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.
2D NMR Methods for Structural Delineation of Copper(II) Complexes of Penicillin and Pilocarpine
Gaggelli, Elena; Gaggelli, Nicola
1994-01-01
A method was developed for delineating the structure of paramagnetic metal complexes. The selective disappearance of cross-peaks in proton-carbon shift correlated 2D NMR maps was shown to uniquely depend upon the scalar and/or dipolar interaction between ligand nuclei and the unpaired electron(s), thus providing a means of identifying binding sites. Copper(II) was shown to form metal complexes with both Penicillin (PNC) and Pilocarpine (PLC) and the structure of the two 1:2 complexes in water solution at physiological pH were determined. PMID:18476239
An inversion method of 2D NMR relaxation spectra in low fields based on LSQR and L-curve
NASA Astrophysics Data System (ADS)
Su, Guanqun; Zhou, Xiaolong; Wang, Lijia; Wang, Yuanjun; Nie, Shengdong
2016-04-01
The low-field nuclear magnetic resonance (NMR) inversion method based on traditional least-squares QR decomposition (LSQR) always produces some oscillating spectra. Moreover, the solution obtained by traditional LSQR algorithm often cannot reflect the true distribution of all the components. Hence, a good solution requires some manual intervention, for especially low signal-to-noise ratio (SNR) data. An approach based on the LSQR algorithm and L-curve is presented to solve this problem. The L-curve method is applied to obtain an improved initial optimal solution by balancing the residual and the complexity of the solutions instead of manually adjusting the smoothing parameters. First, the traditional LSQR algorithm is used on 2D NMR T1-T2 data to obtain its resultant spectra and corresponding residuals, whose norms are utilized to plot the L-curve. Second, the corner of the L-curve as the initial optimal solution for the non-negative constraint is located. Finally, a 2D map is corrected and calculated iteratively based on the initial optimal solution. The proposed approach is tested on both simulated and measured data. The results show that this algorithm is robust, accurate and promising for the NMR analysis.
HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.
Cornilescu, Gabriel; Bahrami, Arash; Tonelli, Marco; Markley, John L; Eghbalnia, Hamid R
2007-08-01
We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic
Increasing the sensitivity of 2D high-resolution NMR methods applied to quadrupolar nuclei
NASA Astrophysics Data System (ADS)
Amoureux, J. P.; Delevoye, L.; Steuernagel, S.; Gan, Z.; Ganapathy, S.; Montagne, L.
2005-02-01
Gan and Kwak recently proposed a soft-pulse added mixing (SPAM) idea in the classical two-pulse multiple-quantum magic-angle spinning scheme. In the SPAM method, a soft π/2 pulse is added after the second hard-pulse (conversion pulse) and all coherence orders in between them are constructively used to obtain the signal. We, here, further extend this idea to distributed samples where the signal mainly results from echo pathways and that from anti-echo pathways dies out after a few t1 increments. We show that, with a combination of SPAM and collection of fewer anti-echoes, an enhancement of the signal to noise ratio by a factor of ca. 3 may be obtained over the z-filtered version. This may prove to be useful even for samples with long T2' relaxation times.
Ultrafast 2D NMR: an emerging tool in analytical spectroscopy.
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
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.
NMR Analysis of Unknowns: An Introduction to 2D NMR Spectroscopy
ERIC Educational Resources Information Center
Alonso, David E.; Warren, Steven E.
2005-01-01
A study combined 1D (one-dimensional) and 2D (two-dimensional) NMR spectroscopy to solve structural organic problems of three unknowns, which include 2-, 3-, and 4-heptanone. Results showed [to the first power]H NMR and [to the thirteenth power]C NMR signal assignments for 2- and 3-heptanone were more challenging than for 4-heptanone owing to the…
In-Cell Protein Structures from 2D NMR Experiments.
Müntener, Thomas; Häussinger, Daniel; Selenko, Philipp; Theillet, Francois-Xavier
2016-07-21
In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells, but it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from a single set of 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (∼50 μM) measured at moderate magnetic field strengths (600 MHz), thus offering an easily accessible alternative for determining intracellular protein structures. PMID:27379949
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.
2D NMR-spectroscopic screening reveals polyketides in ladybugs
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
2D NMR-spectroscopic screening reveals polyketides in ladybugs.
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
Numerical simulation of ( T 2, T 1) 2D NMR and fluid responses
NASA Astrophysics Data System (ADS)
Tan, Mao-Jin; Zou, You-Long; Zhang, Jin-Yan; Zhao, Xin
2012-12-01
One-dimensional nuclear magnetic resonance (1D NMR) logging technology is limited for fluid typing, while two-dimensional nuclear magnetic resonance (2D NMR) logging can provide more parameters including longitudinal relaxation time ( T 1) and transverse relaxation time ( T 2) relative to fluid types in porous media. Based on the 2D NMR relaxation mechanism in a gradient magnetic field, echo train simulation and 2D NMR inversion are discussed in detail. For 2D NMR inversion, a hybrid inversion method is proposed based on the damping least squares method (LSQR) and an improved truncated singular value decomposition (TSVD) algorithm. A series of spin echoes are first simulated with multiple waiting times ( T W s) in a gradient magnetic field for given fluid models and these synthesized echo trains are inverted by the hybrid method. The inversion results are consistent with given models. Moreover, the numerical simulation of various fluid models such as the gas-water, light oil-water, and vicious oil-water models were carried out with different echo spacings ( T E s) and T W s by this hybrid method. Finally, the influences of different signal-to-noise ratios (SNRs) on inversion results in various fluid models are studied. The numerical simulations show that the hybrid method and optimized observation parameters are applicable to fluid typing of gas-water and oil-water models.
Srinivasan, Krishnan; Stalin, Thambusamy
2014-09-15
The formation of host-guest inclusion complex of 2,6-dinitrobenzoic acid (2,6-DNB) with nano-hydrophobic cavity of β-cyclodextrin (β-CD) in solution phase has been studied by UV-visible spectroscopy and electrochemical analysis (cyclic voltammetry, CV). The effect of acid-base concentrations of 2,6-DNB has been studied in presence and absence of β-CD to determination for the ground state acidity constant (pKa). The binding constant of inclusion complex at 303 K was calculated using Benesi-Hildebrand plot and thermodynamic parameter (ΔG) was also calculated. The solid inclusion complex formation between β-CD and 2,6-DNB was confirmed by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD and SEM analysis. A schematic representation of this inclusion process was proposed by molecular docking studies using patch dock server. PMID:24769381
NASA Astrophysics Data System (ADS)
Srinivasan, Krishnan; Stalin, Thambusamy
2014-09-01
The formation of host-guest inclusion complex of 2,6-dinitrobenzoic acid (2,6-DNB) with nano-hydrophobic cavity of β-cyclodextrin (β-CD) in solution phase has been studied by UV-visible spectroscopy and electrochemical analysis (cyclic voltammetry, CV). The effect of acid-base concentrations of 2,6-DNB has been studied in presence and absence of β-CD to determination for the ground state acidity constant (pKa). The binding constant of inclusion complex at 303 K was calculated using Benesi-Hildebrand plot and thermodynamic parameter (ΔG) was also calculated. The solid inclusion complex formation between β-CD and 2,6-DNB was confirmed by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD and SEM analysis. A schematic representation of this inclusion process was proposed by molecular docking studies using patch dock server.
(13)C NMR assignments of regenerated cellulose from solid-state 2D NMR spectroscopy.
Idström, Alexander; Schantz, Staffan; Sundberg, Johan; Chmelka, Bradley F; Gatenholm, Paul; Nordstierna, Lars
2016-10-20
From the assignment of the solid-state (13)C NMR signals in the C4 region, distinct types of crystalline cellulose, cellulose at crystalline surfaces, and disordered cellulose can be identified and quantified. For regenerated cellulose, complete (13)C assignments of the other carbon regions have not previously been attainable, due to signal overlap. In this study, two-dimensional (2D) NMR correlation methods were used to resolve and assign (13)C signals for all carbon atoms in regenerated cellulose. (13)C-enriched bacterial nanocellulose was biosynthesized, dissolved, and coagulated as highly crystalline cellulose II. Specifically, four distinct (13)C signals were observed corresponding to conformationally different anhydroglucose units: two signals assigned to crystalline moieties and two signals assigned to non-crystalline species. The C1, C4 and C6 regions for cellulose II were fully examined by global spectral deconvolution, which yielded qualitative trends of the relative populations of the different cellulose moieties, as a function of wetting and drying treatments. PMID:27474592
In situ fluid typing and quantification with 1D and 2D NMR logging.
Sun, Boqin
2007-05-01
In situ nuclear magnetic resonance (NMR) fluid typing has recently gained momentum due to data acquisition and inversion algorithm enhancement of NMR logging tools. T(2) distributions derived from NMR logging contain information on bulk fluids and pore size distributions. However, the accuracy of fluid typing is greatly overshadowed by the overlap between T(2) peaks arising from different fluids with similar apparent T(2) relaxation times. Nevertheless, the shapes of T(2) distributions from different fluid components are often different and can be predetermined. Inversion with predetermined T(2) distributions allows us to perform fluid component decomposition to yield individual fluid volume ratios. Another effective method for in situ fluid typing is two-dimensional (2D) NMR logging, which results in proton population distribution as a function of T(2) relaxation time and fluid diffusion coefficient (or T(1) relaxation time). Since diffusion coefficients (or T(1) relaxation time) for different fluid components can be very different, it is relatively easy to separate oil (especially heavy oil) from water signal in a 2D NMR map and to perform accurate fluid typing. Combining NMR logging with resistivity and/or neutron/density logs provides a third method for in situ fluid typing. We shall describe these techniques with field examples. PMID:17466778
Fast acquisition of high-resolution 2D NMR spectroscopy in inhomogeneous magnetic fields
NASA Astrophysics Data System (ADS)
Lin, Liangjie; Wei, Zhiliang; Zeng, Qing; Yang, Jian; Lin, Yanqin; Chen, Zhong
2016-05-01
High-resolution nuclear magnetic resonance (NMR) spectroscopy plays an important role in chemical and biological analyses. In this study, we combine the J-coupling coherence transfer module with the echo-train acquisition technique for fast acquisition of high-resolution 2D NMR spectra in magnetic fields with unknown spatial variations. The proposed method shows satisfactory performance on a 5 mM ethyl 3-bromopropionate sample, under a 5-kHz (10 ppm at 11.7 T) B0 inhomogeneous field, as well as under varying degrees of pulse-flip-angle deviations. Moreover, a simulative ex situ NMR measurement is also conducted to show the effectiveness of the proposed pulse sequence.
Isolation and 2D NMR Studies of Alkaloids from Comptonella sessilifoliola1.
Pusset, J; Lopez, J L; Pais, M; Neirabeyeh, M A; Veillon, J M
1991-04-01
Six known furanoquinoline alkaloids have been isolated from the wood and trunk bark of COMPTONELLA SESSILIFOLIOLA (Guillaumin) Hartley (Rutaceae). 2D NMR experiments gave the assignment of all the signals for both (1)H- and (13)C-NMR spectra. Pteleine and kokusaginine were used as models. The two-dimensional carbon-proton correlation experiments, performed for the first time on furanoquinoline alkaloids, led us to correct (13)C-NMR assignments previously described in the literature. PMID:17226139
1D and 2D NMR studies of isobornyl acrylate - Methyl methacrylate copolymers
NASA Astrophysics Data System (ADS)
Khandelwal, Deepika; Hooda, Sunita; Brar, A. S.; Shankar, Ravi
2011-10-01
Isobornyl acrylate - methyl methacrylate (B/M) copolymers of different compositions were synthesized by atom transfer radical polymerization (ATRP) using methyl-2-bromopropionate as an initiator and PMDETA copper complex as catalyst under nitrogen atmosphere at 70 °C. 1H NMR spectrum was used to determine the compositions of copolymer. The copolymer compositions were then used to determine the reactivity ratios of monomers. Reactivity ratios of co-monomers in B/M copolymer, determined from linear Kelen-Tudos method (KT) and non linear Error-in-Variable Method (EVM), are rB = 0.41 ± 0.11, rM = 1.11 ± 0.33 and rB = 0.52, rM = 1.31 respectively. The complete resonance assignments of 1H and 13C{ 1H} NMR spectra were carried out with the help of Distortion less Enhancement by Polarization Transfer (DEPT), two-dimensional Heteronuclear Single Quantum Coherence (HSQC). 2D HSQC assignments were further confirmed by 2D Total Correlation Spectroscopy (TOCSY). The carbonyl carbon of B and M units and methyl carbon of M unit were assigned up to triad compositional and configurational sequences whereas β-methylene carbons were assigned up to tetrad compositional and configurational sequences. Similarly the methine carbon of B unit was assigned up to pentad level. 1,3 and 1,4 bond order couplings of carbonyl carbon and quaternary carbon resonances with methine, methylene and methyl protons were studied in detail using 2D Hetero Nuclear Multiple Bond Correlation (HMBC) spectra.
