternatives for existing desalination and water purification membrane materials. Recent progress in the development of nanoporous graphene based materials has generated enormous potential for water purification technologies. Progress in the development of nanoporous graphene and graphene oxide (GO) membranes, the mechanism of graphene molecular sieve action, structural design, hydrophilic nature, mechanical strength and antifouling properties and the principal challenges associated with nanopore generation are discussed in detail. Subsequently, the recent applications and performance of newly developed 2D materials such as 2D boron nitride (BN) nanosheets, graphyne, molybdenum disulfide (MoS2), tungsten chalcogenides (WS2) and titanium carbide (Ti3C2Tx) are highlighted. In addition, the challenges affecting 2D nanostructures for water purification are highlighted and their applications in the water purification industry are discussed. Though only a few 2D materials have been explored so far for water treatment applications, this emerging field of research is set to attract a great deal of attention in the near future. PMID:27506268

  5. Sparse radar imaging using 2D compressed sensing

    NASA Astrophysics Data System (ADS)

    Hou, Qingkai; Liu, Yang; Chen, Zengping; Su, Shaoying

    2014-10-01

    Radar imaging is an ill-posed linear inverse problem and compressed sensing (CS) has been proved to have tremendous potential in this field. This paper surveys the theory of radar imaging and a conclusion is drawn that the processing of ISAR imaging can be denoted mathematically as a problem of 2D sparse decomposition. Based on CS, we propose a novel measuring strategy for ISAR imaging radar and utilize random sub-sampling in both range and azimuth dimensions, which will reduce the amount of sampling data tremendously. In order to handle 2D reconstructing problem, the ordinary solution is converting the 2D problem into 1D by Kronecker product, which will increase the size of dictionary and computational cost sharply. In this paper, we introduce the 2D-SL0 algorithm into the reconstruction of imaging. It is proved that 2D-SL0 can achieve equivalent result as other 1D reconstructing methods, but the computational complexity and memory usage is reduced significantly. Moreover, we will state the results of simulating experiments and prove the effectiveness and feasibility of our method.

  6. Ultrafast 2D NMR: an emerging tool in analytical spectroscopy.

    PubMed

    Giraudeau, Patrick; Frydman, Lucio

    2014-01-01

    Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry--from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications. PMID:25014342

  7. Ultrafast 2D NMR: An Emerging Tool in Analytical Spectroscopy

    NASA Astrophysics Data System (ADS)

    Giraudeau, Patrick; Frydman, Lucio

    2014-06-01

    Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry—from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications.

  8. Phosphorene: A New High-Mobility 2D Semiconductor

    NASA Astrophysics Data System (ADS)

    Liu, Han; Neal, Adam; Zhu, Zhen; Tomanek, David; Ye, Peide

    2014-03-01

    The rise of 2D crystals has opened various possibilities for future electrical and optical applications. MoS2 n-type transistors are showing great potential in ultra-scaled and low-power electronics. Here, we introduce phosphorene, a name we coined for 2D few-layer black phosphorus, a new 2D material with layered structure. We perform ab initio band structure calculations and show that the fundamental band gap depends sensitively on the number of layers. We observe transport behavior, which shows a mobility variation in the 2D plane. High on-current of 194 mA/mm, high hole mobility up to 286 cm2/V .s and on/off ratio up to 104 was achieved with phosphorene transistors at room temperature. Schottky barrier height at the metal/phosphorene interface was also measured as a function of temperature. We demonstrate a CMOS inverter with combination to MoS2 NMOS transistors, which shows great potential for semiconducting 2D crystals in future electronic, optoelectronic and flexible electronic devices.

  9. Mean flow and anisotropic cascades in decaying 2D turbulence

    NASA Astrophysics Data System (ADS)

    Liu, Chien-Chia; Cerbus, Rory; Gioia, Gustavo; Chakraborty, Pinaki

    2015-11-01

    Many large-scale atmospheric and oceanic flows are decaying 2D turbulent flows embedded in a non-uniform mean flow. Despite its importance for large-scale weather systems, the affect of non-uniform mean flows on decaying 2D turbulence remains unknown. In the absence of mean flow it is well known that decaying 2D turbulent flows exhibit the enstrophy cascade. More generally, for any 2D turbulent flow, all computational, experimental and field data amassed to date indicate that the spectrum of longitudinal and transverse velocity fluctuations correspond to the same cascade, signifying isotropy of cascades. Here we report experiments on decaying 2D turbulence in soap films with a non-uniform mean flow. We find that the flow transitions from the usual isotropic enstrophy cascade to a series of unusual and, to our knowledge, never before observed or predicted, anisotropic cascades where the longitudinal and transverse spectra are mutually independent. We discuss implications of our results for decaying geophysical turbulence.

  10. Synthesis, structure and luminescence property of 2D lanthanide complexes with 3-fluorophthalate and oxalate

    SciTech Connect

    Cha, Yu-E; Li, Xia; Song, Shuang

    2012-12-15

    Complexes [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (Ln=Sm 1, Eu 2, Tb 3 and Dy 4; fpht=3-fluorophthalate and ox=oxalate) have been synthesized and structurally characterized by single crystal X-ray diffraction. The four complexes possess similar 2D framework structures constructed from Ln-fpht double-stranded helices and ox linkages. Complexes 2 and 3 display the characteristic emission {sup 5}D{sub 0}{yields}{sup 7}F{sub J} (J=0-4) transitions of Eu(III) ion and {sup 5}D{sub 4}{yields}{sup 7}F{sub J} (J=6-3) transitions of Tb(III) ion, respectively. The emission decay curves reveal a monoexponential behavior yielding the lifetime values of 0.266{+-}0.002 ms for 2 and 0.733{+-}0.002 ms for 3. The emission spectrum of 1 shows three weak bands corresponding to the characteristic emission {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 5/2}, {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 7/2} and {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 9/2} transitions of Sm(III) ion. The emission spectrum of 4 displays a broad band centered at 438 nm, which comes from the {pi}{sup Low-Asterisk }-{pi} transition of the ligand. - Graphical abstract: Complexes [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (fpht=3-fluorophthalate, ox=oxalate) possess 2D structures. Sm(III), Eu(III) and Tb(III) complexes show the characteristic fluorescent emission of the Ln(III). Dy(III) complex displays ligand-based luminescent behavior. Highlights: Black-Right-Pointing-Pointer [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (fpht=3-fluorophthalate; ox=oxalate) show 2D structures. Black-Right-Pointing-Pointer The 2D structures are constructed from Ln-fpht double-stranded helices and ox linkage. Black-Right-Pointing-Pointer The Sm(III), Eu(III) and Tb(III) complexes show the characteristic emission of the Ln(III) ions. Black-Right-Pointing-Pointer Dy(III) complex displays ligand-based luminescent behavior.

  11. 2D materials for photon conversion and nanophotonics

    NASA Astrophysics Data System (ADS)

    Tahersima, Mohammad H.; Sorger, Volker J.

    2015-09-01

    The field of two-dimensional (2D) materials has the potential to enable unique applications across a wide range of the electromagnetic spectrum. While 2D-layered materials hold promise for next-generation photon-conversion intrinsic limitations and challenges exist that shall be overcome. Here we discuss the intrinsic limitations as well as application opportunities of this new class of materials, and is sponsored by the NSF program Designing Materials to Revolutionize and Engineer our Future (DMREF) program, which links to the President's Materials Genome Initiative. We present general material-related details for photon conversion, and show that taking advantage of the mechanical flexibility of 2D materials by rolling MoS2/graphene/hexagonal boron nitride stack to a spiral solar cell allows for solar absorption up to 90%.

  12. Perception-based reversible watermarking for 2D vector maps

    NASA Astrophysics Data System (ADS)

    Men, Chaoguang; Cao, Liujuan; Li, Xiang

    2010-07-01

    This paper presents an effective and reversible watermarking approach for digital copyright protection of 2D-vector maps. To ensure that the embedded watermark is insensitive for human perception, we only select the noise non-sensitive regions for watermark embedding by estimating vertex density within each polyline. To ensure the exact recovery of original 2D-vector map after watermark extraction, we introduce a new reversible watermarking scheme based on reversible high-frequency wavelet coefficients modification. Within the former-selected non-sensitive regions, our watermarking operates on the lower-order vertex coordinate decimals with integer wavelet transform. Such operation further reduces the visual distortion caused by watermark embedding. We have validated the effectiveness of our scheme on our real-world city river/building 2D-vector maps. We give extensive experimental comparisons with state-of-the-art methods, including embedding capability, invisibility, and robustness over watermark attacking.

  13. Graphene based 2D-materials for supercapacitors

    NASA Astrophysics Data System (ADS)

    Palaniselvam, Thangavelu; Baek, Jong-Beom

    2015-09-01

    Ever-increasing energy demands and the depletion of fossil fuels are compelling humanity toward the development of suitable electrochemical energy conversion and storage devices to attain a more sustainable society with adequate renewable energy and zero environmental pollution. In this regard, supercapacitors are being contemplated as potential energy storage devices to afford cleaner, environmentally friendly energy. Recently, a great deal of attention has been paid to two-dimensional (2D) nanomaterials, including 2D graphene and its inorganic analogues (transition metal double layer hydroxides, chalcogenides, etc), as potential electrodes for the development of supercapacitors with high electrochemical performance. This review provides an overview of the recent progress in using these graphene-based 2D materials as potential electrodes for supercapacitors. In addition, future research trends including notable challenges and opportunities are also discussed.

  14. Simultaneous 2D Strain Sensing Using Polymer Planar Bragg Gratings

    PubMed Central

    Rosenberger, Manuel; Eisenbeil, Waltraud; Schmauss, Bernhard; Hellmann, Ralf

    2015-01-01

    We demonstrate the application of polymer planar Bragg gratings for multi-axial strain sensing and particularly highlight simultaneous 2D strain measurement. A polymer planar Bragg grating (PPBG) fabricated with a single writing step in bulk polymethylmethacrylate is used for measuring both tensile and compressive strain at various angles. It is shown that the sensitivity of the PPBG strongly depends on the angle between the optical waveguide into which the grating is inscribed and the direction along which the mechanical load is applied. Additionally, a 2D PPBG fabricated by writing two Bragg gratings angularly displaced from each other into a single polymer platelet is bonded to a stainless steel plate. The two reflected wavelengths exhibit different sensitivities while tested toward tensile and compressive strain. These characteristics make 2D PPBG suitable for measuring multi-axial tensile and compressive strain. PMID:25686313

  15. Simultaneous 2D strain sensing using polymer planar Bragg gratings.

    PubMed

    Rosenberger, Manuel; Eisenbeil, Waltraud; Schmauss, Bernhard; Hellmann, Ralf

    2015-01-01

    We demonstrate the application of polymer planar Bragg gratings for multi-axial strain sensing and particularly highlight simultaneous 2D strain measurement. A polymer planar Bragg grating (PPBG) fabricated with a single writing step in bulk polymethylmethacrylate is used for measuring both tensile and compressive strain at various angles. It is shown that the sensitivity of the PPBG strongly depends on the angle between the optical waveguide into which the grating is inscribed and the direction along which the mechanical load is applied. Additionally, a 2D PPBG fabricated by writing two Bragg gratings angularly displaced from each other into a single polymer platelet is bonded to a stainless steel plate. The two reflected wavelengths exhibit different sensitivities while tested toward tensile and compressive strain. These characteristics make 2D PPBG suitable for measuring multi-axial tensile and compressive strain. PMID:25686313

  16. Focusing surface wave imaging with flexible 2D array

    NASA Astrophysics Data System (ADS)

    Zhou, Shiyuan; Fu, Junqiang; Li, Zhe; Xu, Chunguang; Xiao, Dingguo; Wang, Shaohan

    2016-04-01

    Curved surface is widely exist in key parts of energy and power equipment, such as, turbine blade cylinder block and so on. Cycling loading and harsh working condition of enable fatigue cracks appear on the surface. The crack should be found in time to avoid catastrophic damage to the equipment. A flexible 2D array transducer was developed. 2D Phased Array focusing method (2DPA), Mode-Spatial Double Phased focusing method (MSDPF) and the imaging method using the flexible 2D array probe are studied. Experiments using these focusing and imaging method are carried out. Surface crack image is obtained with both 2DPA and MSDPF focusing method. It have been proved that MSDPF can be more adaptable for curved surface and more calculate efficient than 2DPA.

  17. 2D bifurcations and Newtonian properties of memristive Chua's circuits

    NASA Astrophysics Data System (ADS)

    Marszalek, W.; Podhaisky, H.

    2016-01-01

    Two interesting properties of Chua's circuits are presented. First, two-parameter bifurcation diagrams of Chua's oscillatory circuits with memristors are presented. To obtain various 2D bifurcation images a substantial numerical effort, possibly with parallel computations, is needed. The numerical algorithm is described first and its numerical code for 2D bifurcation image creation is available for free downloading. Several color 2D images and the corresponding 1D greyscale bifurcation diagrams are included. Secondly, Chua's circuits are linked to Newton's law φ ''= F(t,φ,φ')/m with φ=\\text{flux} , constant m > 0, and the force term F(t,φ,φ') containing memory terms. Finally, the jounce scalar equations for Chua's circuits are also discussed.

  18. Microscale 2D separation systems for proteomic analysis

    PubMed Central

    Xu, Xin; Liu, Ke; Fan, Z. Hugh

    2012-01-01

    Microscale 2D separation systems have been implemented in capillaries and microfabricated channels. They offer advantages of faster analysis, higher separation efficiency and less sample consumption than the conventional methods, such as liquid chromatography (LC) in a column and slab gel electrophoresis. In this article, we review their recent advancement, focusing on three types of platforms, including 2D capillary electrophoresis (CE), CE coupling with capillary LC, and microfluidic devices. A variety of CE and LC modes have been employed to construct 2D separation systems via sophistically designed interfaces. Coupling of different separation modes has also been realized in a number of microfluidic devices. These separation systems have been applied for the proteomic analysis of various biological samples, ranging from a single cell to tumor tissues. PMID:22462786

  19. Progressive-Relapsing MS (PRMS)

    MedlinePlus

    ... the disease process in MS and in MRI technology. Individuals who were previously diagnosed with progressive-relapsing MS would now be ... The National MS Society is Here to Help Need More Information? We ...

  20. Real-time 2-D temperature imaging using ultrasound.

    PubMed

    Liu, Dalong; Ebbini, Emad S

    2010-01-01

    We have previously introduced methods for noninvasive estimation of temperature change using diagnostic ultrasound. The basic principle was validated both in vitro and in vivo by several groups worldwide. Some limitations remain, however, that have prevented these methods from being adopted in monitoring and guidance of minimally invasive thermal therapies, e.g., RF ablation and high-intensity-focused ultrasound (HIFU). In this letter, we present first results from a real-time system for 2-D imaging of temperature change using pulse-echo ultrasound. The front end of the system is a commercially available scanner equipped with a research interface, which allows the control of imaging sequence and access to the RF data in real time. A high-frame-rate 2-D RF acquisition mode, M2D, is used to capture the transients of tissue motion/deformations in response to pulsed HIFU. The M2D RF data is streamlined to the back end of the system, where a 2-D temperature imaging algorithm based on speckle tracking is implemented on a graphics processing unit. The real-time images of temperature change are computed on the same spatial and temporal grid of the M2D RF data, i.e., no decimation. Verification of the algorithm was performed by monitoring localized HIFU-induced heating of a tissue-mimicking elastography phantom. These results clearly demonstrate the repeatability and sensitivity of the algorithm. Furthermore, we present in vitro results demonstrating the possible use of this algorithm for imaging changes in tissue parameters due to HIFU-induced lesions. These results clearly demonstrate the value of the real-time data streaming and processing in monitoring, and guidance of minimally invasive thermotherapy. PMID:19884075

  1. Src Homology 2 Domain Containing Protein 5 (SH2D5) Binds the Breakpoint Cluster Region Protein, BCR, and Regulates Levels of Rac1-GTP*

    PubMed Central

    Gray, Elizabeth J.; Petsalaki, Evangelia; James, D. Andrew; Bagshaw, Richard D.; Stacey, Melissa M.; Rocks, Oliver; Gingras, Anne-Claude; Pawson, Tony

    2014-01-01

    SH2D5 is a mammalian-specific, uncharacterized adaptor-like protein that contains an N-terminal phosphotyrosine-binding domain and a C-terminal Src homology 2 (SH2) domain. We show that SH2D5 is highly enriched in adult mouse brain, particularly in Purkinjie cells in the cerebellum and the cornu ammonis of the hippocampus. Despite harboring two potential phosphotyrosine (Tyr(P)) recognition domains, SH2D5 binds minimally to Tyr(P) ligands, consistent with the absence of a conserved Tyr(P)-binding arginine residue in the SH2 domain. Immunoprecipitation coupled to mass spectrometry (IP-MS) from cultured cells revealed a prominent association of SH2D5 with breakpoint cluster region protein, a RacGAP that is also highly expressed in brain. This interaction occurred between the phosphotyrosine-binding domain of SH2D5 and an NxxF motif located within the N-terminal region of the breakpoint cluster region. siRNA-mediated depletion of SH2D5 in a neuroblastoma cell line, B35, induced a cell rounding phenotype correlated with low levels of activated Rac1-GTP, suggesting that SH2D5 affects Rac1-GTP levels. Taken together, our data provide the first characterization of the SH2D5 signaling protein. PMID:25331951

  2. Design of the LRP airfoil series using 2D CFD

    NASA Astrophysics Data System (ADS)

    Zahle, Frederik; Bak, Christian; Sørensen, Niels N.; Vronsky, Tomas; Gaudern, Nicholas

    2014-06-01

    This paper describes the design and wind tunnel testing of a high-Reynolds number, high lift airfoil series designed for wind turbines. The airfoils were designed using direct gradient- based numerical multi-point optimization based on a Bezier parameterization of the shape, coupled to the 2D Navier-Stokes flow solver EllipSys2D. The resulting airfoils, the LRP2-30 and LRP2-36, achieve both higher operational lift coefficients and higher lift to drag ratios compared to the equivalent FFA-W3 airfoils.

  3. Quantum process tomography by 2D fluorescence spectroscopy

    SciTech Connect

    Pachón, Leonardo A.; Marcus, Andrew H.; Aspuru-Guzik, Alán

    2015-06-07

    Reconstruction of the dynamics (quantum process tomography) of the single-exciton manifold in energy transfer systems is proposed here on the basis of two-dimensional fluorescence spectroscopy (2D-FS) with phase-modulation. The quantum-process-tomography protocol introduced here benefits from, e.g., the sensitivity enhancement ascribed to 2D-FS. Although the isotropically averaged spectroscopic signals depend on the quantum yield parameter Γ of the doubly excited-exciton manifold, it is shown that the reconstruction of the dynamics is insensitive to this parameter. Applications to foundational and applied problems, as well as further extensions, are discussed.

  4. Evaluation of 2D ceramic matrix composites in aeroconvective environments

    NASA Technical Reports Server (NTRS)

    Riccitiello, Salvatore R.; Love, Wendell L.; Balter-Peterson, Aliza

    1992-01-01

    An evaluation is conducted of a novel ceramic-matrix composite (CMC) material system for use in the aeroconvective-heating environments encountered by the nose caps and wing leading edges of such aerospace vehicles as the Space Shuttle, during orbit-insertion and reentry from LEO. These CMCs are composed of an SiC matrix that is reinforced with Nicalon, Nextel, or carbon refractory fibers in a 2D architecture. The test program conducted for the 2D CMCs gave attention to their subsurface oxidation.

  5. Radiative heat transfer in 2D Dirac materials

    DOE PAGESBeta

    Rodriguez-López, Pablo; Tse, Wang -Kong; Dalvit, Diego A. R.

    2015-05-12

    We compute the radiative heat transfer between two sheets of 2D Dirac materials, including topological Chern insulators and graphene, within the framework of the local approximation for the optical response of these materials. In this approximation, which neglects spatial dispersion, we derive both numerically and analytically the short-distance asymptotic of the near-field heat transfer in these systems, and show that it scales as the inverse of the distance between the two sheets. In conclusion, we discuss the limitations to the validity of this scaling law imposed by spatial dispersion in 2D Dirac materials.

  6. Nomenclature for human CYP2D6 alleles.

    PubMed

    Daly, A K; Brockmöller, J; Broly, F; Eichelbaum, M; Evans, W E; Gonzalez, F J; Huang, J D; Idle, J R; Ingelman-Sundberg, M; Ishizaki, T; Jacqz-Aigrain, E; Meyer, U A; Nebert, D W; Steen, V M; Wolf, C R; Zanger, U M

    1996-06-01

    To standardize CYP2D6 allele nomenclature, and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that alleles be designated by CYP2D6 followed by an asterisk and a combination of roman letters and arabic numerals distinct for each allele with the number specifying the key mutation and, where appropriate, a letter specifying additional mutations. Criteria for classification as a separate allele and protein nomenclature are also presented. PMID:8807658

  7. The 2D large deformation analysis using Daubechies wavelet

    NASA Astrophysics Data System (ADS)

    Liu, Yanan; Qin, Fei; Liu, Yinghua; Cen, Zhangzhi

    2010-01-01

    In this paper, Daubechies (DB) wavelet is used for solution of 2D large deformation problems. Because the DB wavelet scaling functions are directly used as basis function, no meshes are needed in function approximation. Using the DB wavelet, the solution formulations based on total Lagrangian approach for two-dimensional large deformation problems are established. Due to the lack of Kroneker delta properties in wavelet scaling functions, Lagrange multipliers are used for imposition of boundary condition. Numerical examples of 2D large deformation problems illustrate that this method is effective and stable.

  8. Optical imaging systems analyzed with a 2D template.

    PubMed

    Haim, Harel; Konforti, Naim; Marom, Emanuel

    2012-05-10

    Present determination of optical imaging systems specifications are based on performance values and modulation transfer function results carried with a 1D resolution template (such as the USAF resolution target or spoke templates). Such a template allows determining image quality, resolution limit, and contrast. Nevertheless, the conventional 1D template does not provide satisfactory results, since most optical imaging systems handle 2D objects for which imaging system response may be different by virtue of some not readily observable spatial frequencies. In this paper we derive and analyze contrast transfer function results obtained with 1D as well as 2D templates. PMID:22614498

  9. 2dF grows up: Echidna for the AAT

    NASA Astrophysics Data System (ADS)

    McGrath, Andrew; Barden, Sam; Miziarski, Stan; Rambold, William; Smith, Greg

    2008-07-01

    We present the concept design of a new fibre positioner and spectrograph system for the Anglo-Australian Telescope, as a proposed enhancement to the Anglo-Australian Observatory's well-known 2dF facility. A four-fold multiplex enhancement is accomplished by replacing the 400-fibre 2dF fibre positioning robot with a 1600-fibre Echidna unit, feeding three clones of the AAOmega optical spectrograph. Such a facility has the capability of a redshift 1 survey of a large fraction of the southern sky, collecting five to ten thousand spectra per night for a million-galaxy survey.

  10. CH2D+, the Search for the Holy Grail

    NASA Astrophysics Data System (ADS)

    Roueff, Evelyne; Gerin, Maryvonne; Lis, Dariusz C.; Wootten, Alwyn; Marcelino, Nuria; Cernicharo, Jose; Tercero, Belen

    2013-10-01

    CH2D+, the singly deuterated counterpart of CH3+, offers an alternative way to mediate formation of deuterated species at temperatures of several tens of Kelvin, as compared to the release of deuterated species from grains. We report a longstanding observational search for this molecular ion, whose rotational spectroscopy is not yet completely secure. We summarize the main spectroscopic properties of this molecule and discuss the chemical network leading to the formation of CH2D+, with explicit account of the ortho/para forms of H2, H3+, and CH3+. Astrochemical models support the presence of this molecular ion in moderately warm environments at a marginal level.

  11. EM 2dV1.0.F

    2012-01-05

    Code is for a layered electric medium with 2d structure. Includes air-earth interface at node z=2.. The electric ex and ez fields are calculated on edges of elemental grid and magnetic field hy is calculated on the face of the elemental grid. The code allows for a layered earth with 2d structures. Solutions of coupled first order Maxwell's equations are solved in the two dimensional environment using a finite- difference scheme on a staggered spationamore » and temporal grid.« less

  12. Noninvasive deep Raman detection with 2D correlation analysis

    NASA Astrophysics Data System (ADS)

    Kim, Hyung Min; Park, Hyo Sun; Cho, Youngho; Jin, Seung Min; Lee, Kang Taek; Jung, Young Mee; Suh, Yung Doug

    2014-07-01

    The detection of poisonous chemicals enclosed in daily necessaries is prerequisite essential for homeland security with the increasing threat of terrorism. For the detection of toxic chemicals, we combined a sensitive deep Raman spectroscopic method with 2D correlation analysis. We obtained the Raman spectra from concealed chemicals employing spatially offset Raman spectroscopy in which incident line-shaped light experiences multiple scatterings before being delivered to inner component and yielding deep Raman signal. Furthermore, we restored the pure Raman spectrum of each component using 2D correlation spectroscopic analysis with chemical inspection. Using this method, we could elucidate subsurface component under thick powder and packed contents in a bottle.