Väänänen, Taito; Koskela, Harri; Hiltunen, Yrjö; Ala-Korpela, Mika
2002-01-01
Understanding relationships between the structure and composition of molecular mixtures and their chemical properties is a main industrial aim. One central field of research is oil chemistry where the key question is how the molecular characteristics of composite hydrocarbon mixtures can be associated with the macroscopic properties of the oil products. Apparently these relationships are complex and often nonlinear and therefore call for advanced spectroscopic techniques. An informative and an increasingly used approach is two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy. In the case of composite hydrocarbons the application of 2D NMR methodologies in a quantitative manner pose many technical difficulties, and, in any case, the resulting spectra contain many overlapping resonances that challenge the analytical work. Here, we present a general methodology, based on quantitative artificial neural network (ANN) analysis, to resolve overlapping information in 2D NMR spectra and to simultaneously assess the relative importance of multiple spectral variables on the sample properties. The results in a set of 2D NMR spectra of oil samples illustrate, first, that use of ANN analysis for quantitative purposes is feasible also in 2D and, second, that this methodology offers an intrinsic opportunity to assess the complex and nonlinear relationships between the molecular composition and sample properties. The presented ANN methodology is not limited to the analysis of NMR spectra but can also be applied in a manner similar to other (multidimensional) spectroscopic data. PMID:12444730
Dubey, Abhinav; Rangarajan, Annapoorni; Pal, Debnath; Atreya, Hanudatta S
2015-12-15
Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) [(13)C-(1)H] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a "uniqueness score" and a "coverage score". Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of decluttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMR-based metabolomics data by reducing existing impediments. PMID:26556218
Lesot, Philippe; Baillif, Vincent; Billault, Isabelle
2008-04-15
The quantitative determination of isotopic (2H/1H)i ratios at natural abundance using the SNIF-NMR protocol is a well-known method for understanding the enzymatic biosynthesis of metabolites. However, this approach is not always successful for analyzing large solutes and, specifically, is inadequate for prochiral molecules such as complete essential unsaturated fatty acids. To overcome these analytical limitations, we use the natural abundance deuterium 2D NMR (NAD 2D NMR) spectroscopy on solutes embedded in polypeptide chiral liquid crystals. This approach, recently explored for measuring (2H/1H)i ratios of small analytes (Lesot, P.; Aroulanda, C.; Billault, I. Anal. Chem. 2004, 76, 2827-2835), is a powerful way to separate the 2H signals of all nonequivalent enantioisotopomers on the basis both of the 2H quadrupolar interactions and of the 2H chemical shift. Two significant advances over our previous work are presented here and allow the complete isotopic analysis of four mono- and polyunsaturated fatty acid methyl esters: methyl oleate (1), methyl linoleate (2), methyl linolenate (3), and methyl vernoleate (4). The first consists of using NMR spectrometers operating at higher magnetic field strength (14.1 T) and equipped with a selective cryoprobe optimized for deuterium nuclei. The second is the development of Q-COSY Fz 2D NMR experiments able to produce phased 2H 2D maps after a double Fourier transformation. This combination of modern hardware and efficient NMR sequences provides a unique tool to analyze the (2H/1H)i ratios of large prochiral molecules (C-18) dissolved in organic solutions of poly(gamma-benzyl-L-glutamate) and requires smaller amounts of solute than previous study on fatty acids. For each compound (1-4), all 2H quadrupolar doublets visible in the 2D spectra have been assigned on the basis of 2H chemical shifts, isotopic data obtained from isotropic quantitative NAD NMR, and by an interspectral comparison of the anisotropic NAD spectra of four
Gated cardiac NMR imaging and 2D echocardiography in the detection of intracardial neoplasm
Go, R.T.; O'Donnell, J.K.; Salcedo, E.E.; Feiglin, D.H.; Underwood, D.A.; MacIntyre, W.J.; Meaney, T.F.
1985-05-01
Noninvasive 2D echocardiography has replaced contrast angiography as the procedure of choice in the diagnosis of intracardiac neoplasm. The purpose of this study was to determine whether intracardiac neoplasm can be detected as well by gated cardiac NMR. Four patients with known intracardiac neoplasm previously diagnosed by 2D echocardiography had gated cardiac NMR imaging using a superconductive 0.6 Tesla magnet. All patients were performed using a Tl weighted spin echo pulse sequence with a TE of 30 msec and TR of one R-R interval. Two-dimensional planar single or multiple slice techniques were used. In one patient, imaging at different times along the R-R interval were performed for cine display. The results of the present study show detection of the intracardiac neoplasm in all four cases by gated cardiac NMR imaging and the results were comparable to 2D echocardiography. The former imaging technique showed superior spatial resolution. Despite its early stage of development, gated cardiac NMR imaging appears at least equal to 2D echocardiography in the detection of intracardiac neoplasm. The availability of multislice coupled with multiframe acquisition techniques now being developed will provide a cinematic display that will be more effective in the display of the tumor in motion within the cardiac chamber involved and facilitate visualization of the relationship of the tumor to adjacent cardiac structures.
2D NMR spectroscopic analyses of archangelicin from the seeds of Angelica archangelica.
Muller, Melanie; Byres, Maureenx; Jaspars, Marcel; Kumarasamy, Yashodharan; Middleton, Moira; Nahar, Lutfun; Shoeb, Mohammad; Sarker, Satyajit D
2004-12-01
A total of six coumarins, bergapten (1), xanthotoxin (2), imperatorin (3), isoimperatorin (4), phellopterin (5) and archangelicin (6), have been isolated from an n-hexane extract of the seeds of Angelica archangelica. The results of comprehensive 2D NMR analyses of archangelicin are discussed. PMID:15634612
Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR
NASA Astrophysics Data System (ADS)
Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio
2016-03-01
A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40 s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5 mm NMR tubes. All these ingredients - particularly the ⩾3000× 1H polarization enhancements over 11.7 T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.
Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR.
Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio
2016-03-01
A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5mm NMR tubes. All these ingredients--particularly the ⩾ 3000× (1)H polarization enhancements over 11.7T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts. PMID:26920830
GEL-STATE NMR OF BALL-MILLED WHOLE CELL WALLS IN DMSO-d6 USING 2D SOLUTION-STATE NMR SPECTROSCOPY
Technology Transfer Automated Retrieval System (TEKTRAN)
Plant cell walls were used for obtaining 2D solution-state NMR spectra without actual solubilization or structural modification. Ball-milled whole cell walls were swelled directly in the NMR tube with DMSO-d6 where they formed a gel. There are relatively few gel-state NMR studies. Most have involved...
Acid epimerization of 20-keto pregnane glycosides is determined by 2D-NMR spectroscopy.
García, Víctor P
2011-05-01
Carbohydrates influence many essential biological events such as apoptosis, differentiation, tumor metastasis, cancer, neurobiology, immunology, development, host-pathogen interactions, diabetes, signal transduction, protein folding, and many other contexts. We now report on the structure determination of pregnane glycosides isolated from the aerial parts of Ceropegia fusca Bolle (Asclepiadaceae). The observation of cicatrizant, vulnerary and cytostatic activities in some humans and animals of Ceropegia fusca Bolle, a species endemic to the Canary Islands, encouraged us to begin a pharmacological study to determine their exact therapeutic properties. High resolution (1)H-NMR spectra of pregnane glycosides very often display well-resolved signals that can be used as starting points in several selective NMR experiments to study scalar (J coupling), and dipolar (NOE) interactions. ROESY is especially suited for molecules such that ωτ(c) ~ 1, where τ(c) are the motional correlation times and ω is the angular frequency. In these cases the NOE is nearly zero, while the rotating-frame Overhauser effect spectroscopy (ROESY) is always positive and increases monotonically for increasing values of τ(c). The ROESY shows dipolar interactions cross peaks even in medium-sized molecules which are helpful in unambiguous assignment of all the interglycosidic linkages. Selective excitation was carried out using a double pulsed-field gradient spin-echo sequence (DPFGSE) in which 180° Gaussian pulses are sandwiched between sine shaped z-gradients. Scalar interactions were studied by homonuclear DPFGSE-COSY and DPFGSE-TOCSY experiments, while DPFGSE-ROESY was used to monitor the spatial environment of the selectively excited proton. Dipolar interactions between nuclei close in space can be detected by the 1D GROESY experiment, which is a one-dimensional counterpart of the 2D ROESY method. The C-12 and C-17 configurations were determined by ROESY experiments. PMID:21431831
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
Gint2D-T2 correlation NMR of porous media
NASA Astrophysics Data System (ADS)
Zhang, Yan; Blümich, Bernhard
2015-03-01
The internal magnetic field gradient induced in porous media by magnetic susceptibility differences at material interfaces impacts diffusion measurements in particular at high magnetic field and can be used to probe the pore structure. Insight about the relationship between pore space and internal gradient Gint can be obtained from 2D Laplace NMR experiments. When measuring distributions of transverse relaxation times T2 in fluid filled porous media, relaxation and diffusion in internal gradients arise simultaneously and data are often interpreted with the assumption that one or the other parameter be constant throughout the sample. To examine this assumption we measure correlations of the distributions of Gint2D and T2 by 2D Laplace NMR for three different kinds of samples, glass beads with different bead diameters saturated with water, glass beads filled with oil and water, and a wet mortar sample. For the first two samples the cases where either the internal gradient or diffusion dominates were examined separately in order to better understand the relationship between Gint and D. These results are useful for assessing the impact of internal gradients and diffusion in unknown samples, such as the mortar sample. The experiments were performed at different magnetic field strengths corresponding to 300 MHz and 700 MHz 1H Larmor frequency to identify the impact of the magnetic field on the internal gradient. Subsequently, spatially resolved Gint2D-T2 maps were obtained to study the sample heterogeneity.
Gint2D-T2 correlation NMR of porous media.
Zhang, Yan; Blümich, Bernhard
2015-03-01
The internal magnetic field gradient induced in porous media by magnetic susceptibility differences at material interfaces impacts diffusion measurements in particular at high magnetic field and can be used to probe the pore structure. Insight about the relationship between pore space and internal gradient G(int) can be obtained from 2D Laplace NMR experiments. When measuring distributions of transverse relaxation times T(2) in fluid filled porous media, relaxation and diffusion in internal gradients arise simultaneously and data are often interpreted with the assumption that one or the other parameter be constant throughout the sample. To examine this assumption we measure correlations of the distributions of G(int)(2)D and T(2) by 2D Laplace NMR for three different kinds of samples, glass beads with different bead diameters saturated with water, glass beads filled with oil and water, and a wet mortar sample. For the first two samples the cases where either the internal gradient or diffusion dominates were examined separately in order to better understand the relationship between G(int) and D. These results are useful for assessing the impact of internal gradients and diffusion in unknown samples, such as the mortar sample. The experiments were performed at different magnetic field strengths corresponding to 300 MHz and 700 MHz (1)H Larmor frequency to identify the impact of the magnetic field on the internal gradient. Subsequently, spatially resolved Gint(2)D-T(2) maps were obtained to study the sample heterogeneity. PMID:25723135
Huang, Yuqing; Zhang, Zhiyong; Chen, Hao; Feng, Jianghua; Cai, Shuhui; Chen, Zhong
2015-01-01
NMR spectroscopy is a commonly used technique for metabolite analyses. Due to the observed macroscopic magnetic susceptibility in biological tissues, current NMR acquisitions in measurements of biological tissues are generally performed on tissue extracts using liquid NMR or on tissues using magic-angle spinning techniques. In this study, we propose an NMR method to achieve high-resolution J-resolved information for metabolite analyses directly from intact biological samples. A dramatic improvement in spectral resolution is evident in our contrastive demonstrations on a sample of pig brain tissue. Metabolite analyses for a postmortem fish from fresh to decayed statuses are presented to further reveal the capability of the proposed method. This method is a previously-unreported high-resolution 2D J-resolved spectroscopy for biological applications without specialised hardware requirements or complicated sample pretreatments. It provides a significant contribution to metabolite analyses of biological samples, and may be potentially applicable to in vivo samples. Furthermore, this method also can be applied to measurements of semisolid and viscous samples. PMID:25670027
Huang, Yuqing; Zhang, Zhiyong; Chen, Hao; Feng, Jianghua; Cai, Shuhui; Chen, Zhong
2015-01-01
NMR spectroscopy is a commonly used technique for metabolite analyses. Due to the observed macroscopic magnetic susceptibility in biological tissues, current NMR acquisitions in measurements of biological tissues are generally performed on tissue extracts using liquid NMR or on tissues using magic-angle spinning techniques. In this study, we propose an NMR method to achieve high-resolution J-resolved information for metabolite analyses directly from intact biological samples. A dramatic improvement in spectral resolution is evident in our contrastive demonstrations on a sample of pig brain tissue. Metabolite analyses for a postmortem fish from fresh to decayed statuses are presented to further reveal the capability of the proposed method. This method is a previously-unreported high-resolution 2D J-resolved spectroscopy for biological applications without specialised hardware requirements or complicated sample pretreatments. It provides a significant contribution to metabolite analyses of biological samples, and may be potentially applicable to in vivo samples. Furthermore, this method also can be applied to measurements of semisolid and viscous samples. PMID:25670027
Real-time reaction monitoring by ultrafast 2D NMR on a benchtop spectrometer.