  13. On 2D bisection method for double eigenvalue problems

    SciTech Connect

    Ji, X.

    1996-06-01

    The two-dimensional bisection method presented in (SIAM J. Matrix Anal. Appl. 13(4), 1085 (1992)) is efficient for solving a class of double eigenvalue problems. This paper further extends the 2D bisection method of full matrix cases and analyses its stability. As in a single parameter case, the 2D bisection method is very stable for the tridiagonal matrix triples satisfying the symmetric-definite condition. Since the double eigenvalue problems arise from two-parameter boundary value problems, an estimate of the discretization error in eigenpairs is also given. Some numerical examples are included. 42 refs., 1 tab.

  14. Experimental validation of equations for 2D DIC uncertainty quantification.

    SciTech Connect

    Reu, Phillip L.; Miller, Timothy J.

    2010-03-01

    Uncertainty quantification (UQ) equations have been derived for predicting matching uncertainty in two-dimensional image correlation a priori. These equations include terms that represent the image noise and image contrast. Researchers at the University of South Carolina have extended previous 1D work to calculate matching errors in 2D. These 2D equations have been coded into a Sandia National Laboratories UQ software package to predict the uncertainty for DIC images. This paper presents those equations and the resulting error surfaces for trial speckle images. Comparison of the UQ results with experimentally subpixel-shifted images is also discussed.

  15. 2D molybdenum disulphide (2D-MoS2) modified electrodes explored towards the oxygen reduction reaction.

    PubMed

    Rowley-Neale, Samuel J; Fearn, Jamie M; Brownson, Dale A C; Smith, Graham C; Ji, Xiaobo; Banks, Craig E

    2016-08-21

    Two-dimensional molybdenum disulphide nanosheets (2D-MoS2) have proven to be an effective electrocatalyst, with particular attention being focused on their use towards increasing the efficiency of the reactions associated with hydrogen fuel cells. Whilst the majority of research has focused on the Hydrogen Evolution Reaction (HER), herein we explore the use of 2D-MoS2 as a potential electrocatalyst for the much less researched Oxygen Reduction Reaction (ORR). We stray from literature conventions and perform experiments in 0.1 M H2SO4 acidic electrolyte for the first time, evaluating the electrochemical performance of the ORR with 2D-MoS2 electrically wired/immobilised upon several carbon based electrodes (namely; Boron Doped Diamond (BDD), Edge Plane Pyrolytic Graphite (EPPG), Glassy Carbon (GC) and Screen-Printed Electrodes (SPE)) whilst exploring a range of 2D-MoS2 coverages/masses. Consequently, the findings of this study are highly applicable to real world fuel cell applications. We show that significant improvements in ORR activity can be achieved through the careful selection of the underlying/supporting carbon materials that electrically wire the 2D-MoS2 and utilisation of an optimal mass of 2D-MoS2. The ORR onset is observed to be reduced to ca. +0.10 V for EPPG, GC and SPEs at 2D-MoS2 (1524 ng cm(-2) modification), which is far closer to Pt at +0.46 V compared to bare/unmodified EPPG, GC and SPE counterparts. This report is the first to demonstrate such beneficial electrochemical responses in acidic conditions using a 2D-MoS2 based electrocatalyst material on a carbon-based substrate (SPEs in this case). Investigation of the beneficial reaction mechanism reveals the ORR to occur via a 4 electron process in specific conditions; elsewhere a 2 electron process is observed. This work offers valuable insights for those wishing to design, fabricate and/or electrochemically test 2D-nanosheet materials towards the ORR. PMID:27448174

  16. Vacuum compatible sample positioning device for matrix assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry imaging

    PubMed Central

    Aizikov, Konstantin; Smith, Donald F.; Chargin, David A.; Ivanov, Sergei; Lin, Tzu-Yung; Heeren, Ron M. A.; O’Connor, Peter B.

    2011-01-01

    The high mass accuracy and resolving power of Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR MS) make them ideal mass detectors for mass spectrometry imaging (MSI), promising to provide unmatched molecular resolution capabilities. The intrinsic low tolerance of FT-ICR MS to RF interference, however, along with typically vertical positioning of the sample, and MSI acquisition speed requirements present numerous engineering challenges in creating robotics capable of achieving the spatial resolution to match. This work discusses a two-dimensional positioning stage designed to address these issues. The stage is capable of operating in ∼1 × 10–8 mbar vacuum. The range of motion is set to 100 mm × 100 mm to accommodate large samples, while the positioning accuracy is demonstrated to be less than 0.4 micron in both directions under vertical load over the entire range. This device was integrated into three different matrix assisted laser desorption/ionization (MALDI) FT-ICR instruments and showed no detectable RF noise. The “oversampling” MALDI-MSI experiments, under which the sample is completely ablated at each position, followed by the target movement of the distance smaller than the laser beam, conducted on the custom-built 7T FT-ICR MS demonstrate the stability and positional accuracy of the stage robotics which delivers high spatial resolution mass spectral images at a fraction of the laser spot diameter. PMID:21639522

  17. Vacuum compatible sample positioning device for matrix assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry imaging

    SciTech Connect

    Aizikov, Konstantin; Lin, Tzu-Yung; Smith, Donald F.; Heeren, Ron M. A.; Chargin, David A.; Ivanov, Sergei; O'Connor, Peter B.

    2011-05-15

    The high mass accuracy and resolving power of Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR MS) make them ideal mass detectors for mass spectrometry imaging (MSI), promising to provide unmatched molecular resolution capabilities. The intrinsic low tolerance of FT-ICR MS to RF interference, however, along with typically vertical positioning of the sample, and MSI acquisition speed requirements present numerous engineering challenges in creating robotics capable of achieving the spatial resolution to match. This work discusses a two-dimensional positioning stage designed to address these issues. The stage is capable of operating in {approx}1 x 10{sup -8} mbar vacuum. The range of motion is set to 100 mm x 100 mm to accommodate large samples, while the positioning accuracy is demonstrated to be less than 0.4 micron in both directions under vertical load over the entire range. This device was integrated into three different matrix assisted laser desorption/ionization (MALDI) FT-ICR instruments and showed no detectable RF noise. The ''oversampling'' MALDI-MSI experiments, under which the sample is completely ablated at each position, followed by the target movement of the distance smaller than the laser beam, conducted on the custom-built 7T FT-ICR MS demonstrate the stability and positional accuracy of the stage robotics which delivers high spatial resolution mass spectral images at a fraction of the laser spot diameter.

  18. ELLIPT2D: A Flexible Finite Element Code Written Python

    SciTech Connect

    Pletzer, A.; Mollis, J.C.

    2001-03-22

    The use of the Python scripting language for scientific applications and in particular to solve partial differential equations is explored. It is shown that Python's rich data structure and object-oriented features can be exploited to write programs that are not only significantly more concise than their counter parts written in Fortran, C or C++, but are also numerically efficient. To illustrate this, a two-dimensional finite element code (ELLIPT2D) has been written. ELLIPT2D provides a flexible and easy-to-use framework for solving a large class of second-order elliptic problems. The program allows for structured or unstructured meshes. All functions defining the elliptic operator are user supplied and so are the boundary conditions, which can be of Dirichlet, Neumann or Robbins type. ELLIPT2D makes extensive use of dictionaries (hash tables) as a way to represent sparse matrices.Other key features of the Python language that have been widely used include: operator over loading, error handling, array slicing, and the Tkinter module for building graphical use interfaces. As an example of the utility of ELLIPT2D, a nonlinear solution of the Grad-Shafranov equation is computed using a Newton iterative scheme. A second application focuses on a solution of the toroidal Laplace equation coupled to a magnetohydrodynamic stability code, a problem arising in the context of magnetic fusion research.

  19. Rheological Properties of Quasi-2D Fluids in Microgravity

    NASA Technical Reports Server (NTRS)

    Stannarius, Ralf; Trittel, Torsten; Eremin, Alexey; Harth, Kirsten; Clark, Noel; Maclennan, Joseph; Glaser, Matthew; Park, Cheol; Hall, Nancy; Tin, Padetha

    2015-01-01

    In recent years, research on complex fluids and fluids in restricted geometries has attracted much attention in the scientific community. This can be attributed not only to the development of novel materials based on complex fluids but also to a variety of important physical phenomena which have barely been explored. One example is the behavior of membranes and thin fluid films, which can be described by two-dimensional (2D) rheology behavior that is quite different from 3D fluids. In this study, we have investigated the rheological properties of freely suspended films of a thermotropic liquid crystal in microgravity experiments. This model system mimics isotropic and anisotropic quasi 2D fluids [46]. We use inkjet printing technology to dispense small droplets (inclusions) onto the film surface. The motion of these inclusions provides information on the rheological properties of the films and allows the study of a variety of flow instabilities. Flat films have been investigated on a sub-orbital rocket flight and curved films (bubbles) have been studied in the ISS project OASIS. Microgravity is essential when the films are curved in order to avoid sedimentation. The experiments yield the mobility of the droplets in the films as well as the mutual mobility of pairs of particles. Experimental results will be presented for 2D-isotropic (smectic-A) and 2D-nematic (smectic-C) phases.

  20. Creation of a scalar potential in 2D dilaton gravity

    SciTech Connect

    Behrndt, K.

    1994-09-01

    The authors investigate quantum corrections of the 2-d dilaton gravity near the singularity. Their motivation comes from a s-wave reduced cosmological solution which is classically singular in the scalar fields (dilaton and moduli). As a result they find, that the singularity disappears and a dilaton/moduli potential is created.

  1. NKG2D ligands mediate immunosurveillance of senescent cells

    PubMed Central

    Moshayev, Zhana; Vadai, Ezra; Wensveen, Felix; Ben-Dor, Shifra; Golani, Ofra; Polic, Bojan; Krizhanovsky, Valery

    2016-01-01

    Cellular senescence is a stress response mechanism that limits tumorigenesis and tissue damage. Induction of cellular senescence commonly coincides with an immunogenic phenotype that promotes self-elimination by components of the immune system, thereby facilitating tumor suppression and limiting excess fibrosis during wound repair. The mechanisms by which senescent cells regulate their immune surveillance are not completely understood. Here we show that ligands of an activating Natural Killer (NK) cell receptor (NKG2D), MICA and ULBP2 are consistently up-regulated following induction of replicative senescence, oncogene-induced senescence and DNA damage - induced senescence. MICA and ULBP2 proteins are necessary for efficient NK-mediated cytotoxicity towards senescent fibroblasts. The mechanisms regulating the initial expression of NKG2D ligands in senescent cells are dependent on a DNA damage response, whilst continuous expression of these ligands is regulated by the ERK signaling pathway. In liver fibrosis, the accumulation of senescent activated stellate cells is increased in mice lacking NKG2D receptor leading to increased fibrosis. Overall, our results provide new insights into the mechanisms regulating the expression of immune ligands in senescent cells and reveal the importance of NKG2D receptor-ligand interaction in protecting against liver fibrosis. PMID:26878797

  2. Discrepant Results in a 2-D Marble Collision

    ERIC Educational Resources Information Center

    Kalajian, Peter

    2013-01-01

    Video analysis of 2-D collisions is an excellent way to investigate conservation of linear momentum. The often-desired experimental design goal is to minimize the momentum loss in order to demonstrate the conservation law. An air table with colliding pucks is an ideal medium for this experiment, but such equipment is beyond the budget of many…

  3. Validation and testing of the VAM2D computer code

    SciTech Connect

    Kool, J.B.; Wu, Y.S. )

    1991-10-01

    This document describes two modeling studies conducted by HydroGeoLogic, Inc. for the US NRC under contract no. NRC-04089-090, entitled, Validation and Testing of the VAM2D Computer Code.'' VAM2D is a two-dimensional, variably saturated flow and transport code, with applications for performance assessment of nuclear waste disposal. The computer code itself is documented in a separate NUREG document (NUREG/CR-5352, 1989). The studies presented in this report involve application of the VAM2D code to two diverse subsurface modeling problems. The first one involves modeling of infiltration and redistribution of water and solutes in an initially dry, heterogeneous field soil. This application involves detailed modeling over a relatively short, 9-month time period. The second problem pertains to the application of VAM2D to the modeling of a waste disposal facility in a fractured clay, over much larger space and time scales and with particular emphasis on the applicability and reliability of using equivalent porous medium approach for simulating flow and transport in fractured geologic media. Reflecting the separate and distinct nature of the two problems studied, this report is organized in two separate parts. 61 refs., 31 figs., 9 tabs.

  4. On Regularity Criteria for the 2D Generalized MHD System

    NASA Astrophysics Data System (ADS)

    Jiang, Zaihong; Wang, Yanan; Zhou, Yong

    2016-06-01

    This paper deals with the problem of regularity criteria for the 2D generalized MHD system with fractional dissipative terms {-Λ^{2α}u} for the velocity field and {-Λ^{2β}b} for the magnetic field respectively. Various regularity criteria are established to guarantee smoothness of solutions. It turns out that our regularity criteria imply previous global existence results naturally.

  5. Dispersionless 2D Toda hierarchy, Hurwitz numbers and Riemann theorem

    NASA Astrophysics Data System (ADS)

    Natanzon, Sergey M.

    2016-01-01

    We describe all formal symmetric solutions of dispersionless 2D Toda hierarchy. This classification we use for solving of two classical problems: 1) The calculation of conformal mapping of an arbitrary simply connected domain to the standard disk; 2) Calculation of 2- Hurwitz numbers of genus 0.

  6. 2D signature for detection and identification of drugs

    NASA Astrophysics Data System (ADS)

    Trofimov, Vyacheslav A.; Varentsova, Svetlana A.; Shen, Jingling; Zhang, Cunlin; Zhou, Qingli; Shi, Yulei

    2011-06-01

    The method of spectral dynamics analysis (SDA-method) is used for obtaining the2D THz signature of drugs. This signature is used for the detection and identification of drugs with similar Fourier spectra by transmitted THz signal. We discuss the efficiency of SDA method for the identification problem of pure methamphetamine (MA), methylenedioxyamphetamine (MDA), 3, 4-methylenedioxymethamphetamine (MDMA) and Ketamine.

  7. RADMC: A 2-D Continuum Radiative Transfer Tool

    NASA Astrophysics Data System (ADS)

    Dullemond, C. P.

    2011-08-01

    RADMC is a 2-D Monte-Carlo code for dust continuum radiative transfer circumstellar disks and envelopes. It is based on the method of Bjorkman & Wood (ApJ 2001, 554, 615), but with several modifications to produce smoother results with fewer photon packages.

  8. Kinematics of segregating granular mixtures in quasi-2D heaps

    NASA Astrophysics Data System (ADS)

    Fan, Yi; Umbanhowar, Paul; Ottino, Julio; Lueptow, Richard

    2012-11-01

    Segregation of granular mixtures of different sized particles in heap flow appears in a variety of contexts. Our recent experiments showed that when bi-disperse mixtures of different sized spherical particles fill a quasi-two dimensional (2D) silo, three different final heap configurations - stratified, segregated, and mixed - occur, depending on either 2D flow rate or heap rise velocity. However, since it is difficult to measure the kinematic details of the segregating granular mixtures in heap flow experimentally, the underlying mechanisms for how 2D flow rate or heap rise velocity influences final particle configurations have not been well understood. In this work, we use the discrete element method (DEM) to simulate heap flow of bi-disperse mixtures in experimental scale quasi-2D heaps. The final particle distributions in the simulations agree quantitatively with experiments. We measure several key kinematic properties of the segregating granular mixtures including the local flow rate, velocity, and flowing layer thickness. We correlate the characteristics of these kinematic properties with the local particle distributions of the mixtures. This provides new insights for understanding the mechanisms of segregation and stratification in heap flow including the linear decrease in flow rate and maximum velocity down the heap as well as the relatively constant flowing layer thickness along the length of the heap. Funded by Dow Chemical Co.

  9. On the phase diagram of 2d Lorentzian Quantum Gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, Jan; Anagnostopoulos, K. N.; Loll, R.

    The phase diagram of 2d Lorentzian quantum gravity (LQG) coupled to conformal matter is studied. A phase transition is observed at c = c crit ( {1}/{2} < c crit < 4) which can be thought of as the analogue of the c = 1 barrier of Euclidean quantum gravity (EQG). The non-trivial properties of the quantum geometry are discussed.

  10. Optoelectronics of supported and suspended 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Bolotin, Kirill

    2014-03-01

    Two-dimensional semiconductors, materials such monolayer molybdenum disulfide (MoS2) are characterized by strong spin-orbit and electron-electron interactions. However, both electronic and optoelectronic properties of these materials are dominated by disorder-related scattering. In this talk, we investigate approaches to reduce scattering and explore physical phenomena arising in intrinsic 2D semiconductors. First, we discuss fabrication of pristine suspended monolayer MoS2 and use photocurrent spectroscopy measurements to study excitons in this material. We observe band-edge and van Hove singularity excitons and estimate their binding energies. Furthermore, we study dissociation of these excitons and uncover the mechanism of their contribution to photoresponse of MoS2. Second, we study strain-induced modification of bandstructures of 2D semiconductors. With increasing strain, we find large and controllable band gap reduction of both single- and bi-layer MoS2. We also detect experimental signatures consistent with strain-induced transition from direct to indirect band gap in monolayer MoS2. Finally, we fabricate heterostructures of dissimilar 2D semiconductors and study their photoresponse. For closely spaced 2D semiconductors we detect charge transfer, while for separation larger than 10nm we observe Forster-like energy transfer between excitations in different layers.

  11. 2-D Imaging of Electron Temperature in Tokamak Plasmas

    SciTech Connect

    T. Munsat; E. Mazzucato; H. Park; C.W. Domier; M. Johnson; N.C. Luhmann Jr.; J. Wang; Z. Xia; I.G.J. Classen; A.J.H. Donne; M.J. van de Pol

    2004-07-08

    By taking advantage of recent developments in millimeter wave imaging technology, an Electron Cyclotron Emission Imaging (ECEI) instrument, capable of simultaneously measuring 128 channels of localized electron temperature over a 2-D map in the poloidal plane, has been developed for the TEXTOR tokamak. Data from the new instrument, detailing the MHD activity associated with a sawtooth crash, is presented.

  12. NKG2D ligands mediate immunosurveillance of senescent cells.

    PubMed

    Sagiv, Adi; Burton, Dominick G A; Moshayev, Zhana; Vadai, Ezra; Wensveen, Felix; Ben-Dor, Shifra; Golani, Ofra; Polic, Bojan; Krizhanovsky, Valery

    2016-02-01

    Cellular senescence is a stress response mechanism that limits tumorigenesis and tissue damage. Induction of cellular senescence commonly coincides with an immunogenic phenotype that promotes self-elimination by components of the immune system, thereby facilitating tumor suppression and limiting excess fibrosis during wound repair. The mechanisms by which senescent cells regulate their immune surveillance are not completely understood. Here we show that ligands of an activating Natural Killer (NK) cell receptor (NKG2D), MICA and ULBP2 are consistently up-regulated following induction of replicative senescence, oncogene-induced senescence and DNA damage - induced senescence. MICA and ULBP2 proteins are necessary for efficient NK-mediated cytotoxicity towards senescent fibroblasts. The mechanisms regulating the initial expression of NKG2D ligands in senescent cells are dependent on a DNA damage response, whilst continuous expression of these ligands is regulated by the ERK signaling pathway. In liver fibrosis, the accumulation of senescent activated stellate cells is increased in mice lacking NKG2D receptor leading to increased fibrosis. Overall, our results provide new insights into the mechanisms regulating the expression of immune ligands in senescent cells and reveal the importance of NKG2D receptor-ligand interaction in protecting against liver fibrosis. PMID:26878797

  13. 2D molybdenum disulphide (2D-MoS2) modified electrodes explored towards the oxygen reduction reaction

    NASA Astrophysics Data System (ADS)

    Rowley-Neale, Samuel J.; Fearn, Jamie M.; Brownson, Dale A. C.; Smith, Graham C.; Ji, Xiaobo; Banks, Craig E.

    2016-08-01

    Two-dimensional molybdenum disulphide nanosheets (2D-MoS2) have proven to be an effective electrocatalyst, with particular attention being focused on their use towards increasing the efficiency of the reactions associated with hydrogen fuel cells. Whilst the majority of research has focused on the Hydrogen Evolution Reaction (HER), herein we explore the use of 2D-MoS2 as a potential electrocatalyst for the much less researched Oxygen Reduction Reaction (ORR). We stray from literature conventions and perform experiments in 0.1 M H2SO4 acidic electrolyte for the first time, evaluating the electrochemical performance of the ORR with 2D-MoS2 electrically wired/immobilised upon several carbon based electrodes (namely; Boron Doped Diamond (BDD), Edge Plane Pyrolytic Graphite (EPPG), Glassy Carbon (GC) and Screen-Printed Electrodes (SPE)) whilst exploring a range of 2D-MoS2 coverages/masses. Consequently, the findings of this study are highly applicable to real world fuel cell applications. We show that significant improvements in ORR activity can be achieved through the careful selection of the underlying/supporting carbon materials that electrically wire the 2D-MoS2 and utilisation of an optimal mass of 2D-MoS2. The ORR onset is observed to be reduced to ca. +0.10 V for EPPG, GC and SPEs at 2D-MoS2 (1524 ng cm-2 modification), which is far closer to Pt at +0.46 V compared to bare/unmodified EPPG, GC and SPE counterparts. This report is the first to demonstrate such beneficial electrochemical responses in acidic conditions using a 2D-MoS2 based electrocatalyst material on a carbon-based substrate (SPEs in this case). Investigation of the beneficial reaction mechanism reveals the ORR to occur via a 4 electron process in specific conditions; elsewhere a 2 electron process is observed. This work offers valuable insights for those wishing to design, fabricate and/or electrochemically test 2D-nanosheet materials towards the ORR.Two-dimensional molybdenum disulphide nanosheets

  14. Recursive anisotropic 2-D Gaussian filtering based on a triple-axis decomposition.

    PubMed

    Lam, Stanley Yiu Man; Shi, Bertram E

    2007-07-01

    We describe a recursive algorithm for anisotropic 2-D Gaussian filtering, based on separating the filter into the cascade of three, rather two, 1-D filters. The filters operate along axes obtained by integer horizontal and/or vertical pixel shifts. This eliminates interpolation, which removes spatial inhomogeneity in the filter, and produces more elliptically shaped kernels. It also results in a more regular filter structure, which facilitates implementation in DSP chips. Finally, it improves matching between filters with the same eccentricity and width, but different orientations. Our analysis and experiments indicate that the computational complexity is similar to an algorithm that operates along two axes (<11 ms for a 512 x 512 image using a 3.2-GHz Pentium 4 PC). On the other hand, given a limited set of basis filter axes, there is an orientation dependent lower bound on the achievable aspect ratios. PMID:17605390

  15. 2D/3D Image Registration using Regression Learning

    PubMed Central

    Chou, Chen-Rui; Frederick, Brandon; Mageras, Gig; Chang, Sha; Pizer, Stephen

    2013-01-01

    In computer vision and image analysis, image registration between 2D projections and a 3D image that achieves high accuracy and near real-time computation is challenging. In this paper, we propose a novel method that can rapidly detect an object’s 3D rigid motion or deformation from a 2D projection image or a small set thereof. The method is called CLARET (Correction via Limited-Angle Residues in External Beam Therapy) and consists of two stages: registration preceded by shape space and regression learning. In the registration stage, linear operators are used to iteratively estimate the motion/deformation parameters based on the current intensity residue between the target projec-tion(s) and the digitally reconstructed radiograph(s) (DRRs) of the estimated 3D image. The method determines the linear operators via a two-step learning process. First, it builds a low-order parametric model of the image region’s motion/deformation shape space from its prior 3D images. Second, using learning-time samples produced from the 3D images, it formulates the relationships between the model parameters and the co-varying 2D projection intensity residues by multi-scale linear regressions. The calculated multi-scale regression matrices yield the coarse-to-fine linear operators used in estimating the model parameters from the 2D projection intensity residues in the registration. The method’s application to Image-guided Radiation Therapy (IGRT) requires only a few seconds and yields good results in localizing a tumor under rigid motion in the head and neck and under respiratory deformation in the lung, using one treatment-time imaging 2D projection or a small set thereof. PMID:24058278

  16. Resonances of piezoelectric plate with embedded 2D electron system

    NASA Astrophysics Data System (ADS)

    Suslov, A. V.

    2009-02-01

    A thin GaAs/AlGaAs plate was studied by the resonant ultrasound spectroscopy (RUS) in the temperature range 0.3-10 K and in magnetic fields of up to 18 T. The resonance frequencies and linewidths were measured. Quantum oscillations of both these values were observed and were associated with the quantum Hall effect occurred in the 2D electron system. For an analysis the sample was treated as a dielectric piezoelectric plate covered on one side by a film with a field dependent conductivity. Screening of the strain-driven electric field was changed due to the variation of the electron relaxation time in the vicinity of the metal-dielectric transitions caused by the magnetic field in the 2D system. The dielectric film does not affect properties of GaAs and thus the resonance frequencies are defined only by the elastic, piezoelectric and dielectric constants of GaAs. A metallic 2D sheet effectively screens the parallel electric field, so the ultrasound wave velocities and resonance frequencies decrease when the sheet conductivity increases. Oscillations of the resonance linewidth reflect the influence of the 2D system on the ultrasound attenuation, which is proportional to the linewidth. A metallic film as well as a dielectric one does not affect this attenuation but at some finite nonzero value of the conductivity the linewidth approaches a maximum. In high magnetic field each oscillation of the conductivity produces one oscillation of a resonance frequency and two linewidth peaks. The observed phenomena can be described by the relaxation type equations and the resonant ultrasound spectroscopy opens another opportunity for contactless studies on 2D electron systems.

  17. The physics of 2D microfluidic droplet ensembles

    NASA Astrophysics Data System (ADS)

    Beatus, Tsevi; Bar-Ziv, Roy H.; Tlusty, Tsvi

    2012-07-01

    We review non-equilibrium many-body phenomena in ensembles of 2D microfluidic droplets. The system comprises of continuous two-phase flow with disc-shaped droplets driven in a channel, at low Reynolds number of 10-4-10-3. The basic physics is that of an effective potential flow, governed by the 2D Laplace equation, with multiple, static and dynamic, boundaries of the droplets and the walls. The motion of the droplets induces dipolar flow fields, which mediate 1/r2 hydrodynamic interaction between the droplets. Summation of these long-range 2D forces over droplet ensembles converges, in contrast to the divergence of the hydrodynamic forces in 3D. In analogy to electrostatics, the strong effect of boundaries on the equations of motion is calculated by means of image dipoles. We first consider the dynamics of droplets flowing in a 1D crystal, which exhibits unique phonon-like excitations, and a variety of nonlinear instabilities-all stemming from the hydrodynamic interactions. Narrowing the channel results in hydrodynamic screening of the dipolar interactions, which changes salient features of the phonon spectra. Shifting from a 1D ordered crystal to 2D disordered ensemble, the hydrodynamic interactions induce collective density waves and shocks, which are superposed on single-droplet randomized motion and dynamic clustering. These collective modes originate from density-velocity coupling, whose outcome is a 1D Burgers equation. The rich observational phenomenology and the tractable theory render 2D droplet ensembles a suitable table-top system for studying non-equilibrium many-body physics with long-range interactions.

  18. 2d-LCA - an alternative to x-wires

    NASA Astrophysics Data System (ADS)

    Puczylowski, Jaroslaw; Hölling, Michael; Peinke, Joachim

    2014-11-01

    The 2d-Laser Cantilever Anemometer (2d-LCA) is an innovative sensor for two-dimensional velocity measurements in fluids. It uses a micostructured cantilever made of silicon and SU-8 as a sensing element and is capable of performing mesurements with extremly high temporal resolutions up to 150 kHz. The size of the cantilever defines its spatial resolution, which is in the order of 150 μm only. Another big feature is a large angular range of 180° in total. The 2d-LCA has been developed as an alternative measurement method to x-wires with the motivation to create a sensor that can operate in areas where the use of hot-wire anemometry is difficult. These areas include measurements in liquids and in near-wall or particle-laden flows. Unlike hot-wires, the resolution power of the 2d-LCA does not decrease with increasing flow velocity, making it particularly suitable for measurements in high speed flows. Comparative measurements with the 2d-LCA and hot-wires have been carried out in order to assess the performance of the new anemometer. The data of both measurement techniques were analyzed using the same stochastic methods including a spectral analysis as well as an inspection of increment statistics and structure functions. Furthermore, key parameters, such as mean values of both velocity components, angles of attack and the characteristic length scales were determined from both data sets. The analysis reveals a great agreement between both anemometers and thus confirms the new approach.

  19. Half-metallicity in 2D organometallic honeycomb frameworks.

    PubMed

    Sun, Hao; Li, Bin; Zhao, Jin

    2016-10-26

    Half-metallic materials with a high Curie temperature (T C) have many potential applications in spintronics. Magnetic metal free two-dimensional (2D) half-metallic materials with a honeycomb structure contain graphene-like Dirac bands with π orbitals and show excellent aspects in transport properties. In this article, by investigating a series of 2D organometallic frameworks with a honeycomb structure using first principles calculations, we study the origin of forming half-metallicity in this kind of 2D organometallic framework. Our analysis shows that charge transfer and covalent bonding are two crucial factors in the formation of half-metallicity in organometallic frameworks. (i) Sufficient charge transfer from metal atoms to the molecules is essential to form the magnetic centers. (ii) These magnetic centers need to be connected through covalent bonding, which guarantee the strong ferromagnetic (FM) coupling. As examples, the organometallic frameworks composed by (1,3,5)-benzenetricarbonitrile (TCB) molecules with noble metals (Au, Ag, Cu) show half-metallic properties with T C as high as 325 K. In these organometallic frameworks, the strong electronegative cyano-groups (CN groups) drive the charge transfer from metal atoms to the TCB molecules, forming the local magnetic centers. These magnetic centers experience strong FM coupling through the d-p covalent bonding. We propose that most of the 2D organometallic frameworks composed by molecule-CN-noble metal honeycomb structures contain similar half metallicity. This is verified by replacing TCB molecules with other organic molecules. Although the TCB-noble metal organometallic framework has not yet been synthesized, we believe the development of synthesizing techniques and facility will enable the realization of them. Our study provides new insight into the 2D half-metallic material design for the potential applications in nanotechnology. PMID:27541575

  20. Infrared imaging of 2-D temperature distribution during cryogen spray cooling.

    PubMed

    Choi, Bernard; Welch, Ashley J

    2002-12-01

    Cryogen spray cooling (CSC) is used in conjunction with pulsed laser irradiation for treatment of dermatologic indications. The main goal of this study was to determine the radial temperature distribution created by CSC and evaluate the importance of radial temperature gradients upon the subsequent analysis of tissue cooling throughout the skin. Since direct measurement of surface temperatures during CSC are hindered by the formation of a liquid cryogen layer, temperature distributions were estimated using a thin, black aluminum sheet. An infrared focal plane array camera was used to determine the 2-D backside temperature distribution during a cryogen spurt, which preliminary measurements have shown is a good indicator of the front-side temperature distribution. The measured temperature distribution was approximately gaussian in shape. Next, the transient temperature distributions in skin were calculated for two cases: 1) the standard 1-D solution which assumes a uniform cooling temperature distribution, and 2) a 2-D solution using a nonuniform surface cooling temperature distribution based upon the back-side infrared temperature measurements. At the end of a 100-ms cryogen spurt, calculations showed that, for the two cases, large discrepancies in temperatures at the surface and at a 60-micron depth were found at radii greater than 2.5 mm. These results suggest that it is necessary to consider radial temperature gradients during cryogen spray cooling of tissue. PMID:12596634

  1. Qualification of a surrogate matrix-based absolute quantification method for amyloid-β₄₂ in human cerebrospinal fluid using 2D UPLC-tandem mass spectrometry.

    PubMed

    Korecka, Magdalena; Waligorska, Teresa; Figurski, Michal; Toledo, Jon B; Arnold, Steven E; Grossman, Murray; Trojanowski, John Q; Shaw, Leslie M

    2014-01-01

    The primary aims of this work were to: 1) establish a calibrator surrogate matrix for quantification of amyloid-β (Aβ)42 in human cerebrospinal fluid (CSF) and preparation of quality control samples for LC-MS-MS methodology, 2) validate analytical performance of the assay, and 3) evaluate its diagnostic utility and compare it with the AlzBio3 immunoassay. The analytical methodology was based on a 2D-UPLC-MS-MS platform. Sample pretreatment used 5 M guanidine hydrochloride and extraction on μElution SPE columns as previously described. A column cleaning procedure involved gradual removal of aqueous solvents by acetonitrile assured consistent long-term chromatography performance. Receiver-operator characteristic (ROC) curve and correlation analyses evaluated the diagnostic utility of UPLC-MS-MS compared to AlzBio3 immunoassay for detection of Alzheimer's disease (AD). The surrogate matrix, artificial CSF containing 4 mg/mL of BSA, provides linear and reproducible calibration comparable to human pooled CSF as calibration matrix. Appropriate cleaning of the trapping and analytical columns provided every-day, trouble-free runs. Analyses of CSF Aβ42 showed that UPLC-MS-MS distinguished neuropathologically-diagnosed AD subjects from healthy controls with at least equivalent diagnostic utility to AlzBio3. Comparison of ROC curves for these two assays showed no statistically significant difference (p = 0.2229). Linear regression analysis of Aβ42 concentrations measured by this mass spectrometry-based method compared to the AlzBio3 immunoassay showed significantly higher but highly correlated results. In conclusion, the newly established surrogate matrix for 2D-UPLC-MS-MS measurement of Aβ42 provides selective, reproducible, and accurate results. The documented analytical performance and diagnostic performance for AD versus controls supports consideration as a candidate reference method. PMID:24625802

  2. A scanning-mode 2D shear wave imaging (s2D-SWI) system for ultrasound elastography.

    PubMed

    Qiu, Weibao; Wang, Congzhi; Li, Yongchuan; Zhou, Juan; Yang, Ge; Xiao, Yang; Feng, Ge; Jin, Qiaofeng; Mu, Peitian; Qian, Ming; Zheng, Hairong

    2015-09-01

    Ultrasound elastography is widely used for the non-invasive measurement of tissue elasticity properties. Shear wave imaging (SWI) is a quantitative method for assessing tissue stiffness. SWI has been demonstrated to be less operator dependent than quasi-static elastography, and has the ability to acquire quantitative elasticity information in contrast with acoustic radiation force impulse (ARFI) imaging. However, traditional SWI implementations cannot acquire two dimensional (2D) quantitative images of the tissue elasticity distribution. This study proposes and evaluates a scanning-mode 2D SWI (s2D-SWI) system. The hardware and image processing algorithms are presented in detail. Programmable devices are used to support flexible control of the system and the image processing algorithms. An analytic signal based cross-correlation method and a Radon transformation based shear wave speed determination method are proposed, which can be implemented using parallel computation. Imaging of tissue mimicking phantoms, and in vitro, and in vivo imaging test are conducted to demonstrate the performance of the proposed system. The s2D-SWI system represents a new choice for the quantitative mapping of tissue elasticity, and has great potential for implementation in commercial ultrasound scanners. PMID:26025508

  3. 2D-2D tunneling field-effect transistors using WSe2/SnSe2 heterostructures

    NASA Astrophysics Data System (ADS)

    Roy, Tania; Tosun, Mahmut; Hettick, Mark; Ahn, Geun Ho; Hu, Chenming; Javey, Ali

    2016-02-01

    Two-dimensional materials present a versatile platform for developing steep transistors due to their uniform thickness and sharp band edges. We demonstrate 2D-2D tunneling in a WSe2/SnSe2 van der Waals vertical heterojunction device, where WSe2 is used as the gate controlled p-layer and SnSe2 is the degenerately n-type layer. The van der Waals gap facilitates the regulation of band alignment at the heterojunction, without the necessity of a tunneling barrier. ZrO2 is used as the gate dielectric, allowing the scaling of gate oxide to improve device subthreshold swing. Efficient gate control and clean interfaces yield a subthreshold swing of ˜100 mV/dec for >2 decades of drain current at room temperature, hitherto unobserved in 2D-2D tunneling devices. The subthreshold swing is independent of temperature, which is a clear signature of band-to-band tunneling at the heterojunction. A maximum switching ratio ION/IOFF of 107 is obtained. Negative differential resistance in the forward bias characteristics is observed at 77 K. This work bodes well for the possibilities of two-dimensional materials for the realization of energy-efficient future-generation electronics.

  4. ICP-MS Workshop

    SciTech Connect

    Carman, April J.; Eiden, Gregory C.

    2014-11-01

    This is a short document that explains the materials that will be transmitted to LLNL and DNN HQ regarding the ICP-MS Workshop held at PNNL June 17-19th. The goal of the information is to pass on to LLNL information regarding the planning and preparations for the Workshop at PNNL in preparation of the SIMS workshop at LLNL.

  5. 2-D linear motion system. Innovative technology summary report

    SciTech Connect

    1998-11-01

    The US Department of Energy's (DOE's) nuclear facility decontamination and decommissioning (D and D) program requires buildings to be decontaminated, decommissioned, and surveyed for radiological contamination in an expeditious and cost-effective manner. Simultaneously, the health and safety of personnel involved in the D and D activities is of primary concern. D and D workers must perform duties high off the ground, requiring the use of manlifts or scaffolding, often, in radiologically or chemically contaminated areas or in areas with limited access. Survey and decontamination instruments that are used are sometimes heavy or awkward to use, particularly when the worker is operating from a manlift or scaffolding. Finding alternative methods of performing such work on manlifts or scaffolding is important. The 2-D Linear Motion System (2-D LMS), also known as the Wall Walker{trademark}, is designed to remotely position tools and instruments on walls for use in such activities as radiation surveys, decontamination, and painting. Traditional (baseline) methods for operating equipment for these tasks require workers to perform duties on elevated platforms, sometimes several meters above the ground surface and near potential sources of contamination. The Wall Walker 2-D LMS significantly improves health and safety conditions by facilitating remote operation of equipment. The Wall Walker 2-D LMS performed well in a demonstration of its precision, accuracy, maneuverability, payload capacity, and ease of use. Thus, this innovative technology is demonstrated to be a viable alternative to standard methods of performing work on large, high walls, especially those that have potential contamination concerns. The Wall Walker was used to perform a final release radiological survey on over 167 m{sup 2} of walls. In this application, surveying using a traditional (baseline) method that employs an aerial lift for manual access was 64% of the total cost of the improved technology

  6. The Column Density Variance-{\\cal M}_s Relationship

    NASA Astrophysics Data System (ADS)

    Burkhart, Blakesley; Lazarian, A.

    2012-08-01

    Although there is a wealth of column density tracers for both the molecular and diffuse interstellar medium, there are few observational studies investigating the relationship between the density variance (σ2) and the sonic Mach number ({\\cal M}_s). This is in part due to the fact that the σ2-{\\cal M}_s relationship is derived, via MHD simulations, for the three-dimensional (3D) density variance only, which is not a direct observable. We investigate the utility of a 2D column density \\sigma _{\\Sigma /\\Sigma _0}^2-{\\cal M}_s relationship using solenoidally driven isothermal MHD simulations and find that the best fit follows closely the form of the 3D density \\sigma _{\\rho /\\rho _0}^2-{\\cal M}_s trend but includes a scaling parameter A such that \\sigma _{\\ln (\\Sigma /\\Sigma _0)}^2=A\\times \\ln (1+b^2{\\cal M}_s^2), where A = 0.11 and b = 1/3. This relation is consistent with the observational data reported for the Taurus and IC 5146 molecular clouds with b = 0.5 and A = 0.16, and b = 0.5 and A = 0.12, respectively. These results open up the possibility of using the 2D column density values of σ2 for investigations of the relation between the sonic Mach number and the probability distribution function (PDF) variance in addition to existing PDF sonic Mach number relations.

  7. High throughput LC-MS/MS method for the simultaneous analysis of multiple vitamin D analytes in serum.

    PubMed

    Jenkinson, Carl; Taylor, Angela E; Hassan-Smith, Zaki K; Adams, John S; Stewart, Paul M; Hewison, Martin; Keevil, Brian G

    2016-03-01

    Recent studies suggest that vitamin D-deficiency is linked to increased risk of common human health problems. To define vitamin D 'status' most routine analytical methods quantify one particular vitamin D metabolite, 25-hydroxyvitamin D3 (25OHD3). However, vitamin D is characterized by complex metabolic pathways, and simultaneous measurement of multiple vitamin D metabolites may provide a more accurate interpretation of vitamin D status. To address this we developed a high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to analyse multiple vitamin D analytes, with particular emphasis on the separation of epimer metabolites. A supportive liquid-liquid extraction (SLE) and LC-MS/MS method was developed to quantify 10 vitamin D metabolites as well as separation of an interfering 7α-hydroxy-4-cholesten-3-one (7αC4) isobar (precursor of bile acid), and validated by analysis of human serum samples. In a cohort of 116 healthy subjects, circulating concentrations of 25-hydroxyvitamin D3 (25OHD3), 3-epi-25-hydroxyvitamin D3 (3-epi-25OHD3), 24,25-dihydroxyvitamin D3 (24R,25(OH)2D3), 1,25-dihydroxyvitamin D3 (1α,25(OH)2D3), and 25-hydroxyvitamin D2 (25OHD2) were quantifiable using 220μL of serum, with 25OHD3 and 24R,25(OH)2D3 showing significant seasonal variations. This high-throughput LC-MS/MS method provides a novel strategy for assessing the impact of vitamin D on human health and disease. PMID:26874878

  8. [Metabolites and metabolic pathways of mesaconitine in rat liver microsomal investigated by using UPLC-MS/MS method in vitro].

    PubMed

    Bi, Yun-Feng; Liu, Shu; Zhang, Rui-Xing; Song, Feng-Rui; Liu, Zhi-Qiang

    2013-12-01

    Mesaconitine was incubated with rat liver microsomes in vitro. The metabolites of mesaconitine in rat liver microsomes were identified by ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method with high resolution power. A typical reaction mixture of 100 mol L-1 Tris-HCI buffer (pH 7.4) containing 0.5 gL-1 microsomal protein and 50 micro molL-1 mesaconitine was prepared. The above reaction mixture was divided into six groups, and the volume of each group was 200 micro L. The incubation mixture was pre-incubated at 37 degrees C for 2 min and the reactions were initiated by adding NADPH generating system. After 90 min incubation at 37 degrees C, 200 micro L of acetonitrile was added to each group to stop the reaction. The metabolites of mesaconitine were investigated by UPLC-MS/MS method. Mesaconitine and 6 metabolites M1-M6 were found in the incubation system. The structures were characterized according to the data from MS/MS spectra and literatures. The metabolic reactions of mesaconitine in rat liver microsomes included the demethylation, deacetylation, dehydrogenation and hydroxylation. The major metabolic pathways of mesaconitine in rat liver microsomes were determined by UPLC-MS/MS on multiple reaction monitoring (MRM) mode combined with specific inhibitors of cytochrome P450 (CYP) isoforms, including alpha-naphthoflavone (CYP1A2), quinine (CYP2D), diethyldithiocarbamate (CYP2E1), ketoconazole (CYP3A) and sulfaphenazole (CYP2C), separately. Mesaconitine was mainly metabolized by CYP3A. CYP2C and CYP2D were also more important CYP isoforms for the metabolism reactions of mesaconitine, but CYP1A2 and CYP2E1 haven't any contribution to MA metabolism in rat liver microsomes. PMID:24689241

  9. Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

    PubMed Central

    Morisawa, Hiraku; Hirota, Mikako; Toda, Tosifusa

    2006-01-01

    Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved. PMID:17018156

  10. MPEG-4-based 2D facial animation for mobile devices

    NASA Astrophysics Data System (ADS)

    Riegel, Thomas B.

    2005-03-01

    The enormous spread of mobile computing devices (e.g. PDA, cellular phone, palmtop, etc.) emphasizes scalable applications, since users like to run their favorite programs on the terminal they operate at that moment. Therefore appliances are of interest, which can be adapted to the hardware realities without loosing a lot of their functionalities. A good example for this is "Facial Animation," which offers an interesting way to achieve such "scalability." By employing MPEG-4, which provides an own profile for facial animation, a solution for low power terminals including mobile phones is demonstrated. From the generic 3D MPEG-4 face a specific 2D head model is derived, which consists primarily of a portrait image superposed by a suited warping mesh and adapted 2D animation rules. Thus the animation process of MPEG-4 need not be changed and standard compliant facial animation parameters can be used to displace the vertices of the mesh and warp the underlying image accordingly.

  11. In search of a 2-dB coding gain

    NASA Technical Reports Server (NTRS)

    Yuen, J. H.; Vo, Q. D.

    1985-01-01

    A recent code search found a (15,1/5), a (14,1/6), and a (15,1/6) convolutional code which, when concatenated with a 10-bit (1023,959) Reed-Solomon (RS) code, achieves a bit-error rate (BER) of 0.000001 at a bit signal-to-noise ratio (SNR) of 0.50 dB, 0.47 dB and 0.42 B, respectively. All of these three codes outperform the Voyager communication system, our baseline, which achieves a BER of 10.000001 at bit SNR of 2.53 db, by more than 2 dB. The 2 dB coding improvement goal was exceeded.

  12. Critical Dynamics in Quenched 2D Atomic Gases

    NASA Astrophysics Data System (ADS)

    Larcher, F.; Dalfovo, F.; Proukakis, N. P.

    2016-05-01

    Non-equilibrium dynamics across phase transitions is a subject of intense investigations in diverse physical systems. One of the key issues concerns the validity of the Kibble-Zurek (KZ) scaling law for spontaneous defect creation. The KZ mechanism has been recently studied in cold atoms experiments. Interesting open questions arise in the case of 2D systems, due to the distinct nature of the Berezinskii-Kosterlitz-Thouless (BKT) transition. Our studies rely on the stochastic Gross-Pitaevskii equation. We perform systematic numerical simulations of the spontaneous emergence and subsequent dynamics of vortices in a uniform 2D Bose gas, which is quenched across the BKT phase transition in a controlled manner, focusing on dynamical scaling and KZ-type effects. By varying the transverse confinement, we also look at the extent to which such features can be seen in current experiments. Financial support from EPSRC and Provincia Autonoma di Trento.

  13. Graphical representations of DNA as 2-D map

    NASA Astrophysics Data System (ADS)

    Randić, Milan

    2004-03-01

    We describe a modification of the compact representation of DNA sequences which transforms the sequence into a 2-D diagram in which the 'spots' have integer coordinates. As a result the accompanying numerical characterization of DNA is quite simple and straightforward. This is an important advantage, particularly when considering DNA sequences having thousands of nucleic bases. The approach starts with the compact representation of DNA based on zigzag spiral template used for placing 'spots' associated with binary codes of the nucleic acids and subsequent suppression of the underlying zigzag curve. As a result, a 2-D map is formed in which all 'spots' have integer coordinates. By using only distances between spots having the same x or the same y coordinate one can construct a 'map profile' using integer arithmetic. The approach is illustrated on DNA sequences of the first exon of human β-globin.

  14. Interpretation of Magnetic Phase Anomalies over 2D Tabular Bodies

    NASA Astrophysics Data System (ADS)

    Subrahmanyam, M.

    2016-05-01

    In this study, phase angle (inverse tangent of the ratio of the horizontal to vertical gradients of magnetic anomalies) profile over two-dimensional tabular bodies has been subjected to detailed analysis for determining the source parameters. Distances between certain characteristic positions on this phase curve are related to the parameters of two-dimensional tabular magnetic sources. In this paper, I have derived the mathematical expressions for these relations. It has been demonstrated here that for locating the origin of the 2D tabular source, knowledge on the type of the model (contact, sheet, dyke, and fault) is not necessary. A procedure is evolved to determine the location, depth, width and magnetization angle of the 2D sources from the mathematical expressions. The method is tested on real field data. The effect of the overlapping bodies is also discussed with two synthetic examples. The interpretation technique is developed for contact, sheet, dike and inclined fault bodies.

  15. Semiregular solid texturing from 2D image exemplars.

    PubMed

    Du, Song-Pei; Hu, Shi-Min; Martin, Ralph R

    2013-03-01

    Solid textures, comprising 3D particles embedded in a matrix in a regular or semiregular pattern, are common in natural and man-made materials, such as brickwork, stone walls, plant cells in a leaf, etc. We present a novel technique for synthesizing such textures, starting from 2D image exemplars which provide cross-sections of the desired volume texture. The shapes and colors of typical particles embedded in the structure are estimated from their 2D cross-sections. Particle positions in the texture images are also used to guide spatial placement of the 3D particles during synthesis of the 3D texture. Our experiments demonstrate that our algorithm can produce higher quality structures than previous approaches; they are both compatible with the input images, and have a plausible 3D nature. PMID:22614330

  16. FPCAS2D user's guide, version 1.0

    NASA Astrophysics Data System (ADS)

    Bakhle, Milind A.

    1994-12-01

    The FPCAS2D computer code has been developed for aeroelastic stability analysis of bladed disks such as those in fans, compressors, turbines, propellers, or propfans. The aerodynamic analysis used in this code is based on the unsteady two-dimensional full potential equation which is solved for a cascade of blades. The structural analysis is based on a two degree-of-freedom rigid typical section model for each blade. Detailed explanations of the aerodynamic analysis, the numerical algorithms, and the aeroelastic analysis are not given in this report. This guide can be used to assist in the preparation of the input data required by the FPCAS2D code. A complete description of the input data is provided in this report. In addition, four test cases, including inputs and outputs, are provided.