Gouilleux, Boris; Charrier, Benoît; Danieli, Ernesto; Dumez, Jean-Nicolas; Akoka, Serge; Felpin, François-Xavier; Rodriguez-Zubiri, Mireia; Giraudeau, Patrick
2015-12-01
Reaction monitoring is widely used to follow chemical processes in a broad range of application fields. Recently, the development of robust benchtop NMR spectrometers has brought NMR under the fume hood, making it possible to monitor chemical reactions in a safe and accessible environment. However, these low-field NMR approaches suffer from limited resolution leading to strong peak overlaps, which can limit their application range. Here, we propose an approach capable of recording ultrafast 2D NMR spectra on a compact spectrometer and of following in real time reactions in the synthetic chemistry laboratory. This approach--whose potential is shown here on a Heck-Matsuda reaction--is highly versatile; the duration of the measurement can be optimized to follow reactions whose time scale ranges from between a few tens of seconds to a few hours. It makes it possible to monitor complex reactions in non-deuterated solvents, and to confirm in real time the molecular structure of the compounds involved in the reaction while giving access to relevant kinetic parameters. PMID:26501887
NASA Astrophysics Data System (ADS)
Ruan, Qing-Xia; Zhou, Ping
2008-07-01
In the present work, we investigated Na + ion effect on the silk fibroin (SF) conformation. Samples are Na +-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na +] increases, partial silk fibroin conformation transit from helix-form to β-form at certain Na + ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR-NMR correlation analysis reveals that silk fibroin undergoes several intermediate states during its conformation transition process as [Na +] increase. The appearance order of the intermediates is followed as: helix and/or random coil → helix-like → β-sheet-like → β-sheet, which is the same as that produced by pH decrease from 6.8 to 4.8 in the resultant regenerated silk fibroin films. The binding sites of Na + to silk fibroin might involve the carbonyl oxygen atom of certain amino acids sequence which could promote the formation of β-sheet conformation. Since the Na +sbnd O bond is weak, the ability of Na + inducing the secondary structure transition is weaker than those of Ca 2+, Cu 2+ and even K +. It is maybe a reason why the sodium content is much lower than potassium in the silkworm gland.
Technology Transfer Automated Retrieval System (TEKTRAN)
Using a newly developed protocol for the differential analysis of arrays of 2D NMR spectra, we were able to rapidly identify two previously unreported indole alkaloids from a library of unfractionated fungal extracts. Differential analyses of NMR spectra thus constitute an effective tool for the non...
2015-01-01
The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ−δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652
Qiu, Feng; McAlpine, James B; Lankin, David C; Burton, Ian; Karakach, Tobias; Chen, Shao-Nong; Pauli, Guido F
2014-04-15
The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ-δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652
Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D (1)H-NMR data.
Gómez, Josep; Brezmes, Jesús; Mallol, Roger; Rodríguez, Miguel A; Vinaixa, Maria; Salek, Reza M; Correig, Xavier; Cañellas, Nicolau
2014-12-01
One of the main challenges in nuclear magnetic resonance (NMR) metabolomics is to obtain valuable metabolic information from large datasets of raw NMR spectra in a high throughput, automatic, and reproducible way. To date, established software packages used to match and quantify metabolites in NMR spectra remain mostly manually operated, leading to low resolution results and subject to inconsistencies not attributable to the NMR technique itself. Here, we introduce a new software package, called Dolphin, able to automatically quantify a set of target metabolites in multiple sample measurements using an approach based on 1D and 2D NMR techniques to overcome the inherent limitations of 1D (1)H-NMR spectra in metabolomics. Dolphin takes advantage of the 2D J-resolved NMR spectroscopy signal dispersion to avoid inconsistencies in signal position detection, enhancing the reliability and confidence in metabolite matching. Furthermore, in order to improve accuracy in quantification, Dolphin uses 2D NMR spectra to obtain additional information on all neighboring signals surrounding the target metabolite. We have compared the targeted profiling results of Dolphin, recorded from standard biological mixtures, with those of two well established approaches in NMR metabolomics. Overall, Dolphin produced more accurate results with the added advantage of being a fully automated and high throughput processing package. PMID:25370160
Novel 2D Triple-Resonance NMR Experiments for Sequential Resonance Assignments of Proteins
NASA Astrophysics Data System (ADS)
Ding, Keyang; Gronenborn, Angela M.
2002-06-01
We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the α- and β-carbon and α-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H N, N, C α, C β, and H α nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D 15N- 1H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.
Differentiation of enantiomers by 2D NMR spectroscopy at 1 T using residual dipolar couplings.
Koos, Martin R M; Danieli, Ernesto; Casanova, Federico; Blümich, Bernhard; Luy, Burkhard
2016-06-01
Differentiating enantiomers using 2D bench-top NMR spectroscopy. Spectrometers working with permanent magnets at 1 T field strength allow the acquisition of 2D data sets. In conjunction with previously reported chiral alignment media, this setup allows the measurement of enantiomeric excess via residual dipolar couplings in stretched gelatine as a result of the reduced line width obtained by 2D J-resolved spectroscopy. PMID:25773020
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
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
Characterization of novel isobenzofuranones by DFT calculations and 2D NMR analysis.
Teixeira, Milena G; Alvarenga, Elson S
2016-08-01
Phthalides are frequently found in naturally occurring substances and exhibit a broad spectrum of biological activities. In the search for compounds with insecticidal activity, phthalides have been used as versatile building blocks for the syntheses of novel potential agrochemicals. In our work, the Diels-Alder reaction between furan-2(5H)-one and cyclopentadiene was used successfully to obtain (3aR,4S,7R,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4R,7S,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (2) and (3aS,4S,7R,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4R,7S,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (3). The endo adduct (2) was brominated to afford (3aR,4R,5R,7R,7aS,8R)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4S,5S,7S,7aR,8S)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (4) and (3aS,4R,5R,6S,7S,7aR)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4S,5S,6R,7R,7aS)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (5). Following the initial analysis of the NMR spectra and the proposed two novel unforeseen products, we have decided to fully analyze the classical and non-classical assay structures with the aid of computational calculations. Computation to predict the (13) C and (1) H chemical shifts for mean absolute error analyses have been carried out by gauge-including atomic orbital method at M06-2X/6-31+G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for all viable conformers. Characterization of the novel unforeseen compounds (4) and (5) were not possible by employing only the experimental NMR data; however, a more conclusive structural identification was performed by comparing the experimental and theoretical (1) H and (13) C chemical shifts by mean absolute error and DP4 probability analyses. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26811211
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
Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR
Jeng, Meifen; Englander, S.W.; Elove, G.A.; Wand, A.J.; Roder, H. )
1990-11-01
Hydrogen exchange and two-dimensional nuclear magnetic resonance (2D NMR) techniques were used to characterize the structure of oxidized horse cytochrome c at acid pH and high ionic strength. Under these conditions, cytochrome c is known to assume a globular conformation (A state) with properties resembling those of the molten globule state described for other proteins. In order to measure the rate of hydrogen-deuterium exchange for individual backbone amide protons in the A state, samples of oxidized cytochrome c were incubated at 20 {degree}C in D{sub 2}O buffer for time periods ranging from 2 min to 500 h. The exchange reaction was then quenched by transferring the protein to native conditions. The extent of exchange for 44 amide protons trapped in the refolded protein was measured by 2D NMR spectroscopy. The results show that this approach can provide detailed information on H-bonded secondary and tertiary structure in partially folded equilibrium forms of a protein. All of the slowly exchanging amide protons in the three major helices of native cytochrome c are strongly protected from exchange at acid pH, indicating that the A state contains native-like elements of helical secondary structure. By contrast, a number of amide protons involved in irregular tertiary H-bonds of the native structure are only marginally protected in the A state, indicating that these H-bonds are unstable or absent. The H-exchange results suggest that the major helices of cytochrome c and their common hydrophobic domain are largely preserved in the globular acidic form while the loop region of the native structure is flexible and partly disordered.
Ionic Liquid–Solute Interactions Studied by 2D NOE NMR Spectroscopy
Khatun, Sufia; Castner, Edward W.
2014-11-26
Intermolecular interactions between a Ru²⁺(bpy)₃ solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {¹H-¹⁹F} HOESY and {¹H-¹H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru²⁺(bpy)₃ solute is rather different from the bulkmore » IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru²⁺(bpy)₃ solute interacts with both the polar head and the nonpolar tail groups of the 1- butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.« less
Ionic Liquid–Solute Interactions Studied by 2D NOE NMR Spectroscopy
Khatun, Sufia; Castner, Edward W.
2014-11-26
Intermolecular interactions between a Ru²⁺(bpy)₃ solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {¹H-¹⁹F} HOESY and {¹H-¹H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru²⁺(bpy)₃ solute is rather different from the bulk IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru²⁺(bpy)₃ solute interacts with both the polar head and the nonpolar tail groups of the 1- butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.
Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software.
Kapaev, Roman R; Toukach, Philip V
2016-06-27
Glycan Optimized Dual Empirical Spectrum Simulation (GODESS) is a web service, which has been recently shown to be one of the most accurate tools for simulation of (1)H and (13)C 1D NMR spectra of natural carbohydrates and their derivatives. The new version of GODESS supports visualization of the simulated (1)H and (13)C chemical shifts in the form of most 2D spin correlation spectra commonly used in carbohydrate research, such as (1)H-(1)H TOCSY, COSY/COSY-DQF/COSY-RCT, and (1)H-(13)C edHSQC, HSQC-COSY, HSQC-TOCSY, and HMBC. Peaks in the simulated 2D spectra are color-coded and labeled according to the signal assignment and can be exported in JCAMP-DX format. Peak widths are estimated empirically from the structural features. GODESS is available free of charge via the Internet at the platform of the Carbohydrate Structure Database project ( http://csdb.glycoscience.ru ). PMID:27227420
HyperSPASM NMR: A new approach to single-shot 2D correlations on DNP-enhanced samples
NASA Astrophysics Data System (ADS)
Donovan, Kevin J.; Frydman, Lucio
2012-12-01
Dissolution DNP experiments are limited to a single or at most a few scans, before the non-Boltzmann magnetization has been consumed. This makes it impractical to record 2D NMR data by conventional, t1-incremented schemes. Here a new approach termed HyperSPASM to establish 2D heteronuclear correlations in a single scan is reported, aimed at dealing with this kind of challenge. The HyperSPASM experiment relies on imposing an amplitude-modulation of the data by a single Δt1 indirect-domain evolution time, and subsequently monitoring the imparted encoding on separate echo and anti-echo pathway signals within a single continuous acquisition. This is implemented via the use of alternating, switching, coherence selection gradients. As a result of these manipulations the phase imparted by a heteronucleus over its indirect domain evolution can be accurately extracted, and 2D data unambiguously reconstructed with a single-shot excitation. The nature of this sequence makes the resulting experiment particularly well suited for collecting indirectly-detected HSQC data on hyperpolarized samples. The potential of the ensuing HyperSPASM method is exemplified with natural-abundance hyperpolarized correlations on model systems.