  17. 2-D Magnetohydrodynamic Modeling of A Pulsed Plasma Thruster

    NASA Technical Reports Server (NTRS)

    Thio, Y. C. Francis; Cassibry, J. T.; Wu, S. T.; Rodgers, Stephen L. (Technical Monitor)

    2002-01-01

    Experiments are being performed on the NASA Marshall Space Flight Center (MSFC) MK-1 pulsed plasma thruster. Data produced from the experiments provide an opportunity to further understand the plasma dynamics in these thrusters via detailed computational modeling. The detailed and accurate understanding of the plasma dynamics in these devices holds the key towards extending their capabilities in a number of applications, including their applications as high power (greater than 1 MW) thrusters, and their use for producing high-velocity, uniform plasma jets for experimental purposes. For this study, the 2-D MHD modeling code, MACH2, is used to provide detailed interpretation of the experimental data. At the same time, a 0-D physics model of the plasma initial phase is developed to guide our 2-D modeling studies.

  18. 2D FEM Heat Transfer & E&M Field Code

    1992-04-02

    TOPAZ and TOPAZ2D are two-dimensional implicit finite element computer codes for heat transfer analysis. TOPAZ2D can also be used to solve electrostatic and magnetostatic problems. The programs solve for the steady-state or transient temperature or electrostatic and magnetostatic potential field on two-dimensional planar or axisymmetric geometries. Material properties may be temperature or potential-dependent and either isotropic or orthotropic. A variety of time and temperature-dependent boundary conditions can be specified including temperature, flux, convection, and radiation.more » By implementing the user subroutine feature, users can model chemical reaction kinetics and allow for any type of functional representation of boundary conditions and internal heat generation. The programs can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in the material surrounding the enclosure. Additional features include thermal contact resistance across an interface, bulk fluids, phase change, and energy balances.« less

  19. 2D ice from first principles: structures and phase transitions

    NASA Astrophysics Data System (ADS)

    Chen, Ji; Schusteritsch, Georg; Pickard, Chris J.; Salzmann, Christoph G.; Michaelides, Angelos

    Despite relevance to disparate areas such as cloud microphysics and tribology, major gaps in the understanding of the structures and phase transitions of low-dimensional water ice remain. Here we report a first principles study of confined 2D ice as a function of pressure. We find that at ambient pressure hexagonal and pentagonal monolayer structures are the two lowest enthalpy phases identified. Upon mild compression the pentagonal structure becomes the most stable and persists up to ca. 2 GPa at which point square and rhombic phases are stable. The square phase agrees with recent experimental observations of square ice confined within graphene sheets. We also find a double layer AA stacked square ice phase, which clarifies the difference between experimental observations and earlier force field simulations. This work provides a fresh perspective on 2D confined ice, highlighting the sensitivity of the structures observed to both the confining pressure and width.

  20. 2-D and 3-D computations of curved accelerator magnets

    SciTech Connect

    Turner, L.R.

    1991-01-01

    In order to save computer memory, a long accelerator magnet may be computed by treating the long central region and the end regions separately. The dipole magnets for the injector synchrotron of the Advanced Photon Source (APS), now under construction at Argonne National Laboratory (ANL), employ magnet iron consisting of parallel laminations, stacked with a uniform radius of curvature of 33.379 m. Laplace's equation for the magnetic scalar potential has a different form for a straight magnet (x-y coordinates), a magnet with surfaces curved about a common center (r-{theta} coordinates), and a magnet with parallel laminations like the APS injector dipole. Yet pseudo 2-D computations for the three geometries give basically identical results, even for a much more strongly curved magnet. Hence 2-D (x-y) computations of the central region and 3-D computations of the end regions can be combined to determine the overall magnetic behavior of the magnets. 1 ref., 6 figs.

  1. 2D FEM Heat Transfer & E&M Field Code

    SciTech Connect

    1992-04-02

    TOPAZ and TOPAZ2D are two-dimensional implicit finite element computer codes for heat transfer analysis. TOPAZ2D can also be used to solve electrostatic and magnetostatic problems. The programs solve for the steady-state or transient temperature or electrostatic and magnetostatic potential field on two-dimensional planar or axisymmetric geometries. Material properties may be temperature or potential-dependent and either isotropic or orthotropic. A variety of time and temperature-dependent boundary conditions can be specified including temperature, flux, convection, and radiation. By implementing the user subroutine feature, users can model chemical reaction kinetics and allow for any type of functional representation of boundary conditions and internal heat generation. The programs can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in the material surrounding the enclosure. Additional features include thermal contact resistance across an interface, bulk fluids, phase change, and energy balances.

  2. MasterChem: cooking 2D-polymers.

    PubMed

    Rodríguez-San-Miguel, D; Amo-Ochoa, P; Zamora, F

    2016-03-18

    2D-polymers are still dominated by graphene and closely related materials such as boron nitride, transition metal sulphides and oxides. However, the rational combination of molecules with suitable design is already showing the high potential of chemistry in this new research field. The aim of this feature article is to illustrate, and provide some perspectives, the current state-of-the-art in the field of synthetic 2D-polymers showing different alternatives to prepare this novel type of polymers based on the rational use of chemistry. This review comprises a brief revision of the essential concepts, the strategies of preparation following the two general approaches, bottom-up and top-down, and a revision of the promising seminal properties showed by some of these nanomaterials. PMID:26790817

  3. Controlling avalanche criticality in 2D nano arrays

    NASA Astrophysics Data System (ADS)

    Zohar, Y. C.; Yochelis, S.; Dahmen, K. A.; Jung, G.; Paltiel, Y.

    2013-05-01

    Many physical systems respond to slowly changing external force through avalanches spanning broad range of sizes. Some systems crackle even without apparent external force, such as bursts of neuronal activity or charge transfer avalanches in 2D molecular layers. Advanced development of theoretical models describing disorder-induced critical phenomena calls for experiments probing the dynamics upon tuneable disorder. Here we show that isomeric structural transitions in 2D organic self-assembled monolayer (SAM) exhibit critical dynamics with experimentally tuneable disorder. The system consists of field effect transistor coupled through SAM to illuminated semiconducting nanocrystals (NCs). Charges photoinduced in NCs are transferred through SAM to the transistor surface and modulate its conductivity. Avalanches of isomeric structural transitions are revealed by measuring the current noise I(t) of the transistor. Accumulated surface traps charges reduce dipole moments of the molecules, decrease their coupling, and thus decrease the critical disorder of the SAM enabling its tuning during experiments.

  4. A 2D MEMS stage for optical applications

    NASA Astrophysics Data System (ADS)

    Ataman, Caglar; Petremand, Yves; Noell, Wilfried; Ürey, Hakan; Epitaux, Marc; de Rooij, Nico F.

    2006-04-01

    A 2D MEMS platform for a microlens scanner application is reported. The platform is fabricated on an SOI wafer with 50 μm thick device layer. Entire device is defined with a single etching step on the same layer. Through four S-shaped beams, the device is capable of producing nonlinear 2D motion from linear 1D translation of two pairs of comb actuator sets. The device has a clear aperture of 2mm by 2mm, which is hallowed from the backside for micro-optics assembly. In this paper, a numerical device model and its validation via experimental characterization results are presented. Integration of the micro-optical components with the stage is also discussed. Additionally, a new driving scheme to minimize the settling time of the device in DC operation is explored.

  5. A Better 2-D Mechanical Energy Conservation Experiment

    NASA Astrophysics Data System (ADS)

    Paesler, Michael

    2012-02-01

    A variety of simple classical mechanics energy conservation experiments are used in teaching laboratories. Typical one-dimensional (1-D) setups may involve falling balls or oscillating springs. Many of these can be quite satisfying in that students can confirm—within a few percent—that mechanical energy is conserved. Students generally have little trouble identifying discrepancies such as the loss of a few percent of the gravitational potential energy due to air friction encountered by a falling ball. Two-dimensional (2-D) systems can require more sophisticated analysis for higher level laboratories, but such systems often incorporate complicating components that can make the exercise academically incomplete and experimentally less accurate. The following describes a simple 2-D energy conservation experiment based on the popular "Newton's Cradle" toy that allows students to account for nearly all of the mechanical energy in the system in an academically complete analysis.

  6. Photonics and optoelectronics of 2D semiconductor transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Mak, Kin Fai; Shan, Jie

    2016-04-01

    Recent advances in the development of atomically thin layers of van der Waals bonded solids have opened up new possibilities for the exploration of 2D physics as well as for materials for applications. Among them, semiconductor transition metal dichalcogenides, MX2 (M = Mo, W; X = S, Se), have bandgaps in the near-infrared to the visible region, in contrast to the zero bandgap of graphene. In the monolayer limit, these materials have been shown to possess direct bandgaps, a property well suited for photonics and optoelectronics applications. Here, we review the electronic and optical properties and the recent progress in applications of 2D semiconductor transition metal dichalcogenides with emphasis on strong excitonic effects, and spin- and valley-dependent properties.

  7. Thermal conductivity measurements in a 2D Yukawa system

    NASA Astrophysics Data System (ADS)

    Nosenko, V.; Ivlev, A.; Zhdanov, S.; Morfill, G.; Goree, J.; Piel, A.

    2007-03-01

    Thermal conductivity was measured for a 2D Yukawa system. First, we formed a monolayer suspension of microspheres in a plasma, i.e., a dusty plasma, which is like a colloidal suspension, but with an extremely low volume fraction and a partially-ionized rarefied gas instead of solvent. In the absence of manipulation, the suspension forms a 2D triangular lattice. To melt this lattice and form a liquid, we used a laser-heating method. Two focused laser beams were moved rapidly around in the monolayer. The kinetic temperature of the particles increased with the laser power applied, and above a threshold a melting transition occurred. We used digital video microscopy for direct imaging and particle tracking. The spatial profiles of the particle kinetic temperature were calculated. Using the heat transport equation with an additional term to account for the energy dissipation due to the gas drag, we analyzed the temperature distribution to derive the thermal conductivity.

  8. Fully automated 2D-3D registration and verification.

    PubMed

    Varnavas, Andreas; Carrell, Tom; Penney, Graeme

    2015-12-01

    Clinical application of 2D-3D registration technology often requires a significant amount of human interaction during initialisation and result verification. This is one of the main barriers to more widespread clinical use of this technology. We propose novel techniques for automated initial pose estimation of the 3D data and verification of the registration result, and show how these techniques can be combined to enable fully automated 2D-3D registration, particularly in the case of a vertebra based system. The initialisation method is based on preoperative computation of 2D templates over a wide range of 3D poses. These templates are used to apply the Generalised Hough Transform to the intraoperative 2D image and the sought 3D pose is selected with the combined use of the generated accumulator arrays and a Gradient Difference Similarity Measure. On the verification side, two algorithms are proposed: one using normalised features based on the similarity value and the other based on the pose agreement between multiple vertebra based registrations. The proposed methods are employed here for CT to fluoroscopy registration and are trained and tested with data from 31 clinical procedures with 417 low dose, i.e. low quality, high noise interventional fluoroscopy images. When similarity value based verification is used, the fully automated system achieves a 95.73% correct registration rate, whereas a no registration result is produced for the remaining 4.27% of cases (i.e. incorrect registration rate is 0%). The system also automatically detects input images outside its operating range. PMID:26387052

  9. A discrete simulation of 2-D fluid flow on TERASYS

    SciTech Connect

    Mullins, P.G.; Krolak, P.D.

    1995-12-01

    A discrete simulation of two-dimensional (2-D) fluid flow, on a recently designed novel architecture called TERASYS is presented. The simulation uses a cellular automaton approach, implemented in a new language called data-parallel bit C (dbC). A performance comparison between our implementation on TERASYS and an implementation on the Connection Machine is discussed. We comment briefly on the suitability of the TERASYS system for modeling fluid flow using cellular automata.

  10. An inverse design method for 2D airfoil

    NASA Astrophysics Data System (ADS)

    Liang, Zhi-Yong; Cui, Peng; Zhang, Gen-Bao

    2010-03-01

    The computational method for aerodynamic design of aircraft is applied more universally than before, in which the design of an airfoil is a hot problem. The forward problem is discussed by most relative papers, but inverse method is more useful in practical designs. In this paper, the inverse design of 2D airfoil was investigated. A finite element method based on the variational principle was used for carrying out. Through the simulation, it was shown that the method was fit for the design.

  11. NASA High-Speed 2D Photogrammetric Measurement System

    NASA Technical Reports Server (NTRS)

    Dismond, Harriett R.

    2012-01-01

    The object of this report is to provide users of the NASA high-speed 2D photogrammetric measurement system with procedures required to obtain drop-model trajectory and impact data for full-scale and sub-scale models. This guide focuses on use of the system for vertical drop testing at the NASA Langley Landing and Impact Research (LandIR) Facility.

  12. Report of the 1988 2-D Intercomparison Workshop, chapter 3

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Brasseur, Guy; Soloman, Susan; Guthrie, Paul D.; Garcia, Rolando; Yung, Yuk L.; Gray, Lesley J.; Tung, K. K.; Ko, Malcolm K. W.; Isaken, Ivar

    1989-01-01

    Several factors contribute to the errors encountered. With the exception of the line-by-line model, all of the models employ simplifying assumptions that place fundamental limits on their accuracy and range of validity. For example, all 2-D modeling groups use the diffusivity factor approximation. This approximation produces little error in tropospheric H2O and CO2 cooling rates, but can produce significant errors in CO2 and O3 cooling rates at the stratopause. All models suffer from fundamental uncertainties in shapes and strengths of spectral lines. Thermal flux algorithms being used in 2-D tracer tranport models produce cooling rates that differ by as much as 40 percent for the same input model atmosphere. Disagreements of this magnitude are important since the thermal cooling rates must be subtracted from the almost-equal solar heating rates to derive the net radiative heating rates and the 2-D model diabatic circulation. For much of the annual cycle, the net radiative heating rates are comparable in magnitude to the cooling rate differences described. Many of the models underestimate the cooling rates in the middle and lower stratosphere. The consequences of these errors for the net heating rates and the diabatic circulation will depend on their meridional structure, which was not tested here. Other models underestimate the cooling near 1 mbar. Suchs errors pose potential problems for future interactive ozone assessment studies, since they could produce artificially-high temperatures and increased O3 destruction at these levels. These concerns suggest that a great deal of work is needed to improve the performance of thermal cooling rate algorithms used in the 2-D tracer transport models.

  13. Statistical analysis of quiet stance sway in 2-D

    PubMed Central

    DiZio, Paul; Lackner, James R.

    2014-01-01

    Subjects exposed to a rotating environment that perturbs their postural sway show adaptive changes in their voluntary spatially directed postural motion to restore accurate movement paths but do not exhibit any obvious learning during passive stance. We have found, however, that a variable known to characterize the degree of stochasticity in quiet stance can also reveal subtle learning phenomena in passive stance. We extended Chow and Collins (Phys Rev E 52(1):909–912, 1995) one-dimensional pinned-polymer model (PPM) to two dimensions (2-D) and then evaluated the model’s ability to make analytical predictions for 2-D quiet stance. To test the model, we tracked center of mass and centers of foot pressures, and compared and contrasted stance sway for the anterior–posterior versus medio-lateral directions before, during, and after exposure to rotation at 10 rpm. Sway of the body during rotation generated Coriolis forces that acted perpendicular to the direction of sway. We found significant adaptive changes for three characteristic features of the mean square displacement (MSD) function: the exponent of the power law defined at short time scales, the proportionality constant of the power law, and the saturation plateau value defined at longer time scales. The exponent of the power law of MSD at a short time scale lies within the bounds predicted by the 2-D PPM. The change in MSD during exposure to rotation also had a power-law exponent in the range predicted by the theoretical model. We discuss the Coriolis force paradigm for studying postural and movement control and the applicability of the PPM model in 2-D for studying postural adaptation. PMID:24477760

  14. Energy level transitions of gas in a 2D nanopore

    SciTech Connect

    Grinyaev, Yurii V.; Chertova, Nadezhda V.; Psakhie, Sergei G.

    2015-10-27

    An analytical study of gas behavior in a 2D nanopore was performed. It is shown that the temperature dependence of gas energy can be stepwise due to transitions from one size-quantized subband to another. Taking into account quantum size effects results in energy level transitions governed by the nanopore size, temperature and gas density. This effect leads to an abrupt change of gas heat capacity in the nanopore at the above varying system parameters.

  15. 2D imaging of functional structures in perfused pig heart

    NASA Astrophysics Data System (ADS)

    Kessler, Manfred D.; Cristea, Paul D.; Hiller, Michael; Trinks, Tobias

    2002-06-01

    In 2000 by 2D-imaging we were able for the first time to visualize in subcellular space functional structures of myocardium. For these experiments we used hemoglobin-free perfused pig hearts in our lab. Step by step we learned to understand the meaning of subcellular structures. Principally, the experiment revealed that in subcellular space very fast changes of light scattering can occur. Furthermore, coefficients of different parameters were determined on the basis of multicomponent system theory.

  16. Multicolor symbology for remotely scannable 2D barcodes

    NASA Astrophysics Data System (ADS)

    Wissner-Gross, Alexander D.; Sullivan, Timothy M.

    2008-03-01

    There has been much recent interest in mobile systems for augmented reality. However, existing visual tagging solutions are not robust at the low resolutions typical of current camera phones or at the low solid angles needed for "across-the-room" reality augmentation. In this paper, we propose a new 2D barcode symbology that uses multiple colors in order to address these challenges. We present preliminary results, showing the detection of example barcodes in this scheme over a range of angles.

  17. 2 1/2 -D compressible reconnection model

    NASA Astrophysics Data System (ADS)

    Skender, M.; Vršnak, B.

    The exact solution of the jump conditions on the RD/SMS discontinuity system in a two-and-half-dimensional (2 1/2 -D) symmetrical reconnection model enables one to analyse the outflowing jet characteristics in dependence on the inflow velocity, and to follow changes in transition to the two-dimensional model. Implications arising from the exact solution and its relevance for solar flares are discussed.

  18. CBEAM. 2-D: a two-dimensional beam field code

    SciTech Connect

    Dreyer, K.A.

    1985-05-01

    CBEAM.2-D is a two-dimensional solution of Maxwell's equations for the case of an electron beam propagating through an air medium. Solutions are performed in the beam-retarded time frame. Conductivity is calculated self-consistently with field equations, allowing sophisticated dependence of plasma parameters to be handled. A unique feature of the code is that it is implemented on an IBM PC microcomputer in the BASIC language. Consequently, it should be available to a wide audience.

  19. Universal Fabrication of 2D Electron Systems in Functional Oxides.

    PubMed

    Rödel, Tobias Chris; Fortuna, Franck; Sengupta, Shamashis; Frantzeskakis, Emmanouil; Fèvre, Patrick Le; Bertran, François; Mercey, Bernard; Matzen, Sylvia; Agnus, Guillaume; Maroutian, Thomas; Lecoeur, Philippe; Santander-Syro, Andrés Felipe

    2016-03-01

    2D electron systems (2DESs) in functional oxides are promising for applications, but their fabrication and use, essentially limited to SrTiO3 -based heterostructures, are hampered by the need for growing complex oxide overlayers thicker than 2 nm using evolved techniques. It is demonstrated that thermal deposition of a monolayer of an elementary reducing agent suffices to create 2DESs in numerous oxides. PMID:26753522

  20. Statistical analysis of quiet stance sway in 2-D.

    PubMed

    Bakshi, Avijit; DiZio, Paul; Lackner, James R

    2014-04-01

    Subjects exposed to a rotating environment that perturbs their postural sway show adaptive changes in their voluntary spatially directed postural motion to restore accurate movement paths but do not exhibit any obvious learning during passive stance. We have found, however, that a variable known to characterize the degree of stochasticity in quiet stance can also reveal subtle learning phenomena in passive stance. We extended Chow and Collins (Phys Rev E 52(1):909-912, 1995) one-dimensional pinned-polymer model (PPM) to two dimensions (2-D) and then evaluated the model's ability to make analytical predictions for 2-D quiet stance. To test the model, we tracked center of mass and centers of foot pressures, and compared and contrasted stance sway for the anterior-posterior versus medio-lateral directions before, during, and after exposure to rotation at 10 rpm. Sway of the body during rotation generated Coriolis forces that acted perpendicular to the direction of sway. We found significant adaptive changes for three characteristic features of the mean square displacement (MSD) function: the exponent of the power law defined at short time scales, the proportionality constant of the power law, and the saturation plateau value defined at longer time scales. The exponent of the power law of MSD at a short time scale lies within the bounds predicted by the 2-D PPM. The change in MSD during exposure to rotation also had a power-law exponent in the range predicted by the theoretical model. We discuss the Coriolis force paradigm for studying postural and movement control and the applicability of the PPM model in 2-D for studying postural adaptation. PMID:24477760

  1. Valley and electric photocurrents in 2D silicon and graphene

    SciTech Connect

    Tarasenko, S. A.; Ivchenko, E. L.; Olbrich, P.; Ganichev, S. D.

    2013-12-04

    We show that the optical excitation of multi-valley systems leads to valley currents which depend on the light polarization. The net electric current, determined by the vector sum of single-valley contributions, vanishes for some peculiar distributions of carriers in the valley and momentum spaces forming a pure valley current. We report on the study of this phenomenon, both experimental and theoretical, for graphene and 2D electron channels on the silicon surface.

  2. Baby universes and fractal structure of 2d gravity

    NASA Astrophysics Data System (ADS)

    Thorleifsson, Gudmar

    1994-04-01

    We extract the string susceptibility exponent γstr by measuring the distribution of baby universes on surfaces in the case of various matter fields coupled to discrete 2d quantum gravity. For c <= 1 the results are in good agreement with the KPZ-formula, if logarithmic corrections are taken into account for c = 1. For c > 1 it is not as clear how to extract γstr but universality with respect to c is observed in the fractal structure.

  3. An Intercomparison of 2-D Models Within a Common Framework

    NASA Technical Reports Server (NTRS)

    Weisenstein, Debra K.; Ko, Malcolm K. W.; Scott, Courtney J.; Jackman, Charles H.; Fleming, Eric L.; Considine, David B.; Kinnison, Douglas E.; Connell, Peter S.; Rotman, Douglas A.; Bhartia, P. K. (Technical Monitor)

    2002-01-01

    A model intercomparison among the Atmospheric and Environmental Research (AER) 2-D model, the Goddard Space Flight Center (GSFC) 2-D model, and the Lawrence Livermore National Laboratory 2-D model allows us to separate differences due to model transport from those due to the model's chemical formulation. This is accomplished by constructing two hybrid models incorporating the transport parameters of the GSFC and LLNL models within the AER model framework. By comparing the results from the native models (AER and e.g. GSFC) with those from the hybrid model (e.g. AER chemistry with GSFC transport), differences due to chemistry and transport can be identified. For the analysis, we examined an inert tracer whose emission pattern is based on emission from a High Speed Civil Transport (HSCT) fleet; distributions of trace species in the 2015 atmosphere; and the response of stratospheric ozone to an HSCT fleet. Differences in NO(y) in the upper stratosphere are found between models with identical transport, implying different model representations of atmospheric chemical processes. The response of O3 concentration to HSCT aircraft emissions differs in the models from both transport-dominated differences in the HSCT-induced perturbations of H2O and NO(y) as well as from differences in the model represent at ions of O3 chemical processes. The model formulations of cold polar processes are found to be the most significant factor in creating large differences in the calculated ozone perturbations

  4. Resolving 2D Amorphous Materials with Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Burson, Kristen M.; Buechner, Christin; Lewandowski, Adrian; Heyde, Markus; Freund, Hans-Joachim

    Novel two-dimensional (2D) materials have garnered significant scientific interest due to their potential technological applications. Alongside the emphasis on crystalline materials, such as graphene and hexagonal BN, a new class of 2D amorphous materials must be pursued. For amorphous materials, a detailed understanding of the complex structure is necessary. Here we present a structural study of 2D bilayer silica on Ru(0001), an insulating material which is weakly coupled to the substrate. Atomic structure has been determined with a dual mode atomic force microscopy (AFM) and scanning tunneling microscopy (STM) sensor in ultra-high vacuum (UHV) at low temperatures, revealing a network of different ring sizes. Liquid AFM measurements with sub-nanometer resolution bridge the gap between clean UHV conditions and the environments that many material applications demand. Samples are grown and characterized in vacuum and subsequently transferred to the liquid AFM. Notably, the key structural features observed, namely nanoscale ring networks and larger holes to the substrate, show strong quantitative agreement between the liquid and UHV microscopy measurements. This provides direct evidence for the structural stability of these silica films for nanoelectronics and other applications. KMB acknowledges support from the Alexander von Humboldt Foundation.

  5. Hunting down magnetic monopoles in 2D topological insulators?

    NASA Astrophysics Data System (ADS)

    He, Xugang; Cmpmsd At Bnl Team

    Contrary to the existence of electric charge, magnetic monopole does not exist in nature. It is thus extraordinary to find that magnetic monopoles can be pictured conceptually in topological insulators. For 2D topological insulators, the topological invariant corresponds to the total flux of an effective magnetic field (the Berry curvature) over the reciprocal space. Upon wrapping the 2D reciprocal space into a compact manifold as a torus, the non-zero total flux can be considered to originate from magnetic monopoles with quantized charge. We will first illustrate the intrinsic difficulty via extending a 2D problem to a 3D reciprocal space, and then demonstrate that analytical continuation to the complex momentum space offers a natural solution in which 1) the magnetic monopoles emerge naturally in pairs each forming a string above and below the real axis possessing opposite charge, and 2) the total charge below the real axis gives exactly the topological invariant. In essence, the robustness of the topology is mapped to the robustness of the total charge in the lower complex plan, a mapping intriguing even mathematically. Finally, we will illustrate the evolution across the topological phase transition, providing a natural description of the metallic nature in the phase boundary, and offering a clear explanation why a change of global topology can be induced via a local change in reciprocal space. Work supported by US DOE BES DE-AC02-98CH10886.

  6. F-theory and 2d (0, 2) theories

    NASA Astrophysics Data System (ADS)

    Schäfer-Nameki, Sakura; Weigand, Timo

    2016-05-01

    F-theory compactified on singular, elliptically fibered Calabi-Yau five-folds gives rise to two-dimensional gauge theories preserving N = (0 , 2) supersymmetry. In this paper we initiate the study of such compactifications and determine the dictionary between the geometric data of the elliptic fibration and the 2d gauge theory such as the matter content in terms of (0 , 2) superfields and their supersymmetric couplings. We study this setup both from a gauge-theoretic point of view, in terms of the partially twisted 7-brane theory, and provide a global geometric description based on the structure of the elliptic fibration and its singularities. Global consistency conditions are determined and checked against the dual M-theory compactification to one dimension. This includes a discussion of gauge anomalies, the structure of the Green-Schwarz terms and the Chern-Simons couplings in the dual M-theory supersymmetric quantum mechanics. Furthermore, by interpreting the resulting 2d (0 , 2) theories as heterotic worldsheet theories, we propose a correspondence between the geometric data of elliptically fibered Calabi-Yau five-folds and the target space of a heterotic gauged linear sigma-model (GLSM). In particular the correspondence between the Landau-Ginsburg and sigma-model phase of a 2d (0 , 2) GLSM is realized via different T-branes or gluing data in F-theory.

  7. Design Application Translates 2-D Graphics to 3-D Surfaces

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Fabric Images Inc., specializing in the printing and manufacturing of fabric tension architecture for the retail, museum, and exhibit/tradeshow communities, designed software to translate 2-D graphics for 3-D surfaces prior to print production. Fabric Images' fabric-flattening design process models a 3-D surface based on computer-aided design (CAD) specifications. The surface geometry of the model is used to form a 2-D template, similar to a flattening process developed by NASA's Glenn Research Center. This template or pattern is then applied in the development of a 2-D graphic layout. Benefits of this process include 11.5 percent time savings per project, less material wasted, and the ability to improve upon graphic techniques and offer new design services. Partners include Exhibitgroup/Giltspur (end-user client: TAC Air, a division of Truman Arnold Companies Inc.), Jack Morton Worldwide (end-user client: Nickelodeon), as well as 3D Exhibits Inc., and MG Design Associates Corp.

  8. Role of defects in frictional properties of 2-D materials

    NASA Astrophysics Data System (ADS)

    Kavalur, Aditya; Kim, Woo Kyun

    Graphene and other 2-D materials have provided a promising prospect to improve the tribological properties of small length scale devices such as MEMS/NEMS due to their low friction coefficient and excellent wear resistance. Several recent research efforts have been devoted to unveiling the physical origin of the superior tribological properties of these 2-D materials from both experimental and theoretical standpoints, however, many of them still remain far from clearly understood. Recently, it was shown that lamellar materials do not conform to the predictions of the Prandtl-Tomlinson model due to additional friction mechanisms of delamination and visco-elastic ploughing. These mechanisms are critical as they explain the low and negative coefficients of friction observed in recent AFM experiments. However, thus far, most simulation and theoretical studies about these novel friction mechanisms have focused on only pristine graphene whereas real graphene sheets prepared by CVD and other conventional techniques possess various forms of defects such as vacancies and non-hexagonal rings. In this study we examine the role of these defects in frictional properties of 2-D materials in relation to delamination and visco-elastic ploughing.

  9. Region-based Statistical Analysis of 2D PAGE Images

    PubMed Central

    Li, Feng; Seillier-Moiseiwitsch, Françoise; Korostyshevskiy, Valeriy R.

    2011-01-01

    A new comprehensive procedure for statistical analysis of two-dimensional polyacrylamide gel electrophoresis (2D PAGE) images is proposed, including protein region quantification, normalization and statistical analysis. Protein regions are defined by the master watershed map that is obtained from the mean gel. By working with these protein regions, the approach bypasses the current bottleneck in the analysis of 2D PAGE images: it does not require spot matching. Background correction is implemented in each protein region by local segmentation. Two-dimensional locally weighted smoothing (LOESS) is proposed to remove any systematic bias after quantification of protein regions. Proteins are separated into mutually independent sets based on detected correlations, and a multivariate analysis is used on each set to detect the group effect. A strategy for multiple hypothesis testing based on this multivariate approach combined with the usual Benjamini-Hochberg FDR procedure is formulated and applied to the differential analysis of 2D PAGE images. Each step in the analytical protocol is shown by using an actual dataset. The effectiveness of the proposed methodology is shown using simulated gels in comparison with the commercial software packages PDQuest and Dymension. We also introduce a new procedure for simulating gel images. PMID:21850152

  10. 2D luminescence imaging of pH in vivo

    PubMed Central

    Schreml, Stephan; Meier, Robert J.; Wolfbeis, Otto S.; Landthaler, Michael; Szeimies, Rolf-Markus; Babilas, Philipp

    2011-01-01

    Luminescence imaging of biological parameters is an emerging field in biomedical sciences. Tools to study 2D pH distribution are needed to gain new insights into complex disease processes, such as wound healing and tumor metabolism. In recent years, luminescence-based methods for pH measurement have been developed. However, for in vivo applications, especially for studies on humans, biocompatibility and reliability under varying conditions have to be ensured. Here, we present a referenced luminescent sensor for 2D high-resolution imaging of pH in vivo. The ratiometric sensing scheme is based on time-domain luminescence imaging of FITC and ruthenium(II)tris-(4,7-diphenyl-1,10-phenanthroline). To create a biocompatible 2D sensor, these dyes were bound to or incorporated into microparticles (aminocellulose and polyacrylonitrile), and particles were immobilized in polyurethane hydrogel on transparent foils. We show sensor precision and validity by conducting in vitro and in vivo experiments, and we show the versatility in imaging pH during physiological and chronic cutaneous wound healing in humans. Implementation of this technique may open vistas in wound healing, tumor biology, and other biomedical fields. PMID:21262842

  11. A 2-D ECE Imaging Diagnostic for TEXTOR

    NASA Astrophysics Data System (ADS)

    Wang, J.; Deng, B. H.; Domier, C. W.; Luhmann, H. Lu, Jr.

    2002-11-01

    A true 2-D extension to the UC Davis ECE Imaging (ECEI) concept is under development for installation on the TEXTOR tokamak in 2003. This combines the use of linear arrays with multichannel conventional wideband heterodyne ECE radiometers to provide a true 2-D imaging system. This is in contrast to current 1-D ECEI systems in which 2-D images are obtained through the use of multiple plasma discharges (varying the scanned emission frequency each discharge). Here, each array element of the 20 channel mixer array measures plasma emission at 16 simultaneous frequencies to form a 16x20 image of the plasma electron temperature Te. Correlation techniques can then be applied to any pair of the 320 image elements to study both radial and poloidal characteristics of turbulent Te fluctuations. The system relies strongly on the development of low cost, wideband (2-18 GHz) IF detection electronics for use in both ECE Imaging as well as conventional heterodyne ECE radiometry. System details, with a strong focus on the wideband IF electronics development, will be presented. *Supported by U.S. DoE Contracts DE-FG03-95ER54295 and DE-FG03-99ER54531.

  12. Dopamine D2/D3 receptor availability and venturesomeness.

    PubMed

    Bernow, Nina; Yakushev, Igor; Landvogt, Christian; Buchholz, Hans-Georg; Smolka, Michael N; Bartenstein, Peter; Lieb, Klaus; Gründer, Gerhard; Vernaleken, Ingo; Schreckenberger, Mathias; Fehr, Christoph

    2011-08-30

    The construct of impulsivity is considered as a major trait of personality. There is growing evidence that the mesolimbic dopamine system plays an important role in the modulation of impulsivity and venturesomeness, the two key components within the impulsivity-construct. The aim of the present study was to explore an association between trait impulsivity measured with self-assessment and the dopaminergic neurotransmission as measured by positron emission tomography (PET) in a cohort of healthy male subjects. In vivo D2/D3 receptor availability was determined with [(18)F]fallypride PET in 18 non-smoking healthy subjects. The character trait impulsivity was measured using the Impulsiveness-Venturesomeness-Empathy questionnaire (I7). Image processing and statistical analysis was performed on a voxel-by-voxel basis using statistical parametric mapping (SPM) software. The I7 subscale venturesomeness correlated positively with the D2/D3 receptor availability within the left temporal cortex and the thalamus. Measures on the I7 subscale impulsiveness and empathy did not correlate with the D2/D3 receptor availability in any brain region investigated. Our results suggest the involvement of extrastriatal dopaminergic neurotransmission in venturesomeness, a component of impulsivity. PMID:21689908

  13. Characterization of Porous Medium Properties Using 2D NMR

    NASA Astrophysics Data System (ADS)

    Sun, Boqin; Dunn, Keh-Jim

    2003-03-01

    We have successfully applied the concept of 2D NMR to the characterization of properties of fluid-saturated porous medium. Using a two-windowed modified CPMG pulse sequence, we were able to explore the magnetic internal filed gradient distribution within the pore space of a fluid-saturated porous medium due to magnetic susceptibility contrast between the solid matrix and pore fluid. Similar scheme is used to identify and quantify different types of pore fluids, such as oil, water, and gas, based on the contrast in their diffusion coefficients. The magic angle spinning technique (MAS) can also be applied in the 2D NMR framework for delineating the chemical shift spectra of the pore fluids in a porous medium at different T1 or T2 relaxation times. The results can be displayed in a two-dimensional plot, with one axis being the T1 or T2 relaxation times, the other axis being the internal field gradient, diffusion coefficient, or chemical shift, and the third axis being the proton population. Our preliminary laboratory work indicates that the 2D NMR approach can be a powerful tool for the characterization of properties of fluid-saturated porous medium, such as fluid typing, oil viscosity determination, surface wettability, etc.

  14. Broadband THz Spectroscopy of 2D Nanoscale Materials

    NASA Astrophysics Data System (ADS)

    Chen, Lu; Tripathi, Shivendra; Huang, Mengchen; Hsu, Jen-Feng; D'Urso, Brian; Lee, Hyungwoo; Eom, Chang-Beom; Irvin, Patrick; Levy, Jeremy

    Two-dimensional (2D) materials such as graphene and transition-metal dichalcogenides (TMDC) have attracted intense research interest in the past decade. Their unique electronic and optical properties offer the promise of novel optoelectronic applications in the terahertz regime. Recently, generation and detection of broadband terahertz (10 THz bandwidth) emission from 10-nm-scale LaAlO3/SrTiO3 nanostructures created by conductive atomic force microscope (c-AFM) lithography has been demonstrated . This unprecedented control of THz emission at 10 nm length scales creates a pathway toward hybrid THz functionality in 2D-material/LaAlO3/SrTiO3 heterostructures. Here we report initial efforts in THz spectroscopy of 2D nanoscale materials with resolution comparable to the dimensions of the nanowire (10 nm). Systems under investigation include graphene, single-layer molybdenum disulfide (MoS2), and tungsten diselenide (WSe2) nanoflakes. 1. Y. Ma, et al., Nano Lett. 13, 2884 (2013). We gratefully acknowledge financial support from the following agencies and grants: AFOSR (FA9550-12-1-0268 (JL, PRI), FA9550-12-1-0342 (CBE)), ONR (N00014-13-1-0806 (JL, CBE), N00014-15-1-2847 (JL)), NSF DMR-1124131 (JL, CBE) and DMR-1234096 (CBE).

  15. Cytochrome P450-2D6 Screening Among Elderly Using Antidepressants (CYSCE)

    ClinicalTrials.gov

    2015-12-09

    Depression; Depressive Disorder; Poor Metabolizer Due to Cytochrome P450 CYP2D6 Variant; Intermediate Metabolizer Due to Cytochrome P450 CYP2D6 Variant; Ultrarapid Metabolizer Due to Cytochrome P450 CYP2D6 Variant

  16. Stereochemistry of 16a-hydroxyfriedelin and 3-Oxo-16-methylfriedel-16-ene established by 2D NMR spectroscopy.

    PubMed

    Duarte, Lucienir Pains; Silva de Miranda, Roqueline Rodrigues; Rodrigues, Salomão Bento Vasconcelos; de Fátima Silva, Grácia Divina; Vieira Filho, Sidney Augusto; Knupp, Vagner Fernandes

    2009-01-01

    Friedelin (1), 3beta-friedelinol (2), 28-hydroxyfriedelin (3), 16alpha-hydroxyfriedelin (4), 30-hydroxyfriedelin (5) and 16alpha,28-dihydroxyfriedelin (6) were isolated through fractionation of the hexane extract obtained from branches of Salacia elliptica. After a week in CDCl(3) solution, 16alpha-hydroxyfriedelin (4) reacted turning into 3-oxo-16-methylfriedel-16-ene (7). This is the first report of a dehydration followed by a Nametkin rearrangement of a pentacyclic triterpene in CDCl(3) solution occurring in the NMR tube. These seven pentacyclic triterpenes was identified through NMR spectroscopy and the stereochemistry of compound 4 and 7 was established by 2D NMR (NOESY) spectroscopy and mass spectrometry (GC-MS). It is also the first time that all the (13)C-NMR and 2D NMR spectral data are reported for compounds 4 and 7. PMID:19214150

  17. Stability-indicating HPLC method development and structural elucidation of novel degradation products in posaconazole injection by LC-TOF/MS, LC-MS/MS and NMR.

    PubMed

    Yang, Yidi; Zhu, Xi; Zhang, Fei; Li, Wei; Wu, Ying; Ding, Li

    2016-06-01

    Stress testing was carried out under acidic, alkaline, oxidative, thermal and photolytic conditions to evaluate the intrinsic stability of posaconazole injection. A total of four degradation products were detected and the drug was found to be susceptible to oxidative and thermal degradations. Three unknown degradants formed under oxidative stress condition were isolated by preparative HPLC and unambiguously elucidated by LC-TOF/MS, LC-MS/MS, (1)H NMR, (13)C NMR and 2D NMR techniques. Based on the spectrometric and spectroscopic information, these novel degradation products were unequivocally assigned as the N-oxides of posaconazole. Probable mechanisms for the formation of the degradants were proposed. A new and selective HPLC method was developed and validated to separate, detect and quantify all the degradants in posaconazole injection. PMID:27023129

  18. Simulation of 2D Fields of Raindrop Size Distributions

    NASA Astrophysics Data System (ADS)

    Berne, A.; Schleiss, M.; Uijlenhoet, R.

    2008-12-01

    The raindrop size distribution (DSD hereafter) is of primary importance for quantitative applications of weather radar measurements. The radar reflectivity~Z (directly measured by radar) is related to the power backscattered by the ensemble of hydrometeors within the radar sampling volume. However, the rain rate~R (the flux of water to the surface) is the variable of interest for many applications (hydrology, weather forecasting, air traffic for example). Usually, radar reflectivity is converted into rain rate using a power law such as Z=aRb. The coefficients a and b of the Z-R relationship depend on the DSD. The variability of the DSD in space and time has to be taken into account to improve radar rain rate estimates. Therefore, the ability to generate a large number of 2D fields of DSD which are statistically homogeneous provides a very useful simulation framework that nicely complements experimental approaches based on DSD data, in order to investigate radar beam propagation through rain as well as radar retrieval techniques. The proposed approach is based on geostatistics for structural analysis and stochastic simulation. First, the DSD is assumed to follow a gamma distribution. Hence a 2D field of DSDs can be adequately described as a 2D field of a multivariate random function consisting of the three DSD parameters. Such fields are simulated by combining a Gaussian anamorphosis and a multivariate Gaussian random field simulation algorithm. Using the (cross-)variogram models fitted on data guaranties that the spatial structure of the simulated fields is consistent with the observed one. To assess its validity, the proposed method is applied to data collected during intense Mediterranean rainfall. As only time series are available, Taylor's hypothesis is assumed to convert time series in 1D range profile. Moreover, DSD fields are assumed to be isotropic so that the 1D structure can be used to simulate 2D fields. A large number of 2D fields of DSD parameters are

  19. Determinants of the substrate specificity of human cytochrome P-450 CYP2D6: design and construction of a mutant with testosterone hydroxylase activity.

    PubMed Central

    Smith, G; Modi, S; Pillai, I; Lian, L Y; Sutcliffe, M J; Pritchard, M P; Friedberg, T; Roberts, G C; Wolf, C R

    1998-01-01

    , the CYP2D6F483I mutant acquired the ability to metabolize testosterone to a novel product, which was identified by MS and proton NMR spectroscopy as 15alpha-hydroxytestosterone. NMR spin relaxation experiments were used to measure distances between the haem iron and protons of testosterone bound to the CYP2D6F483I mutant. These experiments demonstrate that very minor modifications to the active site structure of CYP2D6 can have a profound influence on the substrate specificity of the enzyme. PMID:9560305

  20. NAPS-MS

    PubMed Central

    Gudesblatt, Mark; Kresa-Reahl, Kiren; Brandes, David W.; Sater, Pamela

    2016-01-01

    Background: Patients with multiple sclerosis (MS) have higher rates of fatigue, mood disturbance, and cognitive impairments than healthy populations. Disease-modifying agents may affect sleep. Although patients taking natalizumab often show improvement in fatigue during the first year of therapy, the mechanism behind this effect is unknown. The aim of the NAPS-MS study was to investigate whether natalizumab affected objective measures of sleep as determined by polysomnography (PSG) and multiple sleep latency testing (MSLT) in patients with MS with fatigue or sleepiness initiating therapy. Additional goals were to evaluate changes in measures of fatigue, mood, and cognition and to correlate these measures with objective sleep measures. Methods: Patients underwent PSG and MSLT before their first natalizumab infusion and after their seventh. Patients completed the Modified Fatigue Impact Scale, Fatigue Severity Scale (FSS), Epworth Sleepiness Scale (ESS), and visual analogue scale for fatigue (VAS-F) at their first, fourth, and seventh natalizumab infusions. NeuroTrax cognitive tests and the Hospital Anxiety and Depression Scale (HADS) were performed at the first and seventh natalizumab infusions. Results: Changes in sleep efficiency, wakefulness after sleep onset, and multiple sleep latency from baseline to 6 months of therapy did not reach significance. The FSS, VAS-F, ESS, and HADS scores were significantly improved after 6 months of therapy; cognitive scores were not significantly improved. Conclusions: Although treatment with natalizumab was associated with improvements in fatigue, sleepiness, and mood, changes in objective measures of sleep were not significant. PMID:27551242

  1. Note: Significant increase to the temporal resolution of 2D X-ray detectors using a novel beam chopper system

    SciTech Connect

    Küchemann, Stefan; Mahn, Carsten; Samwer, Konrad

    2014-01-15

    The investigation of short time dynamics using X-ray scattering techniques is commonly limited either by the read out frequency of the detector or by a low intensity. In this paper, we present a chopper system, which can increase the temporal resolution of 2D X-ray detectors by a factor of 13. This technique only applies to amorphous or polycrystalline samples due to their circular diffraction patterns. Using the chopper, we successfully increased the temporal resolution up to 5.1 ms during synchrotron experiments. For the construction, we provide a mathematical formalism, which, in principle, allows an even higher increase of the temporal resolution.

  2. Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

    PubMed Central

    2009-01-01

    The in vitro stationary phase proteome of the human pathogen Shigella dysenteriae serotype 1 (SD1) was quantitatively analyzed in Coomassie Blue G250 (CBB)-stained 2D gels. More than four hundred and fifty proteins, of which 271 were associated with distinct gel spots, were identified. In parallel, we employed 2D-LC-MS/MS followed by the label-free computationally modified spectral counting method APEX for absolute protein expression measurements. Of the 4502 genome-predicted SD1 proteins, 1148 proteins were identified with a false positive discovery rate of 5% and quantitated using 2D-LC-MS/MS and APEX. The dynamic range of the APEX method was approximately one order of magnitude higher than that of CBB-stained spot intensity quantitation. A squared Pearson correlation analysis revealed a reasonably good correlation (R2 = 0.67) for protein quantities surveyed by both methods. The correlation was decreased for protein subsets with specific physicochemical properties, such as low Mr values and high hydropathy scores. Stoichiometric ratios of subunits of protein complexes characterized in E. coli were compared with APEX quantitative ratios of orthologous SD1 protein complexes. A high correlation was observed for subunits of soluble cellular protein complexes in several cases, demonstrating versatile applications of the APEX method in quantitative proteomics. PMID:19563668

  3. Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS)

    PubMed Central

    Widom, Julia R.; Johnson, Neil P.; von Hippel, Peter H.; Marcus, Andrew H.

    2013-01-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analog of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS) – a fluorescence-detected variation of 2D electronic spectroscopy – to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point-dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R12 = 3.5 Å ± 0.5 Å, twist angle θ12 = 5° ± 5°), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV-2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein-nucleic acid complexes. PMID:24223491

  4. Cloning and characterization of a novel human phosphatidic acid phosphatase type 2, PAP2d, with two different transcripts PAP2d_v1 and PAP2d_v2.

    PubMed

    Sun, Liyun; Gu, Shaohua; Sun, Yaqiong; Zheng, Dan; Wu, Qihan; Li, Xin; Dai, Jianfeng; Dai, Jianliang; Ji, Chaoneng; Xie, Yi; Mao, Yumin

    2005-04-01

    This study reports the cloning and characterization of a novel human phosphatidic acid phosphatase type 2 isoform cDNAs (PAP2d) from the foetal brain cDNA library. The PAP2d gene is localized on chromosome 1p21.3. It contains six exons and spans 112 kb of the genomic DNA. By large-scale cDNA sequencing we found two splice variants of PAP2d, PAP2d_v1 and PAP2d_v2. The PAP2d_v1 cDNA is 1722 bp in length and spans an open reading frame from nucleotide 56 to 1021, encoding a 321aa protein. The PAP2d_v2 cDNA is 1707 bp in length encoding a 316aa protein from nucleotide 56-1006. The PAP2d_v1 cDNA is 15 bp longer than the PAP2d_v2 cDNA in the terminal of the fifth exon and it creates different ORF. Both of the proteins contain a well-conserved PAP2 motif. The PAP2d_v1 is mainly expressed in human brain, lung, kidney, testis and colon, while PAP2d_v2 is restricted to human placenta, skeletal muscle, and kidney. The two splice variants are co-expressed only in kidney. PMID:16010976

  5. Human erythrocytes analyzed by generalized 2D Raman correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Wesełucha-Birczyńska, Aleksandra; Kozicki, Mateusz; Czepiel, Jacek; Łabanowska, Maria; Nowak, Piotr; Kowalczyk, Grzegorz; Kurdziel, Magdalena; Birczyńska, Malwina; Biesiada, Grażyna; Mach, Tomasz; Garlicki, Aleksander

    2014-07-01

    The most numerous elements of the blood cells, erythrocytes, consist mainly of two components: homogeneous interior filled with hemoglobin and closure which is the cell membrane. To gain insight into their specific properties we studied the process of disintegration, considering these two constituents, and comparing the natural aging process of human healthy blood cells. MicroRaman spectra of hemoglobin within the single RBC were recorded using 514.5, and 785 nm laser lines. The generalized 2D correlation method was applied to analyze the collected spectra. The time passed from blood donation was regarded as an external perturbation. The time was no more than 40 days according to the current storage limit of blood banks, although, the average RBC life span is 120 days. An analysis of the prominent synchronous and asynchronous cross peaks allow us to get insight into the mechanism of hemoglobin decomposition. Appearing asynchronous cross-peaks point towards globin and heme separation from each other, while synchronous shows already broken globin into individual amino acids. Raman scattering analysis of hemoglobin “wrapping”, i.e. healthy erythrocyte ghosts, allows for the following peculiarity of their behavior. The increasing power of the excitation laser induced alterations in the assemblage of membrane lipids. 2D correlation maps, obtained with increasing laser power recognized as an external perturbation, allows for the consideration of alterations in the erythrocyte membrane structure and composition, which occurs first in the proteins. Cross-peaks were observed indicating an asynchronous correlation between the senescent-cell antigen (SCA) and heme or proteins vibrations. The EPR spectra of the whole blood was analyzed regarding time as an external stimulus. The 2D correlation spectra points towards participation of the selected metal ion centers in the disintegration process.