Golotvin, Sergey S; Vodopianov, Eugene; Pol, Rostislav; Lefebvre, Brent A; Williams, Antony J; Rutkowske, Randy D; Spitzer, Timothy D
2007-10-01
A method for structure validation based on the simultaneous analysis of a 1D (1)H NMR and 2D (1)H - (13)C single-bond correlation spectrum such as HSQC or HMQC is presented here. When compared with the validation of a structure by a 1D (1)H NMR spectrum alone, the advantage of including a 2D HSQC spectrum in structure validation is that it adds not only the information of (13)C shifts, but also which proton shifts they are directly coupled to, and an indication of which methylene protons are diastereotopic. The lack of corresponding peaks in the 2D spectrum that appear in the 1D (1)H spectrum, also gives a clear picture of which protons are attached to heteroatoms. For all these benefits, combined NMR verification was expected and found by all metrics to be superior to validation by 1D (1)H NMR alone. Using multiple real-life data sets of chemical structures and the corresponding 1D and 2D data, it was possible to unambiguously identify at least 90% of the correct structures. As part of this test, challenging incorrect structures, mostly regioisomers, were also matched with each spectrum set. For these incorrect structures, the false positive rate was observed as low as 6%. PMID:17694570
On 2D bisection method for double eigenvalue problems
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.
Interactions of sialic acid with phosphatidylcholine liposomes studied by 2D NMR spectroscopy.
Timoszyk, Anna; Latanowicz, Lidia
2013-01-01
Biological membranes are complex systems which have attracted scientific interest for a long time and for various reasons. The sialic acid-liposome interactions at the molecular level depend on their hydro-lipophilic characteristics. The aim of the present study was to investigate the changes of conformation of the phospholipid (1,2-Diacyl-sn-glycero-3-phosphocholine) and sialic acid (2,8-(N-acetylneuraminic acid)) molecules and the type of interactions induced by the sialic acid molecules on membrane-like systems (liposomes) by 2D NMR (TOCSY, HETCOR, ROESY). The nature of the interaction of sialic acid with the model membrane depends on the structure of the phospholipid headgroups and the hydration of membrane. In ROESY spectra was observed the absence of dipole-dipole couplings within the choline head, between headgroups and glycerol, and between glycerol and fatty acid chains. It indicates an increase of the membrane dynamics in the presence of sialic acid. Moreover, the conformation of sialic acid molecule is changed in the presence of liposomes, which depends on stereochemistry of the chemical groups of the carbon atoms C7 and C8, and oxygen O8. The observed differences between the ROESY spectra of free and liposome bound sialic acid may be a consequence of a changed orientation of the pyranose ring from trans to gauche in the presence of liposomes. The sialic acid penetrate into the phospholipid bilayer to a sufficient depth to allow the dipole interaction. The present result that the correlation signal was found only between the methyl protons from the acetyl group of sialic acid and the methylene tail of phospholipid molecule in the ROESY spectrum indicates that the opposite end of the sialic acid molecule stays in the aqueous phase without interacting with membrane molecules. PMID:24364043
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.
Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques
NASA Astrophysics Data System (ADS)
Topcu, Gulacti; Ulubelen, Ayhan
2007-05-01
In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.
Off-resonance effects on 2D NMR nutation spectra of I = 3/2 quadrupolar nuclei in static samples.
Xia, Y; Deng, F; Ye, C
1995-12-01
The off-resonance effects on 2D NMR nutation of I = 3/2 quadrupolar nuclei are demonstrated with perturbation theory and numerical calculation in static samples. The off-resonant (delta omega) rf field (omega 1) enlarges a nutation frequency and consequently increases the measurement range of nuclear quadrupolar interaction parameters. When omega e > omega Qmax, and arctg(omega 1/delta omega) = +/- 54.7 degrees (magic angle), the satellite lines (produced by coherence transfers) in a nutation spectrum are superimposed with the line of central transition, and hence the nutation spectrum is simplified and its sensitivity is enhanced. The nuclear quadrupolar interaction parameters of 23Na nuclei in Na omega molecular sieve are obtained using 2D NMR nutation. PMID:9053113
2D 1H and 3D 1H-15N NMR of zinc-rubredoxins: contributions of the beta-sheet to thermostability.
Richie, K. A.; Teng, Q.; Elkin, C. J.; Kurtz, D. M.
1996-01-01
Based on 2D 1H-1H and 2D and 3D 1H-15N NMR spectroscopies, complete 1H NMR assignments are reported for zinc-containing Clostridium pasteurianum rubredoxin (Cp ZnRd). Complete 1H NMR assignments are also reported for a mutated Cp ZnRd, in which residues near the N-terminus, namely, Met 1, Lys 2, and Pro 15, have been changed to their counterparts, (-), Ala and Glu, respectively, in rubredoxin from the hyperthermophilic archaeon, Pyrococcus furiosus (Pf Rd). The secondary structure of both wild-type and mutated Cp ZnRds, as determined by NMR methods, is essentially the same. However, the NMR data indicate an extension of the three-stranded beta-sheet in the mutated Cp ZnRd to include the N-terminal Ala residue and Glu 15, as occurs in Pf Rd. The mutated Cp Rd also shows more intense NOE cross peaks, indicating stronger interactions between the strands of the beta-sheet and, in fact, throughout the mutated Rd. However, these stronger interactions do not lead to any significant increase in thermostability, and both the mutated and wild-type Cp Rds are much less thermostable than Pf Rd. These correlations strongly suggest that, contrary to a previous proposal [Blake PR et al., 1992, Protein Sci 1:1508-1521], the thermostabilization mechanism of Pf Rd is not dominated by a unique set of hydrogen bonds or electrostatic interactions involving the N-terminal strand of the beta-sheet. The NMR results also suggest that an overall tighter protein structure does not necessarily lead to increased thermostability. PMID:8732760
NASA Astrophysics Data System (ADS)
Gopinath, T.; Veglia, Gianluigi
2013-05-01
We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.
Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; Li, Mi
2016-04-26
In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involvingmore » with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less
Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V
2015-02-01
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. PMID:25178811
High field and 2D-nmr studies with the aporphine alkaloid glaucine.
Kerr, K M; Kook, A M; Davis, P J
1986-01-01
The aporphine alkaloid glaucine (1) was examined by comparison of the high field (600 MHz) 1H-nmr spectra of 1 vs. racemic 6a,7,7-trideutereoglaucine (4,5), by computer-simulated 1H-nmr spectra at 600 MHz, by using decoupled proton spectra, and two-dimensional COSY and HETCOR experiments with 1 at 500 and 360 MHz, respectively, and using high field (90 MHZ) 13C-nmr of S-(+)-glaucine (1). Emphasis was placed on the resolution of the chemical shifts and coupling constants for the H-4 alpha, H-4 beta, H-5 alpha, H-5 beta, H-6 alpha, H-7 alpha, and H-7 beta alicyclic protons of the molecule, which were previously unassigned. The complete assignment of the alicyclic protons of 1 by 1H-nmr was required for the structural elucidation of deuterated analogs of glaucine, which will be used in microbial transformation studies to determine the stereochemical course of aporphine dehydrogenation by the fungi Fusarium solani (ATCC 12823) and Aspergillus flavipes (ATCC 1030). PMID:3783155
NASA Astrophysics Data System (ADS)
Marković, Violeta; Joksović, Milan D.; Marković, Svetlana; Jakovljević, Ivan
2014-01-01
A distribution of possible isomeric and tautomeric forms of two tautomerizable anthraquinone-thiosemicarbazones with pronounced cytotoxic potential was investigated using 2D NMR and DFT studies. Conformational analysis of the E and Z isomers of both thiosemicarbazones was performed to find out the most stable conformation for each molecule. It was found that superior stability of E-isomers results from ten-membered intramolecular hydrogen bond between thiosemicarbazone N2H and anthraquinone carbonyl group. This hydrogen bond is stronger than that between thiosemicarbazone N2H and ester oxygen, owing to the large partial negative charge on the anthraquinone oxygen.
NASA Astrophysics Data System (ADS)
Tripathi, Neha; Saha, Satyen
2014-06-01
Room temperature ionic liquids are one of the most exciting classes of materials in the last decade. In particular piperidinium (PIP) cation based ionic liquid (IL) (such as PIP14NTf2) have found application in electrochemistry/batteries. In this Letter, 2D NMR (NOESY and HOESY) is employed for studying the interactions present between cations and anions. HOESY spectrum shows that fluorine of NTf2 unusually interacts with all proton of the cation (PIP14). Combined HOESY and NOESY indicate that NTf2 anion is distributed heterogeneously in liquid. Existence of micro heterogeneity in this important class of IL is proposed.
NASA Astrophysics Data System (ADS)
Stalin, T.; Srinivasan, K.; Sivakumar, K.
2014-02-01
The host-guest inclusion complex formation of 2,4-dinitrobenzoic acid (2,4-DNB) with nano-hydrophobic cavity of β-cyclodextrin (β-CD) in solution phase were studied by UV-visible spectrophotometer and electrochemical method (cyclic voltammetry, CV). The prototropic behaviors of 2,4-DNB with and without β-CD and the ground state acidity constant (pKa) of host-guest inclusion complex (2,4-DNB-β-CD) was studied. The binding constant of the inclusion complex at 303 K was calculated using Benesi-Hildebrand plot. The solid inclusion complex formation between β-CD and 2,4-DNB was confirmed by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD and SEM analysis. A schematic representation of this inclusion process is proposed by molecular docking studies using the patch dock server.
Li, Guohua; Li, Jihong; Wang, Wei; Yang, Mei; Zhang, Yuanwei; Sun, Pingchuan; Yuan, Zhi; He, Binglin; Yu, Yaoting
2006-06-01
To remove uremic octapeptide from the blood stream of uremic patients, various modified polyacylamide cross-linked absorbents were prepared. Adsorption experiments showed these absorbents have significant differences in adsorption capacity to the target peptide. In this paper, two-dimension proton nuclear magnetic resonance (2D 1H NMR) spectroscopy was used to investigate the interaction mechanism between the peptide and the adsorbents. Because of the insolubility of the absorbent, some soluble linear polymers with the same functional groups as the absorbents were employed as the model adsorbents in 2D 1H NMR. The preferred binding site for the peptide and polymers was identified to be at the C-terminal carboxyl group of the octapeptide via chemical shift perturbation effects. In this study, we found that hydrogen bonding, electrostatic, and hydrophobic interactions all play a role in the interaction force but had different contributions. Especially, the great chemical shift changes of the aromatic amino acid residues (Trp) during the interaction between butyl-modified polyacrylamide and octapeptide suggested the hydrophobic interaction, incorporated with the electrostatic force, played an important role in the binding reaction in aqueous solutions. This information not only rationally explained the results of the adsorption experiments, but also identified the effective binding site and mechanism, and shall provide a structural basis for designing better affinity-type adsorbents for the target peptide. PMID:16768402
Kleywegt, G J; Boelens, R; Cox, M; Llinás, M; Kaptein, R
1991-05-01
A suite of computer programs (CLAIRE) is described which can be of assistance in the process of assigning 2D 1H NMR spectra of proteins. The programs embody a software implementation of the sequential assignment approach first developed by Wüthrich and co-workers (K. Wüthrich, G. Wider, G. Wagner and W. Braun (1982) J. Mol. Biol. 155, 311). After data-abstraction (peakpicking), the software can be used to detect patterns (spin systems), to find cross peaks between patterns in 2D NOE data sets and to generate assignments that are consistent with all available data and which satisfy a number of constraints imposed by the user. An interactive graphics program called CONPAT is used to control the entire assignment process as well as to provide the essential feedback from the experimental NMR spectra. The algorithms are described in detail and the approach is demonstrated on a set of spectra from the mistletoe protein phoratoxin B, a homolog of crambin. The results obtained compare well with those reported earlier based entirely on a manual assignment process. PMID:1841687
2D exchange 31P NMR spectroscopy of bacteriophage M13 and tobacco mosaic virus.