  6. 2D to 3D conversion implemented in different hardware

    NASA Astrophysics Data System (ADS)

    Ramos-Diaz, Eduardo; Gonzalez-Huitron, Victor; Ponomaryov, Volodymyr I.; Hernandez-Fragoso, Araceli

    2015-02-01

    Conversion of available 2D data for release in 3D content is a hot topic for providers and for success of the 3D applications, in general. It naturally completely relies on virtual view synthesis of a second view given by original 2D video. Disparity map (DM) estimation is a central task in 3D generation but still follows a very difficult problem for rendering novel images precisely. There exist different approaches in DM reconstruction, among them manually and semiautomatic methods that can produce high quality DMs but they demonstrate hard time consuming and are computationally expensive. In this paper, several hardware implementations of designed frameworks for an automatic 3D color video generation based on 2D real video sequence are proposed. The novel framework includes simultaneous processing of stereo pairs using the following blocks: CIE L*a*b* color space conversions, stereo matching via pyramidal scheme, color segmentation by k-means on an a*b* color plane, and adaptive post-filtering, DM estimation using stereo matching between left and right images (or neighboring frames in a video), adaptive post-filtering, and finally, the anaglyph 3D scene generation. Novel technique has been implemented on DSP TMS320DM648, Matlab's Simulink module over a PC with Windows 7, and using graphic card (NVIDIA Quadro K2000) demonstrating that the proposed approach can be applied in real-time processing mode. The time values needed, mean Similarity Structural Index Measure (SSIM) and Bad Matching Pixels (B) values for different hardware implementations (GPU, Single CPU, and DSP) are exposed in this paper.

  7. Progress in 2D photonic crystal Fano resonance photonics

    NASA Astrophysics Data System (ADS)

    Zhou, Weidong; Zhao, Deyin; Shuai, Yi-Chen; Yang, Hongjun; Chuwongin, Santhad; Chadha, Arvinder; Seo, Jung-Hun; Wang, Ken X.; Liu, Victor; Ma, Zhenqiang; Fan, Shanhui

    2014-01-01

    In contrast to a conventional symmetric Lorentzian resonance, Fano resonance is predominantly used to describe asymmetric-shaped resonances, which arise from the constructive and destructive interference of discrete resonance states with broadband continuum states. This phenomenon and the underlying mechanisms, being common and ubiquitous in many realms of physical sciences, can be found in a wide variety of nanophotonic structures and quantum systems, such as quantum dots, photonic crystals, plasmonics, and metamaterials. The asymmetric and steep dispersion of the Fano resonance profile promises applications for a wide range of photonic devices, such as optical filters, switches, sensors, broadband reflectors, lasers, detectors, slow-light and non-linear devices, etc. With advances in nanotechnology, impressive progress has been made in the emerging field of nanophotonic structures. One of the most attractive nanophotonic structures for integrated photonics is the two-dimensional photonic crystal slab (2D PCS), which can be integrated into a wide range of photonic devices. The objective of this manuscript is to provide an in depth review of the progress made in the general area of Fano resonance photonics, focusing on the photonic devices based on 2D PCS structures. General discussions are provided on the origins and characteristics of Fano resonances in 2D PCSs. A nanomembrane transfer printing fabrication technique is also reviewed, which is critical for the heterogeneous integrated Fano resonance photonics. The majority of the remaining sections review progress made on various photonic devices and structures, such as high quality factor filters, membrane reflectors, membrane lasers, detectors and sensors, as well as structures and phenomena related to Fano resonance slow light effect, nonlinearity, and optical forces in coupled PCSs. It is expected that further advances in the field will lead to more significant advances towards 3D integrated photonics, flat

  8. 3D track initiation in clutter using 2D measurements

    NASA Astrophysics Data System (ADS)

    Lin, Lin; Kirubarajan, Thiagalingam; Bar-Shalom, Yaakov

    2001-11-01

    In this paper we present an algorithm for initiating 3-D tracks using range and azimuth (bearing) measurements from a 2-D radar on a moving platform. The work is motivated by the need to track possibly low-flying targets, e.g., cruise missiles, using reports from an aircraft-based surveillance radar. Previous work on this problem considered simple linear motion in a flat earth coordinate frame. Our research extends this to a more realistic scenario where the earth"s curvature is also considered. The target is assumed to be moving along a great circle at a constant altitude. After the necessary coordinate transformations, the measurements are nonlinear functions of the target state and the observability of target altitude is severely limited. The observability, quantified by the Cramer-Rao Lower Bound (CRLB), is very sensitive to the sensor-to-target geometry. The paper presents a Maximum Likelihood (ML) estimator for estimating the target motion parameters in the Earth Centered Earth Fixed coordinate frame from 2-D range and angle measurements. In order to handle the possibility of false measurements and missed detections, which was not considered in, we use the Probabilistic Data Association (PDA) algorithm to weight the detections in a frame. The PDA-based modified global likelihood is optimized using a numerical search. The accuracies obtained by the resulting ML-PDA estimator are quantified using the CRLB for different sensor-target configurations. It is shown that the proposed estimator is efficient, that is, it meets the CRLB. Of particular interest is the achievable accuracy for estimating the target altitude, which is not observed directly by the 2-D radar, but can be only inferred from the range and bearing observations.

  9. 2D induced gravity from the canonically gauged WZNW system

    NASA Astrophysics Data System (ADS)

    Blagojević, M.; Popović, D. S.; Sazdović, B.

    1999-02-01

    Starting from the Kac-Moody structure of the WZNW model for SL(2,R) and using the general canonical formalism, we formulate a gauge theory invariant under local SL(2,R)×SL(2,R) and diffeomorphisms. This theory represents a gauge extension of the WZNW system, defined by a difference of two simple WZNW actions. By performing a partial gauge fixing and integrating out some dynamical variables, we prove that the resulting effective theory coincides with the induced gravity in 2D. The geometric properties of the induced gravity are obtained out of the gauge properties of the WZNW system with the help of the Dirac brackets formalism.

  10. Recent update of the RPLUS2D/3D codes

    NASA Technical Reports Server (NTRS)

    Tsai, Y.-L. Peter

    1991-01-01

    The development of the RPLUS2D/3D codes is summarized. These codes utilize LU algorithms to solve chemical non-equilibrium flows in a body-fitted coordinate system. The motivation behind the development of these codes is the need to numerically predict chemical non-equilibrium flows for the National AeroSpace Plane Program. Recent improvements include vectorization method, blocking algorithms for geometric flexibility, out-of-core storage for large-size problems, and an LU-SW/UP combination for CPU-time efficiency and solution quality.

  11. Quantifying Therapeutic and Diagnostic Efficacy in 2D Microvascular Images

    NASA Technical Reports Server (NTRS)

    Parsons-Wingerter, Patricia; Vickerman, Mary B.; Keith, Patricia A.

    2009-01-01

    VESGEN is a newly automated, user-interactive program that maps and quantifies the effects of vascular therapeutics and regulators on microvascular form and function. VESGEN analyzes two-dimensional, black and white vascular images by measuring important vessel morphology parameters. This software guides the user through each required step of the analysis process via a concise graphical user interface (GUI). Primary applications of the VESGEN code are 2D vascular images acquired as clinical diagnostic images of the human retina and as experimental studies of the effects of vascular regulators and therapeutics on vessel remodeling.

  12. Transport Experiments on 2D Correlated Electron Physics in Semiconductors

    SciTech Connect

    Tsui, Daniel

    2014-03-24

    This research project was designed to investigate experimentally the transport properties of the 2D electrons in Si and GaAs, two prototype semiconductors, in several new physical regimes that were previously inaccessible to experiments. The research focused on the strongly correlated electron physics in the dilute density limit, where the electron potential energy to kinetic energy ratio rs>>1, and on the fractional quantum Hall effect related physics in nuclear demagnetization refrigerator temperature range on samples with new levels of purity and controlled random disorder.

  13. 2D/3D Synthetic Vision Navigation Display

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Kramer, Lynda J.; Arthur, J. J., III; Bailey, Randall E.; Sweeters, jason L.

    2008-01-01

    Flight-deck display software was designed and developed at NASA Langley Research Center to provide two-dimensional (2D) and three-dimensional (3D) terrain, obstacle, and flight-path perspectives on a single navigation display. The objective was to optimize the presentation of synthetic vision (SV) system technology that permits pilots to view multiple perspectives of flight-deck display symbology and 3D terrain information. Research was conducted to evaluate the efficacy of the concept. The concept has numerous unique implementation features that would permit enhanced operational concepts and efficiencies in both current and future aircraft.

  14. Efficient 2d full waveform inversion using Fortran coarray

    NASA Astrophysics Data System (ADS)

    Ryu, Donghyun; Kim, ahreum; Ha, Wansoo

    2016-04-01

    We developed a time-domain seismic inversion program using the coarray feature of the Fortran 2008 standard to parallelize the algorithm. We converted a 2d acoustic parallel full waveform inversion program with Message Passing Interface (MPI) to a coarray program and examined performance of the two inversion programs. The results show that the speed of the waveform inversion program using the coarray is slightly faster than that of the MPI version. The standard coarray lacks features for collective communication; however, it can be improved in following standards since it is introduced recently. The parallel algorithm can be applied for 3D seismic data processing.

  15. Unitary matrix models and 2D quantum gravity

    SciTech Connect

    Dalley, S. . Joseph Henry Labs.); Johnson, C.V.; Morris, T.R. . Dept. of Physics); Watterstam, A. )

    1992-09-21

    In this paper the KdV and modified KdV integrable hierarchies are shown to be different descriptions of the same 2D gravitational system - open-closed string theory. Non-perturbative solutions of the multicritical unitary matrix models map to non-singular solutions of the renormalization group equation for the string susceptibility, [P, Q] = Q. The authors also demonstrate that the large-N solutions of unitary matrix integrals in external fields, studied by Gross and Newman, equal the non-singular pure closed-string solutions of [[bar P], Q] = Q.

  16. 2-D scalable optical controlled phased-array antenna system

    NASA Astrophysics Data System (ADS)

    Chen, Maggie Yihong; Howley, Brie; Wang, Xiaolong; Basile, Panoutsopoulos; Chen, Ray T.

    2006-02-01

    A novel optoelectronically-controlled wideband 2-D phased-array antenna system is demonstrated. The inclusion of WDM devices makes a highly scalable system structure. Only (M+N) delay lines are required to control a M×N array. The optical true-time delay lines are combination of polymer waveguides and optical switches, using a single polymeric platform and are monolithically integrated on a single substrate. The 16 time delays generated by the device are measured to range from 0 to 175 ps in 11.6 ps. Far-field patterns at different steering angles in X-band are measured.

  17. Ring Correlations in Two-Dimensional (2D) Random Networks

    NASA Astrophysics Data System (ADS)

    Sadjadi, Mahdi; Thorpe, M. F.

    Amorphous materials can be characterized by their ring structure. Recently, two experimental groups imaged bilayers of vitreous silica at atomic resolution which provides a direct access to the ring structure of a 2D glass. It has been shown that experimental samples have various ring statistics, obey Aboav-Weaire law and have a distinct area law. In this work, we study correlations between rings as a function of their size and topological separation. We show that correlation is medium-range and vanishes when the separation is about three rings apart. We also present a generalization of the Aboav-Weaire law.

  18. Breakdown of wave diffusion in 2D due to loops.

    PubMed

    Haney, Matthew; Snieder, Roel

    2003-08-29

    The validity of the diffusion approximation for the intensity of multiply scattered waves is tested with numerical simulations in a strongly scattering 2D medium of finite extent. We show that the diffusion equation underestimates the intensity and attribute this to both the neglect of recurrent scattering paths and interference within diffusion theory. We present a theory to quantify this discrepancy based on counting all possible scattering paths between point scatterers. Interference phenomena, due to loop paths, are incorporated in a way similar to coherent backscattering. PMID:14525183

  19. Anomalous Hall Effect in a 2D Rashba Ferromagnet.

    PubMed

    Ado, I A; Dmitriev, I A; Ostrovsky, P M; Titov, M

    2016-07-22

    Skew scattering on rare impurity configurations is shown to dominate the anomalous Hall effect in a 2D Rashba ferromagnet. The mechanism originates in scattering on rare impurity pairs separated by distances of the order of the Fermi wavelength. The corresponding theoretical description goes beyond the conventional noncrossing approximation. The mechanism provides the only contribution to the anomalous Hall conductivity in the most relevant metallic regime and strongly modifies previously obtained results for lower energies in the leading order with respect to impurity strength. PMID:27494487

  20. Ultrathin 2D Metal-Organic Framework Nanosheets.

    PubMed

    Zhao, Meiting; Wang, Yixian; Ma, Qinglang; Huang, Ying; Zhang, Xiao; Ping, Jianfeng; Zhang, Zhicheng; Lu, Qipeng; Yu, Yifu; Xu, Huan; Zhao, Yanli; Zhang, Hua

    2015-12-01

    A facile surfactant-assisted bottom-up synthetic method to prepare a series of freestanding ultrathin 2D M-TCPP (M = Zn, Cu, Cd or Co, TCPP = tetrakis(4-carboxyphenyl)porphyrin) nanosheets with a thickness of sub-10 nm is developed. As a proof-of-concept application, some of them are successfully used as new platforms for DNA detection. The Cu-TCPP nanosheet-based sensor shows excellent fluorescent sensing performance and is used for the simultaneous detection of multiple DNA targets. PMID:26468970

  1. Finite Element Analysis of 2-D Elastic Contacts Involving FGMs

    NASA Astrophysics Data System (ADS)

    Abhilash, M. N.; Murthy, H.

    2014-05-01

    The response of elastic indenters in contact with Functionally Graded Material (FGM) coated homogeneous elastic half space has been presented in the current paper. Finite element analysis has been used due to its ability to handle complex geometry, material, and boundary conditions. Indenters of different typical surface profiles have been considered and the problem has been idealized as a two-dimensional (2D) plane strain problem considering only normal loads. Initially, indenters were considered to be rigid and the results were validated with the solutions presented in the literature. The analysis has then been extended to the case of elastic indenters on FGM-coated half spaces and the results are discussed.

  2. Topology-Preserving Rigid Transformation of 2D Digital Images.

    PubMed

    Ngo, Phuc; Passat, Nicolas; Kenmochi, Yukiko; Talbot, Hugues

    2014-02-01

    We provide conditions under which 2D digital images preserve their topological properties under rigid transformations. We consider the two most common digital topology models, namely dual adjacency and well-composedness. This paper leads to the proposal of optimal preprocessing strategies that ensure the topological invariance of images under arbitrary rigid transformations. These results and methods are proved to be valid for various kinds of images (binary, gray-level, label), thus providing generic and efficient tools, which can be used in particular in the context of image registration and warping. PMID:26270925

  3. VECTUM. Irregular 2D Velocity Vector Field Plotting Package

    SciTech Connect

    McClurg, F.R.; Mousseau, V.A.

    1992-05-04

    VECTUM is a NCAR Graphics based package, for generating a plot of an irregular 2D velocity vector field. The program reads an ASCII database of x, y, u, v, data pairs and produces a plot in Computer Graphics Metafile (CGM) format. The program also uses an ASCII parameter file for controlling annotation details such as the plot title, arrowhead style, scale of vectors, windowing, etc. Simple geometry (i.e. lines, arcs, splines) can be defined to be included with the velocity vectors. NCAR Graphics drivers can be used to display the CGM file into PostScript, HPGL, HDF, etc, output.

  4. A parallel splitting wavelet method for 2D conservation laws

    NASA Astrophysics Data System (ADS)

    Schmidt, Alex A.; Kozakevicius, Alice J.; Jakobsson, Stefan

    2016-06-01

    The current work presents a parallel formulation using the MPI protocol for an adaptive high order finite difference scheme to solve 2D conservation laws. Adaptivity is achieved at each time iteration by the application of an interpolating wavelet transform in each space dimension. High order approximations for the numerical fluxes are computed by ENO and WENO schemes. Since time evolution is made by a TVD Runge-Kutta space splitting scheme, the problem is naturally suitable for parallelization. Numerical simulations and speedup results are presented for Euler equations in gas dynamics problems.

  5. Quantum Oscillations in an Interfacial 2D Electron Gas.

    SciTech Connect

    Zhang, Bingop; Lu, Ping; Liu, Henan; Lin, Jiao; Ye, Zhenyu; Jaime, Marcelo; Balakirev, Fedor F.; Yuan, Huiqiu; Wu, Huizhen; Pan, Wei; Zhang, Yong

    2016-01-01

    Recently, it has been predicted that topological crystalline insulators (TCIs) may exist in SnTe and Pb1-xSnxTe thin films [1]. To date, most studies on TCIs were carried out either in bulk crystals or thin films, and no research activity has been explored in heterostructures. We present here the results on electronic transport properties of the 2D electron gas (2DEG) realized at the interfaces of PbTe/ CdTe (111) heterostructures. Evidence of topological state in this interfacial 2DEG was observed.

  6. The 2d MIT: The Pseudogap and Fermi Liquid Theory

    NASA Astrophysics Data System (ADS)

    Castner, T. G.

    2005-06-01

    Fermi liquid theory for the 2d metal-insulator transition is extended to include the correlation gap in the density-of-states. The results are consistent with the scaling form g=gce[on(To/T)] at T larger than a characteristic T* ∝ xTc (Tc=Ec= mobility edge). The two-component model n1+nloc=n=nc(1+x) for n>nc is required and the theory explains the T-dependence of the data of Hanein et al. for p-type GaAs.

  7. New perspective on matter coupling in 2D quantum gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, J.; Anagnostopoulos, K. N.; Loll, R.

    1999-11-01

    We provide compelling evidence that a previously introduced model of nonperturbative 2D Lorentzian quantum gravity exhibits (two-dimensional) flat-space behavior when coupled to Ising spins. The evidence comes from both a high-temperature expansion and from Monte Carlo simulations of the combined gravity-matter system. This weak-coupling behavior lends further support to the conclusion that the Lorentzian model is a genuine alternative to Liouville quantum gravity in two dimensions, with a different and much ``smoother'' critical behavior.

  8. The quantum spacetime of c > 0 2 d gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, J.; Anagnostopoulos, K. N.; Thorleifsson, G.

    1998-04-01

    We review recent developments in the understanding of the fractal properties of quantum spacetime of 2d gravity coupled to c > 0 conformal matter. In particular we discuss bounds put by numerical simulations using dynamical triangulations on the value of the Hausdorff dimension dH obtained from scaling properties of two point functions defined in terms of geodesic distance. Further insight to the fractal structure of spacetime is obtained from the study of the loop length distribution function which reveals that the 0 < c ≤ 1 system has similar geometric properties with pure gravity, whereas the branched polymer structure becomes clear for c ≥ 5.

  9. Black liquor gasification phase 2D final report

    SciTech Connect

    Kohl, A.L.; Stewart, A.E.

    1988-06-01

    This report covers work conducted by Rockwell International under Amendment 5 to Subcontract STR/DOE-12 of Cooperative Agreement DE-AC-05-80CS40341 between St. Regis Corporation (now Champion International) and the Department of Energy (DOE). The work has been designated Phase 2D of the overall program to differentiate it from prior work under the same subcontract. The overall program is aimed at demonstrating the feasibility of and providing design data for the Rockwell process for gasifying Kraft black liquor. In this process, concentrated black liquor is converted into low-Btu fuel gas and reduced melt by reaction with air in a specially designed gasification reactor.

  10. Real-time SPECT and 2D ultrasound image registration.

    PubMed

    Bucki, Marek; Chassat, Fabrice; Galdames, Francisco; Asahi, Takeshi; Pizarro, Daniel; Lobo, Gabriel

    2007-01-01

    In this paper we present a technique for fully automatic, real-time 3D SPECT (Single Photon Emitting Computed Tomography) and 2D ultrasound image registration. We use this technique in the context of kidney lesion diagnosis. Our registration algorithm allows a physician to perform an ultrasound exam after a SPECT image has been acquired and see in real time the registration of both modalities. An automatic segmentation algorithm has been implemented in order to display in 3D the positions of the acquired US images with respect to the organs. PMID:18044572

  11. Beam-Plasma Instabilities in a 2D Yukawa Lattice

    SciTech Connect

    Kyrkos, S.; Kalman, G. J.; Rosenberg, M.

    2009-06-05

    We consider a 2D Yukawa lattice of grains, with a beam of other charged grains moving in the lattice plane. In contrast to Vlasov plasmas, where the electrostatic instability excited by the beam is only longitudinal, here both longitudinal and transverse instabilities of the lattice phonons can develop. We determine and compare the transverse and longitudinal growth rates. The growth rate spectrum in wave number space exhibits remarkable gaps where no instability can develop. Depending on the system parameters, the transverse instability can be selectively excited.

  12. Secondary-Progressive MS (SPMS)

    MedlinePlus

    ... spite of the medication you are taking, the conversation with your MS care provider might be about ... SPMS is stable without activity or progression, the conversation with your MS care could focus on rehabilitation ...

  13. In vivo 1D and 2D correlation MR spectroscopy of the soleus muscle at 7T

    NASA Astrophysics Data System (ADS)

    Ramadan, Saadallah; Ratai, Eva-Maria; Wald, Lawrence L.; Mountford, Carolyn E.

    2010-05-01

    AimThis study aims to (1) undertake and analyse 1D and 2D MR correlation spectroscopy from human soleus muscle in vivo at 7T, and (2) determine T1 and T2 relaxation time constants at 7T field strength due to their importance in sequence design and spectral quantitation. MethodSix healthy, male volunteers were consented and scanned on a 7T whole-body scanner (Siemens AG, Erlangen, Germany). Experiments were undertaken using a 28 cm diameter detunable birdcage coil for signal excitation and an 8.5 cm diameter surface coil for signal reception. The relaxation time constants, T1 and T2 were recorded using a STEAM sequence, using the 'progressive saturation' method for the T1 and multiple echo times for T2. The 2D L-Correlated SpectroscopY (L-COSY) method was employed with 64 increments (0.4 ms increment size) and eight averages per scan, with a total time of 17 min. ResultsT1 and T2 values for the metabolites of interest were determined. The L-COSY spectra obtained from the soleus muscle provided information on lipid content and chemical structure not available, in vivo, at lower field strengths. All molecular fragments within multiple lipid compartments were chemically shifted by 0.20-0.26 ppm at this field strength. 1D and 2D L-COSY spectra were assigned and proton connectivities were confirmed with the 2D method. ConclusionIn vivo 1D and 2D spectroscopic examination of muscle can be successfully recorded at 7T and is now available to assess lipid alterations as well as other metabolites present with disease. T1 and T2 values were also determined in soleus muscle of male healthy volunteers.

  14. 2D wax-printed paper substrates with extended solvent supply capabilities allow enhanced ion signal in paper spray ionization.

    PubMed

    Damon, Deidre E; Maher, Yosef S; Yin, Mengzhen; Jjunju, Fred P M; Young, Iain S; Taylor, Stephen; Maher, Simon; Badu-Tawiah, Abraham K

    2016-06-21

    Paper-based microfluidic channels were created from solid wax printing, and the resultant 2D wax-printed paper substrates were used for paper spray (PS) mass spectrometry (MS) analysis of small organic compounds. Controlling fluid flow at the tip of the wax-printed paper triangles enabled the use of lower spray voltages (0.5-1 kV) and extended signal lifetime (10 minutes) in PS-MS. High sensitivity (sub ng mL(-1) levels) and quantitation precision (<10% RSD) have been achieved in the analysis of illicit drugs in 4 μL of raw urine (fresh and dry), as well as corrosion inhibitors and pesticides in water samples. The reported study encourages the future development of disposable 3D microfluidic paper-based analytical devices, which function with simple operation but capable of on-chip analyte detection by MS; such a device can replace the traditional complex laboratory procedures for MS analysis to enable on-site in situ sampling with portable mass spectrometers. PMID:27121269

  15. Inhibitory effects of phytochemicals on metabolic capabilities of CYP2D6*1 and CYP2D6*10 using cell-based models in vitro

    PubMed Central

    Qu, Qiang; Qu, Jian; Han, Lu; Zhan, Min; Wu, Lan-xiang; Zhang, Yi-wen; Zhang, Wei; Zhou, Hong-hao

    2014-01-01

    Aim: Herbal products have been widely used, and the safety of herb-drug interactions has aroused intensive concerns. This study aimed to investigate the effects of phytochemicals on the catalytic activities of human CYP2D6*1 and CYP2D6*10 in vitro. Methods: HepG2 cells were stably transfected with CYP2D6*1 and CYP2D6*10 expression vectors. The metabolic kinetics of the enzymes was studied using HPLC and fluorimetry. Results: HepG2-CYP2D6*1 and HepG2-CYP2D6*10 cell lines were successfully constructed. Among the 63 phytochemicals screened, 6 compounds, including coptisine sulfate, bilobalide, schizandrin B, luteolin, schizandrin A and puerarin, at 100 μmol/L inhibited CYP2D6*1- and CYP2D6*10-mediated O-demethylation of a coumarin compound AMMC by more than 50%. Furthermore, the inhibition by these compounds was dose-dependent. Eadie-Hofstee plots demonstrated that these compounds competitively inhibited CYP2D6*1 and CYP2D6*10. However, their Ki values for CYP2D6*1 and CYP2D6*10 were very close, suggesting that genotype-dependent herb-drug inhibition was similar between the two variants. Conclusion: Six phytochemicals inhibit CYP2D6*1 and CYP2D6*10-mediated catalytic activities in a dose-dependent manner in vitro. Thus herbal products containing these phytochemicals may inhibit the in vivo metabolism of co-administered drugs whose primary route of elimination is CYP2D6. PMID:24786236

  16. Preconditioning 2D Integer Data for Fast Convex Hull Computations.

    PubMed

    Cadenas, José Oswaldo; Megson, Graham M; Luengo Hendriks, Cris L

    2016-01-01

    In order to accelerate computing the convex hull on a set of n points, a heuristic procedure is often applied to reduce the number of points to a set of s points, s ≤ n, which also contains the same hull. We present an algorithm to precondition 2D data with integer coordinates bounded by a box of size p × q before building a 2D convex hull, with three distinct advantages. First, we prove that under the condition min(p, q) ≤ n the algorithm executes in time within O(n); second, no explicit sorting of data is required; and third, the reduced set of s points forms a simple polygonal chain and thus can be directly pipelined into an O(n) time convex hull algorithm. This paper empirically evaluates and quantifies the speed up gained by preconditioning a set of points by a method based on the proposed algorithm before using common convex hull algorithms to build the final hull. A speedup factor of at least four is consistently found from experiments on various datasets when the condition min(p, q) ≤ n holds; the smaller the ratio min(p, q)/n is in the dataset, the greater the speedup factor achieved. PMID:26938221

  17. Magnetic gating of a 2D topological insulator.

    PubMed

    Dang, Xiaoqian; Burton, J D; Tsymbal, Evgeny Y

    2016-09-28

    Deterministic control of transport properties through manipulation of spin states is one of the paradigms of spintronics. Topological insulators offer a new playground for exploring interesting spin-dependent phenomena. Here, we consider a ferromagnetic 'gate' representing a magnetic adatom coupled to the topologically protected edge state of a two-dimensional (2D) topological insulator to modulate the electron transmission of the edge state. Due to the locked spin and wave vector of the transport electrons the transmission across the magnetic gate depends on the mutual orientation of the adatom magnetic moment and the current. If the Fermi energy matches an exchange-split bound state of the adatom, the electron transmission can be blocked due to the full back scattering of the incident wave. This antiresonance behavior is controlled by the adatom magnetic moment orientation so that the transmission of the edge state can be changed from 1 to 0. Expanding this consideration to a ferromagnetic gate representing a 1D chain of atoms shows a possibility to control the spin-dependent current of a strip of a 2D topological insulator by magnetization orientation of the ferromagnetic gate. PMID:27437829

  18. MESH2D GRID GENERATOR DESIGN AND USE

    SciTech Connect

    Flach, G.; Smith, F.

    2012-01-20

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j{sub 0}) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations. The overall mesh is constructed from grid zones that are typically then subdivided into a collection of smaller grid cells. The grid zones usually correspond to distinct materials or larger-scale geometric shapes. The structured grid zones are identified through uppercase indices (I,J). Subdivision of zonal regions into grid cells can be done uniformly, or nonuniformly using either a polynomial or geometric skewing algorithm. Grid cells may be concentrated backward, forward, or toward both ends. Figure 1 illustrates the above concepts in the context of a simple four zone grid.

  19. 3D surface configuration modulates 2D symmetry detection.

    PubMed

    Chen, Chien-Chung; Sio, Lok-Teng

    2015-02-01

    We investigated whether three-dimensional (3D) information in a scene can affect symmetry detection. The stimuli were random dot patterns with 15% dot density. We measured the coherence threshold, or the proportion of dots that were the mirror reflection of the other dots in the other half of the image about a central vertical axis, at 75% accuracy with a 2AFC paradigm under various 3D configurations produced by the disparity between the left and right eye images. The results showed that symmetry detection was difficult when the corresponding dots across the symmetry axis were on different frontoparallel or inclined planes. However, this effect was not due to a difference in distance, as the observers could detect symmetry on a slanted surface, where the depth of the two sides of the symmetric axis was different. The threshold was reduced for a hinge configuration where the join of two slanted surfaces coincided with the axis of symmetry. Our result suggests that the detection of two-dimensional (2D) symmetry patterns is subject to the 3D configuration of the scene; and that coplanarity across the symmetry axis and consistency between the 2D pattern and 3D structure are important factors for symmetry detection. PMID:25536469

  20. Mass loss in 2D rotating stellar models

    SciTech Connect

    Lovekin, Caterine; Deupree, Bob

    2010-10-05

    Radiatively driven mass loss is an important factor in the evolution of massive stars . The mass loss rates depend on a number of stellar parameters, including the effective temperature and luminosity. Massive stars are also often rapidly rotating, which affects their structure and evolution. In sufficiently rapidly rotating stars, both the effective temperature and radius vary significantly as a function of latitude, and hence mass loss rates can vary appreciably between the poles and the equator. In this work, we discuss the addition of mass loss to a 2D stellar evolution code (ROTORC) and compare evolution sequences with and without mass loss. Preliminary results indicate that a full 2D calculation of mass loss using the local effective temperature and luminosity can significantly affect the distribution of mass loss in rotating main sequence stars. More mass is lost from the pole than predicted by 1D models, while less mass is lost at the equator. This change in the distribution of mass loss will affect the angular momentum loss, the surface temperature and luminosity, and even the interior structure of the star. After a single mass loss event, these effects are small, but can be expected to accumulate over the course of the main sequence evolution.

  1. Modelling RF sources using 2-D PIC codes

    SciTech Connect

    Eppley, K.R.

    1993-03-01

    In recent years, many types of RF sources have been successfully modelled using 2-D PIC codes. Both cross field devices (magnetrons, cross field amplifiers, etc.) and pencil beam devices (klystrons, gyrotrons, TWT`S, lasertrons, etc.) have been simulated. All these devices involve the interaction of an electron beam with an RF circuit. For many applications, the RF structure may be approximated by an equivalent circuit, which appears in the simulation as a boundary condition on the electric field (``port approximation``). The drive term for the circuit is calculated from the energy transfer between beam and field in the drift space. For some applications it may be necessary to model the actual geometry of the structure, although this is more expensive. One problem not entirely solved is how to accurately model in 2-D the coupling to an external waveguide. Frequently this is approximated by a radial transmission line, but this sometimes yields incorrect results. We also discuss issues in modelling the cathode and injecting the beam into the PIC simulation.

  2. Flatbands in 2D boroxine-linked covalent organic frameworks.

    PubMed

    Wang, Rui-Ning; Zhang, Xin-Ran; Wang, Shu-Fang; Fu, Guang-Sheng; Wang, Jiang-Long

    2016-01-14

    Density functional calculations have been performed to analyze the electronic and mechanical properties of a number of 2D boroxine-linked covalent organic frameworks (COFs), which are experimentally fabricated from di-borate aromatic molecules. Furthermore, the band structures are surprising and show flat-band characteristics which are mainly attributed to the delocalized π-conjugated electrons around the phenyl rings and can be better understood within aromaticity theories. Next, the effects of branch sizes and hydrostatic strains on their band structures are systematically considered within generalized gradient approximations. It is found that their band gaps will start to saturate when the branch size reaches 9. For boroxine-linked COFs with only one benzene ring in the branch, the band gap is robust under compressive strain while it decreases with the tensile strain increasing. When the branch size is equal or greater than 2, their band gaps will monotonously increase with the strain increasing in the range of [-1.0, 2.0] Å. All boroxine-linked COFs are semiconductors with controllable band gaps, depending on the branch length and the applied strain. In comparison with other 2D materials, such as graphene, hexagonal boron nitride, and even γ-graphyne, all boroxine-linked COFs are much softer and even more stable. That is, they can maintain the planar features under a larger compressive strain, which means that they are good candidates in flexible electronics. PMID:26662215

  3. Magnetic gating of a 2D topological insulator

    NASA Astrophysics Data System (ADS)

    Dang, Xiaoqian; Burton, J. D.; Tsymbal, Evgeny Y.

    2016-09-01

    Deterministic control of transport properties through manipulation of spin states is one of the paradigms of spintronics. Topological insulators offer a new playground for exploring interesting spin-dependent phenomena. Here, we consider a ferromagnetic ‘gate’ representing a magnetic adatom coupled to the topologically protected edge state of a two-dimensional (2D) topological insulator to modulate the electron transmission of the edge state. Due to the locked spin and wave vector of the transport electrons the transmission across the magnetic gate depends on the mutual orientation of the adatom magnetic moment and the current. If the Fermi energy matches an exchange-split bound state of the adatom, the electron transmission can be blocked due to the full back scattering of the incident wave. This antiresonance behavior is controlled by the adatom magnetic moment orientation so that the transmission of the edge state can be changed from 1 to 0. Expanding this consideration to a ferromagnetic gate representing a 1D chain of atoms shows a possibility to control the spin-dependent current of a strip of a 2D topological insulator by magnetization orientation of the ferromagnetic gate.

  4. Sigma-delta cellular neural network for 2D modulation.

    PubMed

    Aomori, Hisashi; Otake, Tsuyoshi; Takahashi, Nobuaki; Tanaka, Mamoru

    2008-01-01

    Although sigma-delta modulation is widely used for analog-to-digital (A/D) converters, sigma-delta concepts are only for 1D signals. Signal processing in the digital domain is extremely useful for 2D signals such as used in image processing, medical imaging, ultrasound imaging, and so on. The intricate task that provides true 2D sigma-delta modulation is feasible in the spatial domain sigma-delta modulation using the discrete-time cellular neural network (DT-CNN) with a C-template. In the proposed architecture, the A-template is used for a digital-to-analog converter (DAC), the C-template works as an integrator, and the nonlinear output function is used for the bilevel output. In addition, due to the cellular neural network (CNN) characteristics, each pixel of an image corresponds to a cell of a CNN, and each cell is connected spatially by the A-template. Therefore, the proposed system can be thought of as a very large-scale and super-parallel sigma-delta modulator. Moreover, the spatio-temporal dynamics is designed to obtain an optimal reconstruction signal. The experimental results show the excellent reconstruction performance and capabilities of the CNN as a sigma-delta modulator. PMID:18215502

  5. New Approach for 2D Readout of GEM Detectors

    SciTech Connect

    Hasell, Douglas K

    2011-10-29

    Detectors based on Gas Electron Multiplication (GEM) technology are becoming more and more widely used in nuclear and high energy physics and are being applied in astronomy, medical physics, industry, and homeland security. GEM detectors are thin, low mass, insensitive to magnetic fields, and can currently provide position resolutions down to {approx}50 microns. However, the designs for reconstructing the position, in two dimensions (2D), of the charged particles striking a GEM detector are often complicated to fabricate and expensive. The objective of this proposal is to investigate a simpler procedure for producing the two dimensional readout layer of GEM detectors using readily available printed circuit board technology which can be tailored to the detector requirements. We will use the established GEM laboratory and facilities at M.I.T. currently employed in developing GEM detectors for the STAR forward tracking upgrade to simplify the testing and evaluation of the new 2D readout designs. If this new design proves successful it will benefit future nuclear and high energy physics experiments already being planned and will similarly extend and simplify the application of GEM technology to other branches of science, medicine, and industry. These benefits would be not only in lower costs for fabrication but also it increased flexibility for design and application.

  6. The effects of aging on haptic 2D shape recognition.

    PubMed

    Overvliet, Krista E; Wagemans, J; Krampe, Ralf T

    2013-12-01

    We use the image-mediation model (Klatzky & Lederman, 1987) as a framework to investigate potential sources of adult age differences in the haptic recognition of two-dimensional (2D) shapes. This model states that the low-resolution, temporally sequential, haptic input is translated into a visual image, which is then reperceived through the visual processors, before it is matched against a long-term memory representation and named. In three experiments we tested groups of 12 older (mean age 73.11) and three groups of 12 young adults (mean age 22.80) each. In Experiment 1 we confirm age-related differences in haptic 2D shape recognition, and we show the typical age × complexity interaction. In Experiment 2 we show that if we facilitate the visual translation process, age differences become smaller, but only with simple shapes and not with the more complex everyday objects. In Experiment 3 we target the last step in the model (matching and naming) for complex stimuli. We found that age differences in exploration time were considerably reduced when this component process was facilitated by providing a category name. We conclude that the image-mediation model can explain adult-age differences in haptic recognition, particularly if the role of working memory in forming the transient visual image is considered. Our findings suggest that sensorimotor skills thought to rely on peripheral processes for the most part are critically constrained by age-related changes in central processing capacity in later adulthood. PMID:23978010

  7. Using dispersive medium to control excitons in 2D materials

    NASA Astrophysics Data System (ADS)

    Klots, Andrey; Bolotin, Kirill I.

    Excitons in 2D materials (2DMs) are known to be sensitive to the surrounding environment. This makes it possible to modify 2D excitons by depositing materials with controlled dielectric constant on top of 2DMs. This possibility becomes especially interesting if we consider materials with dielectric permittivity ɛ that depends both on wavevector k (this happens if the medium is spatially non-uniform) and frequency ω. Here, we develop platforms to control ɛ (k , ω) and explore resulting changes in light-matter interactions of 2DMs. To examine the effect of wavevector-dependent permittivity of the medium, we study absorption/photoluminescence of graphene and MoS2 in the vicinity of highly non-uniform medium - an array of metal nanoparticles, 3-5 nm in diameter. In this case absorption of light can lead to creation of excitons with non-zero momentum. These dark states are not accessible via regular absorption spectroscopy. We study the case of frequency-dependent permittivity by surrounding MoS2 by a highly-dispersive media (e.g. dielectric liquids, graphene and VO2) . We demonstrate non-trivial frequency-dependent renormalization of the quasiparticle bandgap and exciton binding energies.

  8. Suspended 2-D photonic crystal aluminum nitride membrane reflector.

    PubMed

    Ho, Chong Pei; Pitchappa, Prakash; Soon, Bo Woon; Lee, Chengkuo

    2015-04-20

    We experimentally demonstrated a free-standing two-dimensional (2-D) photonic crystal (PhC) aluminum nitride (AlN) membrane to function as a free space (or out-of-plane) reflector working in the mid infrared region. By etching circular holes of radius 620nm in a 330nm thick AlN slab, greater than 90% reflection was measured from 3.08μm to 3.78μm, with the peak reflection of 96% at 3.16μm. Due to the relatively low refractive index of AlN, we also investigated the importance of employing methods such as sacrificial layer release to enhance the performance of the PhC. In addition, characterization of the AlN based PhC was also done up to 450°C to examine the impact of thermo-optic effect on the performance. Despite the high temperature operation, the redshift in the peak reflection wavelengths of the device was estimated to be only 14.1nm. This equates to a relatively low thermo-optic coefficient 2.22 × 10(-5) K(-1) for AlN. Such insensitivity to thermo-optic effect makes AlN based 2-D PhC a promising technology to be used as photonic components for high temperature applications such as Fabry-Perot interferometer used for gas sensing in down-hole oil drilling and ruggedized electronics. PMID:25969099

  9. 2D NMR-spectroscopic screening reveals polyketides in ladybugs

    PubMed Central

    Deyrup, Stephen T.; Eckman, Laura E.; McCarthy, Patrick H.; Smedley, Scott R.; Meinwald, Jerrold; Schroeder, Frank C.

    2011-01-01

    Small molecules of biological origin continue to yield the most promising leads for drug design, but systematic approaches for exploring nature’s cache of structural diversity are lacking. Here, we demonstrate the use of 2D NMR spectroscopy to screen a library of biorationally selected insect metabolite samples for partial structures indicating the presence of new chemical entities. This NMR-spectroscopic survey enabled detection of novel compounds in complex metabolite mixtures without prior fractionation or isolation. Our screen led to discovery and subsequent isolation of two families of tricyclic pyrones in Delphastus catalinae, a tiny ladybird beetle that is employed commercially as a biological pest control agent. The D. catalinae pyrones are based on 23-carbon polyketide chains forming 1,11-dioxo-2,6,10-trioxaanthracene and 4,8-dioxo-1,9,13-trioxaanthracene derivatives, representing ring systems not previously found in nature. This study highlights the utility of 2D NMR-spectroscopic screening for exploring nature’s structure space and suggests that insect metabolomes remain vastly underexplored. PMID:21646540

  10. 2D NMR-spectroscopic screening reveals polyketides in ladybugs.

    PubMed

    Deyrup, Stephen T; Eckman, Laura E; McCarthy, Patrick H; Smedley, Scott R; Meinwald, Jerrold; Schroeder, Frank C

    2011-06-14

    Small molecules of biological origin continue to yield the most promising leads for drug design, but systematic approaches for exploring nature's cache of structural diversity are lacking. Here, we demonstrate the use of 2D NMR spectroscopy to screen a library of biorationally selected insect metabolite samples for partial structures indicating the presence of new chemical entities. This NMR-spectroscopic survey enabled detection of novel compounds in complex metabolite mixtures without prior fractionation or isolation. Our screen led to discovery and subsequent isolation of two families of tricyclic pyrones in Delphastus catalinae, a tiny ladybird beetle that is employed commercially as a biological pest control agent. The D. catalinae pyrones are based on 23-carbon polyketide chains forming 1,11-dioxo-2,6,10-trioxaanthracene and 4,8-dioxo-1,9,13-trioxaanthracene derivatives, representing ring systems not previously found in nature. This study highlights the utility of 2D NMR-spectroscopic screening for exploring nature's structure space and suggests that insect metabolomes remain vastly underexplored. PMID:21646540

  11. Dynamic sector processing using 2D assignment for rotating radars

    NASA Astrophysics Data System (ADS)

    Habtemariam, Biruk K.; Tharmarasa, R.; Pelletier, M.; Kirubarajan, T.

    2011-09-01

    Electronically scanned array radars as well as mechanically steered rotating antennas return measurements with different time stamps during the same scan while sweeping form one region to another. Data association algorithms process the measurements at the end of the scan in order to satisfy the common one measurement per track assumption. Data processing at the end of a full scan resulted in delayed target state update. This issue becomes more apparent while tracking fast moving targets with low scan rate sensors. In this paper, we present new dynamic sector processing algorithm using 2D assignment for continuously scanning radars. A complete scan can be divided into sectors, which could be as small as a single detection, depending on the scanning rate and sparsity of targets. Data association followed by filtering and target state update is done dynamically while sweeping from one end to another. Along with the benefit of immediate track updates, continuous tracking results in challenges such as multiple targets spanning multiple sectors and targets crossing consecutive sectors. Also, associations performed in the current sector may require changes in association done in previous sectors. Such difficulties are resolved by the proposed 2D assignment algorithm that implements an incremental Hungarian assignment technique. The algorithm offers flexibility with respect to assignment variables for fusing of measurements received in consecutive sectors. Furthermore the proposed technique can be extended to multiframe assignment for jointly processing data from multiple scanning radars. Experimental results based on rotating radars are presented.

  12. A Hierarchical Control Strategy For 2-D Object Recognition

    NASA Astrophysics Data System (ADS)

    Cullen, Mark F.; Kuszmaul, Christopher L.; Ramsey, Timothy S.

    1988-02-01

    A control strategy for 2-D object recognition has been implemented on a hardware configuration which includes a Symbolics Lisp Machine (TM) as a front-end processor to a 16,384 processor Connection Machine (TM). The goal of this ongoing research program is to develop an image analysis system as an aid to human image interpretation experts. Our efforts have concentrated on 2-D object recognition in aerial imagery specifically, the detection and identification of aircraft near the Danbury, CT airport. Image processing functions to label and extract image features are implemented on the Connection Machine for robust computation. A model matching function was also designed and implemented on the CM for object recognition. In this paper we report on the integration of these algorithms on the CM, with a hierarchical control strategy to focus and guide the object recognition task to particular objects and regions of interest in imagery. It will be shown that these tech-nigues may be used to manipulate imagery on the order of 2k x 2k pixels in near-real-time.

  13. 2D Gridded Surface Data Value-Added Product

    SciTech Connect

    Tang, Q; Xie, S

    2015-08-30

    This report describes the Atmospheric Radiation Measurement (ARM) Best Estimate (ARMBE) 2-dimensional (2D) gridded surface data (ARMBE2DGRID) value-added product. Spatial variability is critically important to many scientific studies, especially those that involve processes of great spatial variations at high temporal frequency (e.g., precipitation, clouds, radiation, etc.). High-density ARM sites deployed at the Southern Great Plains (SGP) allow us to observe the spatial patterns of variables of scientific interests. The upcoming megasite at SGP with its enhanced spatial density will facilitate the studies at even finer scales. Currently, however, data are reported only at individual site locations at different time resolutions for different datastreams. It is difficult for users to locate all the data they need and requires extra effort to synchronize the data. To address these problems, the ARMBE2DGRID value-added product merges key surface measurements at the ARM SGP sites and interpolates the data to a regular 2D grid to facilitate the data application.

  14. Frictional drag between two dilute 2D hole layers

    NASA Astrophysics Data System (ADS)

    Pillarisetty, R.; Noh, H.; Tsui, D. C.; de Poortere, E. P.; Tutuc, E.; Shayegan, M.

    2002-03-01

    We present results of drag measurements on 2D hole systems in the low density limit (rs ranging from 19 to 39), close to their apparent B=0 metal to insulator transitions at p ~ 8.5×10^9 cm-2. The drag resistivity(ρ_D) of our sample, with a 300 Å center to center quantum well separation, is 1.5 kΩ/ Box for 1.5×10^10 cm-2 at 1 K. This is sufficiently large to allow measurements at dilution fridge temperatures to study whether the 2D hole systems show non-Fermi liquid behavior. We find that for Talt0.5T_F, the data exhibit a slightly stronger than T^2 dependence. As the temperature is further increased we find a crossover to a linear dependence, and ρ_D/T^2 vs T exhibits a peak similar to that observed in previous experiments involving phonon mediated electron-electron scattering and plasmon enhancement. Unlike these previous reports, which exhibited a local maxima in ρD around matched densities, our samples show a clearly monotonic dependence upon either layer density. These results will be discussed in light of interaction effects expected in such a large rs regime.

  15. Marginal fluctuations as instantons on M2/D2-branes

    NASA Astrophysics Data System (ADS)

    Naghdi, M.

    2014-03-01

    We introduce some (anti-) M/D-branes through turning on the corresponding field strengths of the 11- and 10-dimensional supergravity theories over spaces, where we use and for the internal spaces. Indeed, when we add M2/D2-branes on the same directions with the near horizon branes of the Aharony-Bergman-Jafferis-Maldacena model, all symmetries and supersymmetries are preserved trivially. In this case, we obtain a localized object just in the horizon. This normalizable bulk massless scalar mode is a singlet of and , and it agrees with a marginal boundary operator of the conformal dimension of . However, after performing a special conformal transformation, we see that the solution is localized in the Euclideanized space and is attributable to the included anti-M2/D2-branes, which are also necessary to ensure that there is no back-reaction. The resultant theory now breaks all supersymmetries to , while the other symmetries are so preserved. The dual boundary operator is then set up from the skew-whiffing of the representations and for the supercharges and scalars, respectively, while the fermions remain fixed in of the original theory. Besides, we also address another alternate bulk to boundary matching procedure through turning on one of the gauge fields of the full gauge group along the same lines with a similar situation to the one faced in the AdS/CFT correspondence. The latter approach covers the difficulty already faced with in the bulk-boundary matching procedure for as well.

  16. Predicting non-square 2D dice probabilities

    NASA Astrophysics Data System (ADS)

    Pender, G. A. T.; Uhrin, M.