Magusin, P C; Hemminga, M A
1995-01-01
Two-dimensional (2D) exchange 31P nuclear magnetic resonance spectroscopy is used to study the slow overall motion of the rod-shaped viruses M13 and tobacco mosaic virus in concentrated gels. Even for short mixing times, observed diagonal spectra differ remarkably from projection spectra and one-dimensional spectra. Our model readily explains this to be a consequence of the T2e anisotropy caused by slow overall rotation of the viruses about their length axis. 2D exchange spectra recorded for 30% (w/w) tobacco mosaic virus with mixing times < 1 s do not show any off-diagonal broadening, indicating that its overall motion occurs in the sub-Hz frequency range. In contrast, the exchange spectra obtained for 30% M13 show significant off-diagonal intensity for mixing times of 0.01 s and higher. A log-gaussian distribution around 25 Hz of overall diffusion coefficients mainly spread between 1 and 10(3) Hz faithfully reproduces the 2D exchange spectra of 30% M13 recorded at various mixing times in a consistent way. A small but notable change in diagonal spectra at increasing mixing time is not well accounted for by our model and is probably caused by 31P spin diffusion. PMID:7756532
Vergara, Fredd; Shino, Amiu; Kikuchi, Jun
2016-01-01
Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of ¹H-(13)C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae. PMID:27598144
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.
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
Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5†
Ralph, John
2014-01-01
NMR fingerprinting of the components of finely divided plant cell walls swelled in DMSO has been recently described. Cell wall gels, produced directly in the NMR tube with perdeutero-dimethylsulfoxide, allowed the acquisition of well resolved/dispersed 2D 13C–1H correlated solution-state NMR spectra of the entire array of wall polymers, without the need for component fractionation. That is, without actual solubilization, and without apparent structural modification beyond that inflicted by the ball milling and ultrasonication steps, satisfactorily interpretable spectra can be acquired that reveal compositional and structural details regarding the polysaccharide and lignin components in the wall. Here, the profiling method has been improved by using a mixture of perdeuterated DMSO and pyridine (4:1, v/v). Adding pyridine provided not only easier sample handling because of the better mobility compared to the DMSO-d6-only system but also considerably elevated intensities and improved resolution of the NMR spectra due to the enhanced swelling of the cell walls. This modification therefore provides a more rapid method for comparative structural evaluation of plant cell walls than is currently available. We examined loblolly pine (Pinus taeda, a gymnosperm), aspen (Populus tremuloides, an angiosperm), kenaf (Hibiscus cannabinus, an herbaceous plant), and corn (Zea mays L., a grass, i.e., from the Poaceae family). In principle, lignin composition (notably, the syringyl : guaiacyl : p-hydroxyphenyl ratio) can be quantified without the need for lignin isolation. Correlations for p-coumarate units in the corn sample are readily seen, and a variety of the ferulate correlations are also well resolved; ferulates are important components responsible for cell wall cross-linking in grasses. Polysaccharide anomeric correlations were tentatively assigned for each plant sample based on standard samples and various literature data. With the new potential for chemometric analysis
Gopinath, T.; Mote, Kaustubh R; Veglia, Gianluigi
2016-01-01
We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins aligned in mechanically or magnetically lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living 15N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through 15N-15N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish 15N-15N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments. PMID:25749871
Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi
2015-05-01
We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments. PMID:25749871
NASA Astrophysics Data System (ADS)
Brzozowski, K.; Stawikowski, M.; Ślusarz, R.; Sikorska, E.; Lesner, A.; Łęgowska, A.; Rolka, K.
2015-11-01
Trypsin inhibitor SFTI-1 is the smallest and the most potent among BBI inhibitors. It is also an interesting object for SAR studies since it is cyclic 14 amino acid molecule which additionally contains disulfide bridge. We showed that elimination of head-to-tail cycliztion did not influence its activity. Moreover peptoid monomers of Nlys and Nphe introduced in the substrate specificity P1 position of monocyclic SFTI-1 preserved trypsin and chymotripsin inhibitory activity respectively and made P1-P1‧ bond proteolytically stable. These findings motivated us to perform conformational analysis of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy and molecular dynamics calculations. Obtained structure occurred to be in a good agreement with published structures for wild-type SFTI-1, its monocyclic analog with disulfide bridge only as well as one containing Nlys peptoid monomer in P1 position.
Carr, M.D.; Birdsall, B.; Jimenez-Barbero, J.; Polshakov, V.I.; McCormick, J.E.; Feeney, J.; Frenkiel, T.A.; Bauer, C.J. ); Roberts, G.C.K. )
1991-06-25
Three-dimensional (3D) heteronuclear NMR techniques have been used to make sequential {sup 1}H and {sup 15}H resonance assignments for most of the residues of Lactobacillus casei dihydrofolate reductase (DHFR), a monomeric protein of molecular mass 18,300 Da. A uniformly {sup 15}N-labeled sample of the protein was prepared and its complex with methotrexate (MTX) studied by 3D {sup 15}N/{sup 1}H nuclear Overhauserheteronuclear multiple quantum coherence (NOESY-HMQC), Harmann-Hahn-heteronuclear multiple quantum coherence (HOHAHA-HMQC), and HMQC-NOESY-HMQC experiments. These experiments overcame most of the spectral overlap problems caused by chemical shift degeneracies in 2D spectra and allowed the {sup 1}H-{sup 1}H through-space and through-bond connectivities to be identified unambiguously, leading to the resonance assignments. The novel HMQC-NOESY-HMQC experiment allows NOE cross peaks to be detected between NH protons even when their {sup 1}H chemical shifts are degenerate as long as the amide {sup 15}N chemical shifts are nondegenerate. The 3D experiments, in combination with conventional 2D NOESY, COSY, and HOHAHA experiments on unlabelled and selectively deuterated DHFR, provide backbone assignments for 146 of the 162 residues and side-chain assignments for 104 residues of the protein. Data from the NOE-based experiments and identification of the slowly exchanging amide protons provide detailed information about the secondary structure of the binary complex of the protein with methotrexate.
NMR Methods to Study Dynamic Allostery
Grutsch, Sarina; Brüschweiler, Sven; Tollinger, Martin
2016-01-01
Nuclear magnetic resonance (NMR) spectroscopy provides a unique toolbox of experimental probes for studying dynamic processes on a wide range of timescales, ranging from picoseconds to milliseconds and beyond. Along with NMR hardware developments, recent methodological advancements have enabled the characterization of allosteric proteins at unprecedented detail, revealing intriguing aspects of allosteric mechanisms and increasing the proportion of the conformational ensemble that can be observed by experiment. Here, we present an overview of NMR spectroscopic methods for characterizing equilibrium fluctuations in free and bound states of allosteric proteins that have been most influential in the field. By combining NMR experimental approaches with molecular simulations, atomistic-level descriptions of the mechanisms by which allosteric phenomena take place are now within reach. PMID:26964042
NASA Astrophysics Data System (ADS)
Ruessink, B. H.; De Kanter, F. J. J.; MaClean, C.
Zero-quantum NMR, selectively detected by 2D NMR, is applied to observe small 1H- 1H dipolar couplings in a polar liquid partially oriented by a strong electric field. The normal (single-quantum) 1H spectrum is severely broadened, which prevents the observation of small couplings. The results from the zero-quantum proton spectrum are used to calculate the 2H and 14N quadrupole coupling constants of 2-deutero-2-propenenitrile from the 2H and 14N NMR spectra.
Luo, Wenbin; Yao, Xiaolan; Hong, Mei
2005-05-01
One of the main mechanisms of membrane protein folding is by spontaneous insertion into the lipid bilayer from the aqueous environment. The bacterial toxin, colicin Ia, is one such protein. To shed light on the conformational changes involved in this dramatic transfer from the polar to the hydrophobic milieu, we carried out 2D magic-angle spinning (13)C NMR experiments on the water-soluble and membrane-bound states of the channel-forming domain of colicin Ia. Proton-driven (13)C spin diffusion spectra of selectively (13)C-labeled protein show unequivocal attenuation of cross-peaks after membrane binding. This attenuation can be assigned to distance increases but not reduction of the diffusion coefficient. Analysis of the statistics of the interhelical and intrahelical (13)C-(13)C distances in the soluble protein structure indicates that the observed cross-peak reduction is well correlated with a high percentage of short interhelical contacts in the soluble protein. This suggests that colicin Ia channel domain becomes open and extended upon membrane binding, thus lengthening interhelical distances. In comparison, cross-peaks with similar intensities between the two states are dominated by intrahelical contacts in the soluble state. This suggests that the membrane-bound structure of colicin Ia channel domain may be described as a "molten globule", in which the helical secondary structure is retained while the tertiary structure is unfolded. This study demonstrates that (13)C spin diffusion NMR is a valuable tool for obtaining qualitative long-range distance constraints on membrane protein folding. PMID:15853348
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.
Pham, Tran N; Watson, Simon A; Edwards, Andrew J; Chavda, Manisha; Clawson, Jacalyn S; Strohmeier, Mark; Vogt, Frederick G
2010-10-01
Solid-state NMR (SSNMR) can provide detailed structural information about amorphous solid dispersions of pharmaceutical small molecules. In this study, the ability of SSNMR experiments based on dipolar correlation, spin diffusion, and relaxation measurements to characterize the structure of solid dispersions is explored. Observation of spin diffusion effects using the 2D (1)H-(13)C cross-polarization heteronuclear correlation (CP-HETCOR) experiment is shown to be a useful probe of association between the amorphous drug and polymer that is capable of directly proving glass solution formation. Dispersions of acetaminophen and indomethacin in different polymers are examined using this approach, as well as (1)H double-quantum correlation experiments to probe additional structural features. (1)H-(19)F CP-HETCOR serves a similar role for fluorinated drug molecules such as diflunisal in dispersions, providing a rapid means to prove the formation of a glass solution. Phase separation is detected using (13)C, (19)F, and (23)Na-detected (1)H T(1) experiments in crystalline and amorphous solid dispersions that contain small domains. (1)H T(1) measurements of amorphous nanosuspensions of trehalose and dextran illustrate the ability of SSNMR to detect domain size effects in dispersions that are not glass solutions via spin diffusion effects. Two previously unreported amorphous solid dispersions involving up to three components and containing voriconazole and telithromycin are analyzed using these experiments to demonstrate the general applicability of the approach. PMID:20681586
Blondeel, Eric J M; Ho, Raymond; Schulze, Steffen; Sokolenko, Stanislav; Guillemette, Simon R; Slivac, Igor; Durocher, Yves; Guillemette, J Guy; McConkey, Brendan J; Chang, David; Aucoin, Marc G
2016-09-20
Expression of recombinant proteins exerts stress on cell culture systems, affecting the expression of endogenous proteins, and contributing to the depletion of nutrients and accumulation of waste metabolites. In this work, 2D-DIGE proteomics was employed to analyze differential expression of proteins following stable transfection of a Chinese Hamster Ovary (CHO) cell line to constitutively express a heavy-chain monoclonal antibody. Thirty-four proteins of significant differential expression were identified and cross-referenced with cellular functions and metabolic pathways to identify points of cell stress. Subsequently, 1D-(1)H NMR metabolomics experiments analyzed cultures to observe nutrient depletion and waste metabolite accumulations to further examine these cell stresses and pathways. From among fifty metabolites tracked in time-course, eight were observed to be completely depleted from the production media, including: glucose, glutamine, proline, serine, cystine, asparagine, choline, and hypoxanthine, while twenty-three excreted metabolites were also observed to accumulate. The differentially expressed proteins, as well as the nutrient depletion and accumulation of these metabolites corresponded with upregulated pathways and cell systems related to anaplerotic TCA-replenishment, NADH/NADPH replenishment, tetrahydrofolate cycle C1 cofactor conversions, limitations to lipid synthesis, and redox modulation. A nutrient cocktail was assembled to improve the growth medium and alleviate these cell stresses to achieve a ∼75% improvement to peak cell densities. PMID:27496566
Sidebottom, Philip J
2016-08-01
Non-uniform sampling allows the routine, rapid acquisition of 2D NMR data. When the number of points in the NUS schedule is low, the quality of the data obtained is very dependent of the schedule used. A simple proceedure for finding optimium schedules has been developed and is demonstrated for the multiplicity edited HSQC experiment. PMID:27160788
Fast triangulated vortex methods for the 2D Eulen equations
NASA Astrophysics Data System (ADS)
Russo, Giovanni; Strain, John A.
1994-04-01
Vortex methods for inviscid incompressible two-dimensional fluid flow are usually based on blob approximations. This paper presents a vortex method in which the vorticity is approximated by a piecewise polynomial interpolant on a Delaunay triangulation of the vortices. An efficient reconstruction of the Delaunay triangulation at each step makes the method accurate for long times. The vertices of the triangulation move with the fluid velocity, which is reconstructed from the vorticity via a simplified fast multipole method for the Biot-Savart law with a continuous source distribution. The initial distribution of vortices is constructed from the initial vorticity field by an adaptive approximation method which produces good accuracy even for discontinuous initial data. Numerical results show that the method is highly accurate over long time intervals. Experiments with single and multiple circular and elliptical rotating patches of both piecewise constant and smooth vorticity indicate that the method produces much smaller errors than blob methods with the same number of degrees of freedom, at little additional cost. Generalizations to domains with boundaries, viscous flow, and three space dimensions are discussed.
Fast triangulated vortex methods for the 2D Euler equations
Russo, G. ); Strain, J.A. )
1994-04-01
Vortex methods for inviscid incompressible two-dimensional fluid flow are usually based on blob approximations. This paper presents a vortex method in which the vorticity is approximated by a piecewise polynomial interpolant on a Delaunay triangulation of the vortices. An efficient reconstruction of the Delaunay triangulation at each step makes the method accurate for long times. The vertices of the triangulation move with the fluid velocity, which is reconstructed from the vorticity via a simplified fast multipole method for the Biot-Savart law with a continuous source distribution. The initial distribution of vortices is constructed from the initial vorticity field by an adaptive approximation method which produces good accuracy even for discontinuous initial data. Numerical results show that the method is highly accurate over long time intervals. Experiments with single and multiple circular and elliptical rotating patches of both piecewise constant and smooth vorticity indicate that the method produces much smaller errors than blob methods with the same number of degrees of freedom, at little additional cost. Generalizations to domains with boundaries, viscous flow, and three space dimensions are discussed. 52 refs., 28 figs., 2 tabs.
13C and 1H chemical shift assignments and conformation confirmation of trimedlure-Y via 2-D NMR
NASA Astrophysics Data System (ADS)
Warthen, J. D.; Waters, R. M.; McGovern, T. P.
The conformation of 1,1-dimethylethyl 5-chloro- cis-2-methylcyclohexane-1-carboxylate (trimedlure-Y) was confirmed as 1,2,5 equatorial, axial, equatorial via 13C, 1H, APT, CSCM and COSY NMR analyses. The carbon and proton nuclei in trimedlure-Y and the previously unassigned eight cyclohexyl protons (1.50-2.60 ppm) in 1,1-dimethylethyl 5-chloro- trans-2-methylcyclohexane-1-carboxylate (trimedlure-B 1; 1,2,5 equatorial, equatorial, equatorial) were also characterized by these methods. The effects of the 2-CH 3 in the axial or equatorial conformation upon the chemical shifts of the other nuclei in the molecule are discussed.
THE CONTOUR METHOD: SIMPLE 2-D MAPPING OF RESIDUAL STRESSES
M. PRIME; A. GONZALES
2000-06-01
We present an entirely new method for measuring residual stress that is extremely simple to apply yet more powerful than existing techniques. In this method, a part is carefully cut in two. The contour of the resulting new surface is measured to determine the displacements normal to the surface caused by the release of the residual stresses. Analytically, the opposite of these measured displacements are applied as boundary conditions to the surface in a finite element model. By Bueckner's superposition principle, this gives the original residual stresses normal to the plane of the cut. Unlike other relaxation methods for measuring residual stress, the measured data can be used to solve directly for the stresses without a tedious inversion technique. At the same time, an arbitrary two-dimensional variation in stresses can be determined. We demonstrate the method on a steel specimen with a known residual stress profile.
NASA Astrophysics Data System (ADS)
Deshmukh, Ashish P.; Pacheco, Carlos; Hay, Michael B.; Myneni, Satish C. B.
2007-07-01
Carboxyl groups are abundant in natural organic molecules (NOM) and play a major role in their reactivity. The structural environments of carboxyl groups in IHSS soil and river humic samples were investigated using 2D NMR (heteronuclear and homonuclear correlation) spectroscopy. Based on the 1H- 13C heteronuclear multiple-bond correlation (HMBC) spectroscopy results, the carboxyl environments in NOM were categorized as Type I (unsubstituted and alkyl-substituted aliphatic/alicyclic), Type II (functionalized carbon substituted), Type IIIa, b (heteroatom and olefin substituted), and Type IVa, b (5-membered heterocyclic aromatic and 6-membered aromatic). The most intense signal in the HMBC spectra comes from the Type I carboxyl groups, including the 2JCH and 3JCH couplings of unsubstituted aliphatic and alicyclic acids, though this spectral region also includes the 3JCH couplings of Type II and III structures. Type II and III carboxyls have small but detectable 2JCH correlations in all NOM samples except for the Suwannee River humic acid. Signals from carboxyls bonded to 5-membered aromatic heterocyclic fragments (Type IVa) are observed in the soil HA and Suwannee River FA, while correlations to 6-membered aromatics (Type IVb) are only observed in Suwannee River HA. In general, aromatic carboxylic acids may be present at concentrations lower than previously imagined in these samples. Vibrational spectroscopy results for these NOM samples, described in an accompanying paper [Hay M. B. and Myneni S. C. B. (2007) Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy. Geochim. Cosmochim. Acta (in press)], suggest that Type II and Type III carboxylic acids with α substituents (e.g., -OH, -OR, or -CO 2H) constitute the majority of carboxyl structures in all humic substances examined. Furoic and salicylic acid structures (Type IV) are also feasible fragments, albeit as minor constituents. The
3D-2D registration of cerebral angiograms: a method and evaluation on clinical images.
Mitrovic, Uroš; Špiclin, Žiga; Likar, Boštjan; Pernuš, Franjo
2013-08-01
Endovascular image-guided interventions (EIGI) involve navigation of a catheter through the vasculature followed by application of treatment at the site of anomaly using live 2D projection images for guidance. 3D images acquired prior to EIGI are used to quantify the vascular anomaly and plan the intervention. If fused with the information of live 2D images they can also facilitate navigation and treatment. For this purpose 3D-2D image registration is required. Although several 3D-2D registration methods for EIGI achieve registration accuracy below 1 mm, their clinical application is still limited by insufficient robustness or reliability. In this paper, we propose a 3D-2D registration method based on matching a 3D vasculature model to intensity gradients of live 2D images. To objectively validate 3D-2D registration methods, we acquired a clinical image database of 10 patients undergoing cerebral EIGI and established "gold standard" registrations by aligning fiducial markers in 3D and 2D images. The proposed method had mean registration accuracy below 0.65 mm, which was comparable to tested state-of-the-art methods, and execution time below 1 s. With the highest rate of successful registrations and the highest capture range the proposed method was the most robust and thus a good candidate for application in EIGI. PMID:23649179
NASA Astrophysics Data System (ADS)
Johnson, Robert L.; Anderson, Jason M.; Shanks, Brent H.; Fang, Xiaowen; Hong, Mei; Schmidt-Rohr, Klaus
2013-09-01
Two robust combinations of spectral editing techniques with 2D 13Csbnd 13C NMR have been developed for characterizing the aromatic components of 13C-enriched low-temperature carbon materials. One method (exchange with protonated and nonprotonated spectral editing, EXPANSE) selects cross peaks of protonated and nearby nonprotonated carbons, while the other technique, dipolar-dephased double-quantum/single-quantum (DQ/SQ) NMR, selects signals of bonded nonprotonated carbons. Both spectra are free of a diagonal ridge, which has many advantages: Cross peaks on the diagonal or of small intensity can be detected, and residual spinning sidebands or truncation artifacts associated with the diagonal ridge are avoided. In the DQ/SQ experiment, dipolar dephasing of the double-quantum coherence removes protonated-carbon signals; this approach also eliminates the need for high-power proton decoupling. The initial magnetization is generated with minimal fluctuation by combining direct polarization, cross polarization, and equilibration by 13C spin diffusion. The dipolar dephased DQ/SQ spectrum shows signals from all linkages between aromatic rings, including a distinctive peak from polycondensed aromatics. In EXPANSE NMR, signals of protonated carbons are selected in the first spectral dimension by short cross polarization combined with dipolar dephasing difference. This removes ambiguities of peak assignment to overlapping signals of nonprotonated and protonated aromatic carbons, e.g. near 125 ppm. Spin diffusion is enhanced by dipolar-assisted rotational resonance. Before detection, Csbnd H dipolar dephasing by gated decoupling is applied, which selects signals of nonprotonated carbons. Thus, only cross peaks due to magnetization originating from protonated C and ending on nearby nonprotonated C are retained. Combined with the chemical shifts deduced from the cross-peak position, this double spectral editing defines the bonding environment of aromatic, COO, and Cdbnd O carbons
Muthu, Dhanasekaran; Shokhireva, Tatiana K.; Garrett, Sarah A.; Goren, Allena M.; Zhang, Hongjun
2014-01-01
Nitrophorin 2, one of the four NO–storing and –releasing proteins found in the saliva of the blood-sucking bug Rhodnius prolixus, has a more ruffled heme and a high preference for a particular heme orientation (B), compared to those of NP1 and NP4, which show no preference (A:B ~ 1:1), suggesting that it fits more tightly in the β-barrel protein. In this work we have prepared a series of “Belt” mutants of NP2(D1A) and (ΔM0)NP2 aimed at reducing the size of aromatic or other residues that surround the heme, and investigated them as the high-spin aqua and low-spin N-methylimidazole (NMeIm) complexes. The “Belt” mutants included Y38A, Y38F, F42A, F66A, Y85A, Y85F, Y104A, I120T and a triple mutant of NP2(D1A), the F42L,L106F,I120T mutant. Although I120 has been mainly considered to be a distal pocket residue, the CδH3 of I120 lies directly above the heme 3-methyl, at 2.67 Å, of heme orientation B, or 2-vinyl of A, and it thus plays a role as a “Belt” mutant, a role that turns out to be extremely important in creating the strong favoring of the B heme orientation (A:B = 1:14) for NP2(D1A) or 1:12 for (ΔM0)NP2. The results show that the 1D 1H NMR spectra of the high-spin forms are quite sensitive to changes in the shape of the heme binding cavity. The single mutation I120T eliminates the favorability of the B heme orientation by producing a heme A:B orientation of 1:1, while the single mutation F42A reverses the heme orientation from A:B = 1:14 seen for NP2(D1A) to 10:1 for NP2(D1A,F42A). The most extreme ratio was found for the triple mutant of NP2(D1A), NP2(D1A,F42L,L105F,I120T), in which A:B ~25:1, a ΔG change of about −3.5 kcal/mol or −14.1 kJ/mol with respect to NP2(D1A). The seating of the heme is modified as well in that mutant and several others, by rotations of the heme by up to 4° from the seating observed in NP2(D1A), in order to relieve steric interactions between a vinyl β-carbon and a protein side chain, or to fill a cavity
Trefi, Saleh; Gilard, Véronique; Balayssac, Stéphane; Malet-Martino, Myriam; Martino, Robert
2008-03-13
A simple and selective (19)F NMR method has been validated for the quantitation of fluoxetine (FLX) and fluvoxamine (FLV) in methanol solutions and in human plasma and urine. The regression equations for FLX and FLV showed a good linearity in the range of 1.4-620 microg mL(-1) (3.3 x 10(-6)-1.8 x 10(-3) mol L(-1)) with a limit of detection of approximately 0.5 microg mL(-1) (1.3 x 10(-6) mol L(-1)) and a limit of quantification of approximately 2 microg mL(-1) (4.6 x 10(-6) mol L(-1)). The precision of the assay depends on the concentrations and is comprised between 1.5 and 9.5% for a range of concentrations between 1.2 x 10(-3) and 3.2 x 10(-6) mol L(-1). The accuracy evaluated through recovery studies ranged from approximately 96 to 103% in methanol solutions and in urine, and from approximately 93 to 104% in plasma, with standard deviations <7.5%. The low sensitivity of the method precludes its use for the assay of these antidepressants in biofluids at least at therapeutic doses as the ranges of FLX and FLV plasma levels are 0.15-0.5 microg mL(-1) and 0.15-0.25 microg mL(-1), respectively. The method was applied successfully to the determination of FLX and FLV contents in pharmaceutical samples (brand-named and generic) purchased in several countries or via the Internet. All the commercial formulations contain the active ingredient in the range 94-103% of stated concentration. A "signature" of the formulations (solid and liquid) was obtained with 2D Diffusion-Ordered SpectroscopY (DOSY) (1)H NMR which allowed the characterisation of the active ingredient and excipients present in the formulations studied. Finally, the DOSY separation of FLX and FLV whose molecular weights are very close was obtained by using beta-cyclodextrin as host-guest complexing agent. PMID:18206329
NASA Astrophysics Data System (ADS)
Ben Ali, Karim; Lafon, Olivier; Zimmermann, Herbert; Guittet, Eric; Lesot, Philippe
2007-08-01
We describe several homo- and heteronuclear 2D NMR strategies dedicated to the analysis of anisotropic 2H spectra of a mixture of dideuterated unlike/like stereoisomers with two remote stereogenic centers, using weakly orienting chiral liquid crystals. To this end, we propose various 2D correlation experiments, denoted "D(H) nD" or "D(H) nC" (with n = 1, 2), that involve two heteronuclear polarization transfers of INEPT-type with one or two proton relays. The analytical expressions of correlation signals for four pulse sequences reported here were calculated using the product-operators formalism for spin I = 1 and S = 1/2. The features and advantages of each scheme are presented and discussed. The efficiency of these 2D sequences is illustrated using various deuterated model molecules, dissolved in organic solutions of polypeptides made of poly- γ-benzyl- L-glutamate (PBLG) or poly- ɛ-carbobenzyloxy- L-lysine (PCBLL) and NMR numerical simulations.