    2014-07-01

    The prediction of the final state probabilities of a general cuboid randomly thrown onto a surface is a problem that naturally arises in the minds of men and women familiar with regular cubic dice and the basic concepts of probability. Indeed, it was considered by Newton in 1664 (Newton 1967 The Mathematical Papers of Issac Newton vol I (Cambridge: Cambridge University Press) pp 60-1). In this paper we make progress on the 2D problem (which can be realized in 3D by considering a long cuboid, or alternatively a rectangular cross-sectioned dreidel). For the two-dimensional case we suggest that the ratio of the probabilities of landing on each of the two sides is given by \\frac{\\sqrt{{{k}^{2}}+{{l}^{2}}}-k}{\\sqrt{{{k}^{2}}+{{l}^{2}}}-l}\\frac{arctan \\frac{l}{k}}{arctan \\frac{k}{l}} where k and l are the lengths of the two sides. We test this theory both experimentally and computationally, and find good agreement between our theory, experimental and computational results. Our theory is known, from its derivation, to be an approximation for particularly bouncy or ‘grippy’ surfaces where the die rolls through many revolutions before settling. On real surfaces we would expect (and we observe) that the true probability ratio for a 2D die is a somewhat closer to unity than predicted by our theory. This problem may also have wider relevance in the testing of physics engines.

  17. Preconditioning 2D Integer Data for Fast Convex Hull Computations

    PubMed Central

    2016-01-01

    In order to accelerate computing the convex hull on a set of n points, a heuristic procedure is often applied to reduce the number of points to a set of s points, s ≤ n, which also contains the same hull. We present an algorithm to precondition 2D data with integer coordinates bounded by a box of size p × q before building a 2D convex hull, with three distinct advantages. First, we prove that under the condition min(p, q) ≤ n the algorithm executes in time within O(n); second, no explicit sorting of data is required; and third, the reduced set of s points forms a simple polygonal chain and thus can be directly pipelined into an O(n) time convex hull algorithm. This paper empirically evaluates and quantifies the speed up gained by preconditioning a set of points by a method based on the proposed algorithm before using common convex hull algorithms to build the final hull. A speedup factor of at least four is consistently found from experiments on various datasets when the condition min(p, q) ≤ n holds; the smaller the ratio min(p, q)/n is in the dataset, the greater the speedup factor achieved. PMID:26938221

  18. The unitary conformal field theory behind 2D Asymptotic Safety

    NASA Astrophysics Data System (ADS)

    Nink, Andreas; Reuter, Martin

    2016-02-01

    Being interested in the compatibility of Asymptotic Safety with Hilbert space positivity (unitarity), we consider a local truncation of the functional RG flow which describes quantum gravity in d > 2 dimensions and construct its limit of exactly two dimensions. We find that in this limit the flow displays a nontrivial fixed point whose effective average action is a non-local functional of the metric. Its pure gravity sector is shown to correspond to a unitary conformal field theory with positive central charge c = 25. Representing the fixed point CFT by a Liouville theory in the conformal gauge, we investigate its general properties and their implications for the Asymptotic Safety program. In particular, we discuss its field parametrization dependence and argue that there might exist more than one universality class of metric gravity theories in two dimensions. Furthermore, studying the gravitational dressing in 2D asymptotically safe gravity coupled to conformal matter we uncover a mechanism which leads to a complete quenching of the a priori expected Knizhnik-Polyakov-Zamolodchikov (KPZ) scaling. A possible connection of this prediction to Monte Carlo results obtained in the discrete approach to 2D quantum gravity based upon causal dynamical triangulations is mentioned. Similarities of the fixed point theory to, and differences from, non-critical string theory are also described. On the technical side, we provide a detailed analysis of an intriguing connection between the Einstein-Hilbert action in d > 2 dimensions and Polyakov's induced gravity action in two dimensions.

  19. Facial biometrics based on 2D vector geometry

    NASA Astrophysics Data System (ADS)

    Malek, Obaidul; Venetsanopoulos, Anastasios; Androutsos, Dimitrios

    2014-05-01

    The main challenge of facial biometrics is its robustness and ability to adapt to changes in position orientation, facial expression, and illumination effects. This research addresses the predominant deficiencies in this regard and systematically investigates a facial authentication system in the Euclidean domain. In the proposed method, Euclidean geometry in 2D vector space is being constructed for features extraction and the authentication method. In particular, each assigned point of the candidates' biometric features is considered to be a 2D geometrical coordinate in the Euclidean vector space. Algebraic shapes of the extracted candidate features are also computed and compared. The proposed authentication method is being tested on images from the public "Put Face Database". The performance of the proposed method is evaluated based on Correct Recognition (CRR), False Acceptance (FAR), and False Rejection (FRR) rates. The theoretical foundation of the proposed method along with the experimental results are also presented in this paper. The experimental results demonstrate the effectiveness of the proposed method.

  20. Three-bosons in 2D with a magnetic field

    NASA Astrophysics Data System (ADS)

    Rittenhouse, Seth; Johnson, Brad; Wray, Andrew; D'Incao, Jose

    2016-05-01

    Systems of interacting particles in reduced dimensions in the presence of external fields can exhibit a number of surprising behaviors, for instance the emergence of the fractional quantum Hall effect. Examining few-body interactions and effects can lead to significant insights within these systems. In this talk we examine a system of three bosons confined to two dimensions in the presence of a perpendicular magnetic field within the framework of the adiabatic hyperspherical method. For the case of zero-range, regularized pseudo-potential interactions, we find that the system is nearly separable in hyperspherical coordinates and that, away from a set of narrow avoided crossings, the full energy eigenspectrum as a function of the 2D s-wave scattering length is well described by ignoring coupling between adiabatic hyperradial potentials. In the case of weak attractive or repulsive interactions, we find the lowest three-body energy states exhibit even/odd parity oscillations as a function of total internal 2D angular momentum and that for weak repulsive interactions, the universal lowest energy interacting state has an internal angular momentum of M=3. We also discuss the effect of including finite range and higher partial-wave interactions.

  1. Atmospheric Outflows from Hot Jupiters: 2D MHD Simulations

    NASA Astrophysics Data System (ADS)

    Uribe, A.; Matsakos, T.; Konigl, A.

    2015-01-01

    Recent observations of stellar hydrogen Ly-α line absorption during transits of some hot Jupiter exoplanets suggest the presence of a dense, fast wind that is blowing from planetary atmosphere tep{2003Natur.422..143V,2007ApJ...671L..61B}. Modeling efforts include 1D hydrodynamic models tep{2009ApJ...693...23M,2004Icar..170..167Y,2007P&SS...55.1426G} and 2D isothermal magnetized wind models tep{2014arXiv1404.5817T}, among others. In this work, we model the 2D structure of the irradiated upper atmosphere of a hot Jupiter planet and its interaction with the planetary magnetic field. We calculate self consistently the heating by stellar UV radiation and the cooling of the atmosphere by Ly-α emission. We solve for the ionization structure assuming a 100% hydrogen atmosphere, accounting for the radiative ionization, recombination and advection of the gas. We show the effect of stellar tides and planetary magnetic field on the planet outflow and calculate the Ly-α transmission spectra of the resulting atmosphere.

  2. Graphene as a platform to study 2D electronic transitions

    NASA Astrophysics Data System (ADS)

    Bouchiat, Vincent; Kessler, Brian; Girit, Caglar; Zettl, Alex

    2010-03-01

    The easily accessible 2D electron gas in graphene provides an ideal platform on which to tune, via application of an electrostatic gate, the coupling between electronically ordered dopants deposited on its surface. To demonstrate this concept, we have measured arrays of superconducting clusters deposited on Graphene capable to induce via the proximity effect a gate-tunable superconducting transition. Using a simple fabrication procedure based on metal layer dewetting, doped graphene sheets can be decorated with a non percolating network on nanoscale tin clusters. This hybrid material displays a two-step superconducting transition. The higher transition step is gate independent and corresponds to the transition of the tin clusters to the superconducting state. The lower transition step towards a real zero resistance state exhibiting a well developped supercurrent, is strongly gate-tunable and is quantitatively described by Berezinskii-Kosterlitz-Thouless 2D vortex unbinding. Our simple self-assembly method and tunable coupling can readily be extended to other electronic order parameters such as ferro/antiferromagnetism, charge/spin density waves using similar decoration techniques. [1] B. M. Kessler, C.O. Girit, A. Zettl, and V. Bouchiat, Tunable Superconducting Phase Transition in Metal-Decorated Graphene Sheets submitted to PRL, arXiv:0907.3661

  3. Local currents in a 2D topological insulator

    NASA Astrophysics Data System (ADS)

    Dang, Xiaoqian; Burton, J. D.; Tsymbal, Evgeny Y.

    2015-12-01

    Symmetry protected edge states in 2D topological insulators are interesting both from the fundamental point of view as well as from the point of view of potential applications in nanoelectronics as perfectly conducting 1D channels and functional elements of circuits. Here using a simple tight-binding model and the Landauer-Büttiker formalism we explore local current distributions in a 2D topological insulator focusing on effects of non-magnetic impurities and vacancies as well as finite size effects. For an isolated edge state, we show that the local conductance decays into the bulk in an oscillatory fashion as explained by the complex band structure of the bulk topological insulator. We demonstrate that although the net conductance of the edge state is topologically protected, impurity scattering leads to intricate local current patterns. In the case of vacancies we observe vortex currents of certain chirality, originating from the scattering of current-carrying electrons into states localized at the edges of hollow regions. For finite size strips of a topological insulator we predict the formation of an oscillatory band gap in the spectrum of the edge states, the emergence of Friedel oscillations caused by an open channel for backscattering from an impurity and antiresonances in conductance when the Fermi energy matches the energy of the localized state created by an impurity.

  4. Modelling RF sources using 2-D PIC codes

    SciTech Connect

    Eppley, K.R.

    1993-03-01

    In recent years, many types of RF sources have been successfully modelled using 2-D PIC codes. Both cross field devices (magnetrons, cross field amplifiers, etc.) and pencil beam devices (klystrons, gyrotrons, TWT'S, lasertrons, etc.) have been simulated. All these devices involve the interaction of an electron beam with an RF circuit. For many applications, the RF structure may be approximated by an equivalent circuit, which appears in the simulation as a boundary condition on the electric field ( port approximation''). The drive term for the circuit is calculated from the energy transfer between beam and field in the drift space. For some applications it may be necessary to model the actual geometry of the structure, although this is more expensive. One problem not entirely solved is how to accurately model in 2-D the coupling to an external waveguide. Frequently this is approximated by a radial transmission line, but this sometimes yields incorrect results. We also discuss issues in modelling the cathode and injecting the beam into the PIC simulation.

  5. Conformal Laplace superintegrable systems in 2D: polynomial invariant subspaces

    NASA Astrophysics Data System (ADS)

    Escobar-Ruiz, M. A.; Miller, Willard, Jr.

    2016-07-01

    2nd-order conformal superintegrable systems in n dimensions are Laplace equations on a manifold with an added scalar potential and 2n-1 independent 2nd order conformal symmetry operators. They encode all the information about Helmholtz (eigenvalue) superintegrable systems in an efficient manner: there is a 1-1 correspondence between Laplace superintegrable systems and Stäckel equivalence classes of Helmholtz superintegrable systems. In this paper we focus on superintegrable systems in two-dimensions, n = 2, where there are 44 Helmholtz systems, corresponding to 12 Laplace systems. For each Laplace equation we determine the possible two-variate polynomial subspaces that are invariant under the action of the Laplace operator, thus leading to families of polynomial eigenfunctions. We also study the behavior of the polynomial invariant subspaces under a Stäckel transform. The principal new results are the details of the polynomial variables and the conditions on parameters of the potential corresponding to polynomial solutions. The hidden gl 3-algebraic structure is exhibited for the exact and quasi-exact systems. For physically meaningful solutions, the orthogonality properties and normalizability of the polynomials are presented as well. Finally, for all Helmholtz superintegrable solvable systems we give a unified construction of one-dimensional (1D) and two-dimensional (2D) quasi-exactly solvable potentials possessing polynomial solutions, and a construction of new 2D PT-symmetric potentials is established.

  6. Preliminary abatement device evaluation: 1D-2D KGM cyclone design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cyclones are predominately used in controlling cotton gin particulate matter (PM) emissions. The most commonly used cyclone designs are the 2D-2D and 1D-3D; however other designs such as the 1D-2D KGM have or are currently being used. A 1D-2D cyclone has a barrel length equal to the barrel diamete...

  7. 50 CFR Table 2d to Part 679 - Species Codes-Non-FMP Species

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Species Codes-Non-FMP Species 2d Table 2d to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OF THE EXCLUSIVE ECONOMIC ZONE OFF ALASKA Pt. 679, Table 2d Table 2d to Part...

  8. 50 CFR Table 2d to Part 679 - Species Codes-Non-FMP Species

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Species Codes-Non-FMP Species 2d Table 2d to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND... ALASKA Pt. 679, Table 2d Table 2d to Part 679—Species Codes—Non-FMP Species General use...

  9. 50 CFR Table 2d to Part 679 - Species Codes-Non-FMP Species

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Species Codes-Non-FMP Species 2d Table 2d to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND... ALASKA Pt. 679, Table 2d Table 2d to Part 679—Species Codes—Non-FMP Species General use...

  10. 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).

  11. Interactive initialization of 2D/3D rigid registration

    SciTech Connect

    Gong, Ren Hui; Güler, Özgür; Kürklüoglu, Mustafa; Lovejoy, John; Yaniv, Ziv

    2013-12-15

    Purpose: Registration is one of the key technical components in an image-guided navigation system. A large number of 2D/3D registration algorithms have been previously proposed, but have not been able to transition into clinical practice. The authors identify the primary reason for the lack of adoption with the prerequisite for a sufficiently accurate initial transformation, mean target registration error of about 10 mm or less. In this paper, the authors present two interactive initialization approaches that provide the desired accuracy for x-ray/MR and x-ray/CT registration in the operating room setting. Methods: The authors have developed two interactive registration methods based on visual alignment of a preoperative image, MR, or CT to intraoperative x-rays. In the first approach, the operator uses a gesture based interface to align a volume rendering of the preoperative image to multiple x-rays. The second approach uses a tracked tool available as part of a navigation system. Preoperatively, a virtual replica of the tool is positioned next to the anatomical structures visible in the volumetric data. Intraoperatively, the physical tool is positioned in a similar manner and subsequently used to align a volume rendering to the x-ray images using an augmented reality (AR) approach. Both methods were assessed using three publicly available reference data sets for 2D/3D registration evaluation. Results: In the authors' experiments, the authors show that for x-ray/MR registration, the gesture based method resulted in a mean target registration error (mTRE) of 9.3 ± 5.0 mm with an average interaction time of 146.3 ± 73.0 s, and the AR-based method had mTREs of 7.2 ± 3.2 mm with interaction times of 44 ± 32 s. For x-ray/CT registration, the gesture based method resulted in a mTRE of 7.4 ± 5.0 mm with an average interaction time of 132.1 ± 66.4 s, and the AR-based method had mTREs of 8.3 ± 5.0 mm with interaction times of 58 ± 52 s. Conclusions: Based on the

  12. Experimental validation of 2D profile photoresist shrinkage model

    NASA Astrophysics Data System (ADS)

    Bunday, Benjamin; Cordes, Aaron; Self, Andy; Ferry, Lorena; Danilevsky, Alex

    2011-03-01

    For many years, lithographic resolution has been the main obstacle in allowing the pace of transistor densification to meet Moore's Law. For the 32 nm node and beyond, new lithography techniques will be used, including immersion ArF (iArF) lithography and extreme ultraviolet lithography (EUVL). As in the past, these techniques will use new types of photoresists with the capability to print smaller feature widths and pitches. These smaller feature sizes will also require the use of thinner layers of photoresists, such as under 100 nm. In previous papers, we focused on ArF and iArF photoresist shrinkage. We evaluated the magnitude of shrinkage for both R&D and mature resists as a function of chemical formulation, lithographic sensitivity, scanning electron microscope (SEM) beam condition, and feature size. Shrinkage results were determined by the well accepted methodology described in SEMATECH's CD-SEM Unified Specification. In other associated works, we first developed a 1-D model for resist shrinkage for the bottom linewidth and then a 2-D profile model that accounted for shrinkage of all aspects of a trapezoidal profile along a given linescan. A fundamental understanding of the phenomenology of the shrinkage trends was achieved, including how the shrinkage behaves differently for different sized and shaped features. In the 1-D case, calibration of the parameters to describe the photoresist material and the electron beam was all that was required to fit the models to real shrinkage data, as long as the photoresist was thick enough that the beam could not penetrate the entire layer of resist. The later 2-D model included improvements for solving the CD shrinkage in thin photoresists, which is now of great interest for upcoming realistic lithographic processing to explore the change in resist profile with electron dose and to predict the influence of initial resist profile on shrinkage characteristics. The 2-D model also included shrinkage due to both the primary

  13. Magnetoresistance in Co/2D MoS2/Co and Ni/2D MoS2/Ni junctions.

    PubMed

    Zhang, Han; Ye, Meng; Wang, Yangyang; Quhe, Ruge; Pan, Yuanyuan; Guo, Ying; Song, Zhigang; Yang, Jinbo; Guo, Wanlin; Lu, Jing

    2016-06-28

    Semiconducting single-layer (SL) and few-layer MoS2 have a flat surface, free of dangling bonds. Using density functional theory coupled with non-equilibrium Green's function method, we investigate the spin-polarized transport properties of Co/2D MoS2/Co and Ni/2D MoS2/Ni junctions with MoS2 layer numbers of N = 1, 3, and 5. Well-defined interfaces are formed between MoS2 and metal electrodes. The junctions with a SL MoS2 spacer are almost metallic owing to the strong coupling between MoS2 and the ferromagnets, while those are tunneling with a few layer MoS2 spacer. Both large magnetoresistance and tunneling magnetoresistance are found when fcc or hcp Co is used as an electrode. Therefore, flat single- and few-layer MoS2 can serve as an effective nonmagnetic spacer in a magnetoresistance or tunneling magnetoresistance device with a well-defined interface. PMID:27257639

  14. Role of cytochrome P450 2D6 genetic polymorphism in carvedilol hydroxylation in vitro

    PubMed Central

    Wang, Zhe; Wang, Li; Xu, Ren-ai; Zhan, Yun-yun; Huang, Cheng-ke; Dai, Da-peng; Cai, Jian-ping; Hu, Guo-xin

    2016-01-01

    Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic enzyme that catalyzes the metabolism of a great number of therapeutic drugs. Up to now, >100 allelic variants of CYP2D6 have been reported. Recently, we identified 22 novel variants in the Chinese population in these variants. The purpose of this study was to examine the enzymatic activity of the variants toward the CYP2D6 substrate carvedilol in vitro. The CYP2D6 proteins, including CYP2D6.1 (wild type), CYP2D6.2, CYP2D6.10, and 22 other novel CYP2D6 variants, were expressed from insect microsomes and incubated with carvedilol ranging from 1.0 μM to 50 μM at 37°C for 30 minutes. After termination, the carvedilol metabolites were extracted and detected using ultra-performance liquid chromatography tandem mass-spectrometry. Among the 24 CYP2D6 variants, CYP2D6.92 and CYP2D6.96 were catalytically inactive and the remaining 22 variants exhibited significantly decreased intrinsic clearance values (ranging from ~25% to 95%) compared with CYP2D6.1. The present data in vitro suggest that the newly found variants significantly reduced catalytic activities compared with CYP2D6.1. Given that CYP2D6 protein activities could affect carvedilol plasma levels, these findings are greatly relevant to personalized medicine. PMID:27354764

  15. Role of cytochrome P450 2D6 genetic polymorphism in carvedilol hydroxylation in vitro.

    PubMed

    Wang, Zhe; Wang, Li; Xu, Ren-Ai; Zhan, Yun-Yun; Huang, Cheng-Ke; Dai, Da-Peng; Cai, Jian-Ping; Hu, Guo-Xin

    2016-01-01

    Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic enzyme that catalyzes the metabolism of a great number of therapeutic drugs. Up to now, >100 allelic variants of CYP2D6 have been reported. Recently, we identified 22 novel variants in the Chinese population in these variants. The purpose of this study was to examine the enzymatic activity of the variants toward the CYP2D6 substrate carvedilol in vitro. The CYP2D6 proteins, including CYP2D6.1 (wild type), CYP2D6.2, CYP2D6.10, and 22 other novel CYP2D6 variants, were expressed from insect microsomes and incubated with carvedilol ranging from 1.0 μM to 50 μM at 37°C for 30 minutes. After termination, the carvedilol metabolites were extracted and detected using ultra-performance liquid chromatography tandem mass-spectrometry. Among the 24 CYP2D6 variants, CYP2D6.92 and CYP2D6.96 were catalytically inactive and the remaining 22 variants exhibited significantly decreased intrinsic clearance values (ranging from ~25% to 95%) compared with CYP2D6.1. The present data in vitro suggest that the newly found variants significantly reduced catalytic activities compared with CYP2D6.1. Given that CYP2D6 protein activities could affect carvedilol plasma levels, these findings are greatly relevant to personalized medicine. PMID:27354764

  16. Steady 2D Detonations and the DSD Theory

    NASA Astrophysics Data System (ADS)

    Lubyatinsky, S. N.; Loboiko, B. G.; Filin, V. P.; Kostitsin, O. V.; Smirnov, E. B.

    2006-07-01

    In the framework of the simplest DSD theory we obtained ODEs describing steady 2D detonation front shapes for slab, cylinder, and rib geometries. It was found that one solution (a steady detonation front shape) corresponds to several combinations of the confinement material and the defining charge dimension (slab thickness, cylinder radius, or inner rib radius). Comparing experimental data for these combinations and analyzing the shape difference at the edge provide information on the D(κ) relation at low D. The analysis of the data on IHE ribs detonation indicates that as D decreases total curvature κ tends to a limit of about 0.1 mm-1, i.e., double the reciprocal critical diameter. This correction makes the DSD theory consistent with the experimental critical diameter.

  17. 2D numerical modelling of meandering channel formation

    NASA Astrophysics Data System (ADS)

    XIAO, Y.; ZHOU, G.; YANG, F. S.

    2016-03-01

    A 2D depth-averaged model for hydrodynamic sediment transport and river morphological adjustment was established. The sediment transport submodel takes into account the influence of non-uniform sediment with bed surface armoring and considers the impact of secondary flow in the direction of bed-load transport and transverse slope of the river bed. The bank erosion submodel incorporates a simple simulation method for updating bank geometry during either degradational or aggradational bed evolution. Comparison of the results obtained by the extended model with experimental and field data, and numerical predictions validate that the proposed model can simulate grain sorting in river bends and duplicate the characteristics of meandering river and its development. The results illustrate that by using its control factors, the improved numerical model can be applied to simulate channel evolution under different scenarios and improve understanding of patterning processes.

  18. Discrepant Results in a 2-D Marble Collision

    NASA Astrophysics Data System (ADS)

    Kalajian, Peter

    2013-03-01

    Video analysis of 2-D collisions is an excellent way to investigate conservation of linear momentum. The often-desired experimental design goal is to minimize the momentum loss in order to demonstrate the conservation law. An air table with colliding pucks is an ideal medium for this experiment, but such equipment is beyond the budget of many schools. Substituting marbles on a table for air pucks introduces angular momentum and sliding friction so that simple video analysis will demonstrate that linear momentum is not conserved.1,2 Nevertheless, these labs offer students insights into the real-world application of physics. During a recent classroom trial, an unexpected result forced my students to think creatively and critically about what happened in the experiment.

  19. Measurement of topological invariants in a 2D photonic system

    NASA Astrophysics Data System (ADS)

    Mittal, Sunil; Ganeshan, Sriram; Fan, Jingyun; Vaezi, Abolhassan; Hafezi, Mohammad

    2016-03-01

    A hallmark feature of topological physics is the presence of one-way propagating chiral modes at the system boundary. The chirality of edge modes is a consequence of the topological character of the bulk. For example, in a non-interacting quantum Hall model, edge modes manifest as mid-gap states between two topologically distinct bulk bands. The bulk-boundary correspondence dictates that the number of chiral edge modes, a topological invariant called the winding number, is completely determined by the bulk topological invariant, the Chern number. Here, for the first time, we measure the winding number in a 2D photonic system. By inserting a unit flux quantum at the edge, we show that the edge spectrum resonances shift by the winding number. This experiment provides a new approach for unambiguous measurement of topological invariants, independent of the microscopic details, and could possibly be extended to probe strongly correlated topological orders.

  20. 2D and 3D heterogeneous photonic integrated circuits

    NASA Astrophysics Data System (ADS)

    Yoo, S. J. Ben

    2014-03-01

    Exponential increases in the amount of data that need to be sensed, communicated, and processed are continuing to drive the complexity of our computing, networking, and sensing systems. High degrees of integration is essential in scalable, practical, and cost-effective microsystems. In electronics, high-density 2D integration has naturally evolved towards 3D integration by stacking of memory and processor chips with through-silicon-vias. In photonics, too, we anticipate highdegrees of 3D integration of photonic components to become a prevailing method in realizing future microsystems for information and communication technologies. However, compared to electronics, photonic 3D integration face a number of challenges. This paper will review two methods of 3D photonic integration --- fs laser inscription and layer stacking, and discuss applications and future prospects.