2D barcodes: a novel and simple method for denture identification.
Sudheendra, Udyavara S; Sowmya, Kasetty; Vidhi, Mathur; Shreenivas, Kallianpur; Prathamesh, Joshi
2013-01-01
Several methods of denture marking have been described in the literature. However, most of them are expensive, time-consuming, and do not permit the incorporation of large amounts of information. We propose a novel and simple method incorporating 2D codes which has several advantages over the existing methods. A 2D code was generated in the dental office and inserted into a maxillary denture. The code was then read using software downloaded into a mobile phone giving access to the website containing details about the patient. The denture was also subjected to durability tests, which did not hamper the efficacy of the 2D code. 2D coding for dentures is a simple, less expensive method with the potential of storing a large amount of information that can be accessed on-site by the forensic investigator, thus allowing quick identification of the denture wearer. PMID:22971078
Lesot, Philippe; Serhan, Zeinab; Aroulanda, Christie; Billault, Isabelle
2012-12-01
In this work, we report and discuss on the use and limitations of the natural abundance deuterium two-dimensional NMR spectroscopy in polypeptide chiral and achiral aligning media in the studies of homogenous triglycerides at 14.1 T. As illustrative examples, two triglycerides with short and long alkyl chains were investigated: the 1,3-di(butanoyloxy)propan-2-yl butanoate or tributyrin (TB) and the 1,3-di(tetradecanoyloxy)propan-2-yl tetradecanoate or trimyristin (TM). If both flexible compounds are theoretically of C(s) symmetry on average, according to the Altmann's definition (Proc. Roy. Soc., 1967, A298, 184.), the analysis of spectral data in terms of enantiotopic and diastereotopic discriminations shows noticeable differences related to their orientational ordering behavior inside the mesophases. Although from NMR analysis viewpoint, TB behaves as a C(s) symmetry molecule as expected, the NMR results obtained for TM suggest a behavior that could be formally predicted for a C(3v) symmetry molecule on average. This conclusion was nicely supported by the comparison with the tri-n-propylorthoformate, a real C(3v) symmetry solute on average on the NMR timescale. This difference of effective orientational behavior could originate from the difference of size and shape between lateral and central alkyl chains of the solute molecule. PMID:23280656
Device and methods for "gold standard" registration of clinical 3D and 2D cerebral angiograms
NASA Astrophysics Data System (ADS)
Madan, Hennadii; Likar, Boštjan; Pernuš, Franjo; Å piclin, Žiga
2015-03-01
Translation of any novel and existing 3D-2D image registration methods into clinical image-guidance systems is limited due to lack of their objective validation on clinical image datasets. The main reason is that, besides the calibration of the 2D imaging system, a reference or "gold standard" registration is very difficult to obtain on clinical image datasets. In the context of cerebral endovascular image-guided interventions (EIGIs), we present a calibration device in the form of a headband with integrated fiducial markers and, secondly, propose an automated pipeline comprising 3D and 2D image processing, analysis and annotation steps, the result of which is a retrospective calibration of the 2D imaging system and an optimal, i.e., "gold standard" registration of 3D and 2D images. The device and methods were used to create the "gold standard" on 15 datasets of 3D and 2D cerebral angiograms, whereas each dataset was acquired on a patient undergoing EIGI for either aneurysm coiling or embolization of arteriovenous malformation. The use of the device integrated seamlessly in the clinical workflow of EIGI. While the automated pipeline eliminated all manual input or interactive image processing, analysis or annotation. In this way, the time to obtain the "gold standard" was reduced from 30 to less than one minute and the "gold standard" of 3D-2D registration on all 15 datasets of cerebral angiograms was obtained with a sub-0.1 mm accuracy.
NASA Astrophysics Data System (ADS)
Berdagué, Philippe; Lesot, Philippe; Jacob, Jérémy; Terwilliger, Valery J.; Le Milbeau, Claude
2016-01-01
The hydrogen isotopic composition (δD or (D/H) value) of molecular biomarkers preserved in sedimentary archives is increasingly used to provide clues about the evolution of past climatic conditions. The rationale is that intact biomarkers retain isotopic information related to the climatic conditions that prevailed at the time of their synthesis. Some of these biomarkers may be degraded during diagenesis, however. The extent to which these degradations alter the original δD value of the source biomarker is presently debated and the capacity to resolve this question by determination of compound-specific δD values alone is limited. The "bulk" or "global" δD value of any molecule is in fact a composite of δD values at each site within this molecule (δDi or (D/H)i with i = number of hydrogen/deuterium atoms in the considered molecule). Determination of this site-specific δDi value in biomarkers could not only yield outstanding paleoenvironmental information but also help forecast the impacts of diagenesis and define essential steps in biosynthetic pathways. This task is analytically challenging. Here, we examined the capabilities of natural abundance deuterium 2D-NMR (NAD 2D-NMR) using homopolypeptide liquid crystals as an NMR solvent to: (i) analyze the NAD spectra of biomakers; (ii) determine the site-specific distribution of hydrogen in the nine methyl groups (δDMei with i = 23-31) of miliacin, a pentacyclic triterpene of the amyrin family and key biomarker for broomcorn millet in sedimentary archives. Relative (D/H)Mei values were established by anisotropic NAD 2D-NMR. Then absolute δDMei values were obtained by determining δDMei value of the methoxy group of miliacin using two independent approaches: isotropic NAD NMR (SNIF-NMR™) and GC-irMS. The resulting isotope profile for miliacin shows, for the first time, large variations in δDMei values that can directly be explained by biosynthetic processes. This approach has also the potential to permit
NMR and MRI apparatus and method
Clarke, John; Kelso, Nathan; Lee, SeungKyun; Moessle, Michael; Myers, Whittier; McDermott, Robert; ten Haken, Bernard; Pines, Alexander; Trabesinger, Andreas
2007-03-06
Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. Additional signal to noise benefits are obtained by use of a low noise polarization coil, comprising litz wire or superconducting materials. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.
Laussac, J.P.; Lefrancier, P.; Dardenne, M.; Bach, J.F.; Marraud, M.; Cung, M.T.
1988-11-16
The interaction between aluminum and thymulin, a linear nonapeptide of thymic origin isolated from serum, was investigated by means of one- and two-dimensional NMR experiments. These experiments were performed in dimethyl-d/sub 6/ sulfoxide solution at different metal:peptide ratios. The results lead the following conclusions: (i) the Al(III) complexation corresponds to a fast exchange on the NMR time scale; (ii) the evolution of /sup 1/H and /sup 13/C NMR chemical shifts indicates the existence of one type of complex with a 1:2 stoichiometry, associating two peptide molecules and one Al(III) ion; (iii) analysis of the spectra suggests that Al(III) has a specific binding site involving the Asn/sup 9/COO/sup /minus// terminal group and the hydroxyl group of the Ser/sup 4/ residue; (iv) from the NOESY data a conformation has been proposed and compared to the biologically active Zn(II)-thymulin complex. 23 refs., 6 figs., 1 tab.
van Winden, Wouter A; van Gulik, Walter M; Schipper, Dick; Verheijen, Peter J T; Krabben, Preben; Vinke, Jacobus L; Heijnen, Joseph J
2003-07-01
At present two alternative methods are available for analyzing the fluxes in a metabolic network: (1) combining measurements of net conversion rates with a set of metabolite balances including the cofactor balances, or (2) leaving out the cofactor balances and fitting the resulting free fluxes to measured (13)C-labeling data. In this study these two approaches are applied to the fluxes in the glycolysis and pentose phosphate pathway of Penicillium chrysogenum growing on either ammonia or nitrate as the nitrogen source, which is expected to give different pentose phosphate pathway fluxes. The presented flux analyses are based on extensive sets of 2D [(13)C, (1)H] COSY data. A new concept is applied for simulation of this type of (13)C-labeling data: cumulative bondomer modeling. The outcomes of the (13)C-labeling based flux analysis substantially differ from those of the pure metabolite balancing approach. The fluxes that are determined using (13)C-labeling data are shown to be highly dependent on the chosen metabolic network. Extending the traditional nonoxidative pentose phosphate pathway with additional transketolase and transaldolase reactions, extending the glycolysis with a fructose 6-phosphate aldolase/dihydroxyacetone kinase reaction sequence or adding a phosphoenolpyruvate carboxykinase reaction to the model considerably improves the fit of the measured and the simulated NMR data. The results obtained using the extended version of the nonoxidative pentose phosphate pathway model show that the transketolase and transaldolase reactions need not be assumed reversible to get a good fit of the (13)C-labeling data. Strict statistical testing of the outcomes of (13)C-labeling based flux analysis using realistic measurement errors is demonstrated to be of prime importance for verifying the assumed metabolic model. PMID:12740935
A MODIFIED LIGHT TRANSMISSION VISUALIZATION METHOD FOR DNAPL SATURATION MEASUREMENTS IN 2-D MODELS
In this research, a light transmission visualization (LTV) method was used to quantify dense non-aqueous phase liquids (DNAPL) saturation in two-dimensional (2-D), two fluid phase systems. The method is an expansion of earlier LTV methods and takes into account both absorption an...
Gerbaud, Guillaume; Hediger, Sabine; Bardet, Michel; Favennec, Laurent; Zenasni, Aziz; Beynet, Julien; Gourhant, Olivier; Jousseaume, Vincent
2009-11-14
In the research field of the sub-65 nm semiconductor industry, organosilicate SiOCH films with low dielectric constant (k < 2.4) need to be developed in order to improve the performance of integrated circuits [International Roadmap for Semiconductors (ITRS), San Jose, CA, 2004]. One way to produce SiOCH films of low dielectric constant is to introduce pores into the film. This is usually obtained in two steps. Firstly, co-deposition of a matrix precursor, with a sacrificial organic porogen, either by plasma enhanced chemical vapor deposition (PECVD) or spin-coating. Secondly, application of a specific thermal treatment to remove the porogen and create the porosity. This last step can be improved by adding to the thermal process a super-critical CO(2) treatment, an UV irradiation or an electronic bombardment (e-beam). In this study, the two deposition processes as well as the various treatments applied to eliminate the porogens were evaluated and compared using high-resolution solid-state NMR. For this purpose, hybrid (containing porogens) and porous films were extensively characterized on the basis of their (1)H, (13)C and (29)Si high-resolution NMR spectra. Information was obtained concerning the crosslinking of the Si skeleton. Spectral features could be correlated to the processes used. Isotropic chemical shift analyses and 2D correlation NMR experiments were used to show the existence and nature of the interactions between the matrix precursor and the organic porogen. PMID:19851550
Hartmann-Hahn 2D-map to optimize the RAMP-CPMAS NMR experiment for pharmaceutical materials.
Suzuki, Kazuko; Martineau, Charlotte; Fink, Gerhard; Steuernagel, Stefan; Taulelle, Francis
2012-02-01
Cross polarization-magic angle spinning (CPMAS) is the most used experiment for solid-state NMR measurements in the pharmaceutical industry, with the well-known variant RAMP-CPMAS its dominant implementation. The experimental work presented in this contribution focuses on the entangled effects of the main parameters of such an experiment. The shape of the RAMP-CP pulse has been considered as well as the contact time duration, and a particular attention also has been devoted to the radio-frequency (RF) field inhomogeneity. (13)C CPMAS NMR spectra have been recorded with a systematic variation of (13)C and (1)H constant radiofrequency field pair values and represented as a Hartmann-Hahn matching two-dimensional map. Such a map yields a rational overview of the intricate optimal conditions necessary to achieve an efficient CP magnetization transfer. The map also highlights the effects of sweeping the RF by the RAMP-CP pulse on the number of Hartmann-Hahn matches crossed and how RF field inhomogeneity helps in increasing the CP efficiency by using a larger fraction of the sample. In the light of the results, strategies for optimal RAMP-CPMAS measurements are suggested, which lead to a much higher efficiency than constant amplitude CP experiment. PMID:22367881
Removal of t1 noise from metabolomic 2D 1H- 13C HSQC NMR spectra by Correlated Trace Denoising
NASA Astrophysics Data System (ADS)
Poulding, Simon; Charlton, Adrian J.; Donarski, James; Wilson, Julie C.
2007-12-01
The presence of t1 noise artefacts in 2D phase-cycled Heteronuclear Single Quantum Coherence (HSQC) spectra constrains the use of this experiment despite its superior sensitivity. This paper proposes a new processing algorithm, working in the frequency-domain, for reducing t1 noise. The algorithm has been developed for use in contexts, such as metabolomic studies, where existing denoising techniques cannot always be applied. Two test cases are presented that show the algorithm to be effective in improving the SNR of peaks embedded within t1 noise by a factor of more than 2, while retaining the intensity and shape of genuine peaks.
NMR Stark Spectroscopy: New Methods to Calibrate NMR Sensitivity to Electric Fields
NASA Astrophysics Data System (ADS)
Tarasek, Matthew R.
The influence of electrostatics on NMR parameters is well accepted. Thus, NMR is a promising route to probe electrical features within molecules and materials. However, applications of NMR Stark effects (E-field induced changes in spin energy levels) have been elusive. I have developed new approaches to resolve NMR Stark effects from an applied E field. This calibrates nuclear probes whose spectral response might later be used to evaluate internal E fields that are critical to function, such as those due to local charge distributions or sample structure. I will present two novel experimental approaches for direct calibration of NMR quadrupolar Stark effects (QSEs). In the first, steady-state (few-second) excitation by an E field at twice the NMR frequency (2ω 0) is used to saturate spin magnetization. The extent of saturation vs. E-field amplitude calibrates the QSE response rate, while measurements vs sample orientation determine tensorial character. The second method instead synchronizes short (few µs) pulses of the 2ω0 E field with a multiple-pulse NMR sequence. This, “POWER” (Perturbations Observed With Enhanced Resolution) approach enables more accurate measure of small QSEs (i.e. few Hz spectral changes). A 2nd key advantage is the ability to define tensorial response without reorienting the sample, but instead varying the phase of the 2ω0 field. I will describe these experiments and my home-built NMR “Stark probe”, employed on a conventional wide-bore solid-state NMR system. Results with GaAs demonstrate each method, while extensions to a wider array of molecular and material systems may now be possible using these methods.
2D 31P solid state NMR spectroscopy, electronic structure and thermochemistry of PbP7
NASA Astrophysics Data System (ADS)
Benndorf, Christopher; Hohmann, Andrea; Schmidt, Peer; Eckert, Hellmut; Johrendt, Dirk; Schäfer, Konrad; Pöttgen, Rainer
2016-03-01
Phase pure polycrystalline PbP7 was prepared from the elements via a lead flux. Crystalline pieces with edge-lengths up to 1 mm were obtained. The assignment of the previously published 31P solid state NMR spectrum to the seven distinct crystallographic sites was accomplished by radio-frequency driven dipolar recoupling (RFDR) experiments. As commonly found in other solid polyphosphides there is no obvious correlation between the 31P chemical shift and structural parameters. PbP7 decomposes incongruently under release of phosphorus forming liquid lead as remainder. The thermal decomposition starts at T>550 K with a vapor pressure almost similar to that of red phosphorus. Electronic structure calculations reveal PbP7 as a semiconductor according to the Zintl description and clearly shows the stereo-active Pb-6s2 lone pairs in the electron localization function ELF.
Tritiation methods and tritium NMR spectroscopy
Jaiswal, D.K.; Morimoto, H.; Salijoughian, M.; Williams, P.G.
1991-09-01
We have used a simple process for the production of highly tritiated water and characterized the product species by {sup 1}H and {sup 3}H NMR spectroscopy. The water is readily manipulated and used in subsequent reactions either as T{sub 2}O, CH{sub 3}COOT or CF{sub 3}COOT. Development of tritiated diimide has progressed to the point where cis-hydrogenated products at 1-20 Ci/mmole S.A. are possible. Tri-n-butyl tin tritide has been produced at >95% tritium content and well characterized by multinuclear NMR techniques. 27 refs., 3 figs.
Dynamic Analysis of 2D Electromagnetic Resonant Optical Scanner Using 3D Finite Element Method
NASA Astrophysics Data System (ADS)
Hirata, Katsuhiro; Hong, Sara; Maeda, Kengo
The optical scanner is a scanning device in which a laser beam is reflected by a mirror that can be rotated or oscillated. In this paper, we propose a new 2D electromagnetic resonant optical scanner that employs electromagnets and leaf springs. Torque characteristics and resonance characteristics of the scanner are analyzed using the 3D finite element method. The validity of the analysis is shown by comparing the characteristics inferred from the analysis with the characteristics of the prototype. Further, 2D resonance is investigated by introducing a superimposed-frequency current in a single coil.
2D and 3D Method of Characteristic Tools for Complex Nozzle Development
NASA Technical Reports Server (NTRS)
Rice, Tharen
2003-01-01
This report details the development of a 2D and 3D Method of Characteristic (MOC) tool for the design of complex nozzle geometries. These tools are GUI driven and can be run on most Windows-based platforms. The report provides a user's manual for these tools as well as explains the mathematical algorithms used in the MOC solutions.
2D-3D hybrid stabilized finite element method for tsunami runup simulations
NASA Astrophysics Data System (ADS)
Takase, S.; Moriguchi, S.; Terada, K.; Kato, J.; Kyoya, T.; Kashiyama, K.; Kotani, T.
2016-09-01
This paper presents a two-dimensional (2D)-three-dimensional (3D) hybrid stabilized finite element method that enables us to predict a propagation process of tsunami generated in a hypocentral region, which ranges from offshore propagation to runup to urban areas, with high accuracy and relatively low computational costs. To be more specific, the 2D shallow water equation is employed to simulate the propagation of offshore waves, while the 3D Navier-Stokes equation is employed for the runup in urban areas. The stabilized finite element method is utilized for numerical simulations for both of the 2D and 3D domains that are independently discretized with unstructured meshes. The multi-point constraint and transmission methods are applied to satisfy the continuity of flow velocities and pressures at the interface between the resulting 2D and 3D meshes, since neither their spatial dimensions nor node arrangements are consistent. Numerical examples are presented to demonstrate the performance of the proposed hybrid method to simulate tsunami behavior, including offshore propagation and runup to urban areas, with substantially lower computation costs in comparison with full 3D computations.
2D-3D hybrid stabilized finite element method for tsunami runup simulations
NASA Astrophysics Data System (ADS)
Takase, S.; Moriguchi, S.; Terada, K.; Kato, J.; Kyoya, T.; Kashiyama, K.; Kotani, T.
2016-05-01
This paper presents a two-dimensional (2D)-three-dimensional (3D) hybrid stabilized finite element method that enables us to predict a propagation process of tsunami generated in a hypocentral region, which ranges from offshore propagation to runup to urban areas, with high accuracy and relatively low computational costs. To be more specific, the 2D shallow water equation is employed to simulate the propagation of offshore waves, while the 3D Navier-Stokes equation is employed for the runup in urban areas. The stabilized finite element method is utilized for numerical simulations for both of the 2D and 3D domains that are independently discretized with unstructured meshes. The multi-point constraint and transmission methods are applied to satisfy the continuity of flow velocities and pressures at the interface between the resulting 2D and 3D meshes, since neither their spatial dimensions nor node arrangements are consistent. Numerical examples are presented to demonstrate the performance of the proposed hybrid method to simulate tsunami behavior, including offshore propagation and runup to urban areas, with substantially lower computation costs in comparison with full 3D computations.
Simulation of surface tension in 2D and 3D with smoothed particle hydrodynamics method
NASA Astrophysics Data System (ADS)
Zhang, Mingyu
2010-09-01
The methods for simulating surface tension with smoothed particle hydrodynamics (SPH) method in two dimensions and three dimensions are developed. In 2D surface tension model, the SPH particle on the boundary in 2D is detected dynamically according to the algorithm developed by Dilts [G.A. Dilts, Moving least-squares particle hydrodynamics II: conservation and boundaries, International Journal for Numerical Methods in Engineering 48 (2000) 1503-1524]. The boundary curve in 2D is reconstructed locally with Lagrangian interpolation polynomial. In 3D surface tension model, the SPH particle on the boundary in 3D is detected dynamically according to the algorithm developed by Haque and Dilts [A. Haque, G.A. Dilts, Three-dimensional boundary detection for particle methods, Journal of Computational Physics 226 (2007) 1710-1730]. The boundary surface in 3D is reconstructed locally with moving least squares (MLS) method. By transforming the coordinate system, it is guaranteed that the interface function is one-valued in the local coordinate system. The normal vector and curvature of the boundary surface are calculated according to the reconstructed boundary surface and then surface tension force can be calculated. Surface tension force acts only on the boundary particle. Density correction is applied to the boundary particle in order to remove the boundary inconsistency. The surface tension models in 2D and 3D have been applied to benchmark tests for surface tension. The ability of the current method applying to the simulation of surface tension in 2D and 3D is proved.
High-Order Spectral Volume Method for 2D Euler Equations
NASA Technical Reports Server (NTRS)
Wang, Z. J.; Zhang, Laiping; Liu, Yen; Kwak, Dochan (Technical Monitor)
2002-01-01
The Spectral Volume (SV) method is extended to the 2D Euler equations. The focus of this paper is to study the performance of the SV method on multidimensional non-linear systems. Implementation details including total variation diminishing (TVD) and total variation bounded (TVB) limiters are presented. Solutions with both smooth features and discontinuities are utilized to demonstrate the overall capability of the SV method.
NMR Methods, Applications and Trends for Groundwater Evaluation and Management
NASA Astrophysics Data System (ADS)
Walsh, D. O.; Grunewald, E. D.
2011-12-01
Nuclear magnetic resonance (NMR) measurements have a tremendous potential for improving groundwater characterization, as they provide direct detection and measurement of groundwater and unique information about pore-scale properties. NMR measurements, commonly used in chemistry and medicine, are utilized in geophysical investigations through non-invasive surface NMR (SNMR) or downhole NMR logging measurements. Our recent and ongoing research has focused on improving the performance and interpretation of NMR field measurements for groundwater characterization. Engineering advancements have addressed several key technical challenges associated with SNMR measurements. Susceptibility of SNMR measurements to environmental noise has been dramatically reduced through the development of multi-channel acquisition hardware and noise-cancellation software. Multi-channel instrumentation (up to 12 channels) has also enabled more efficient 2D and 3D imaging. Previous limitations in measuring NMR signals from water in silt, clay and magnetic geology have been addressed by shortening the instrument dead-time from 40 ms to 4 ms, and increasing the power output. Improved pulse sequences have been developed to more accurately estimate NMR relaxation times and their distributions, which are sensitive to pore size distributions. Cumulatively, these advancements have vastly expanded the range of environments in which SNMR measurements can be obtained, enabling detection of groundwater in smaller pores, in magnetic geology, in the unsaturated zone, and nearby to infrastructure (presented here in case studies). NMR logging can provide high-resolution estimates of bound and mobile water content and pore size distributions. While NMR logging has been utilized in oil and gas applications for decades, its use in groundwater investigations has been limited by the large size and high cost of oilfield NMR logging tools and services. Recently, engineering efforts funded by the US Department of
Abdelall, Eman K A; Kamel, Gehan M
2016-08-01
Two new series of 1,5-diaryl pyrazoles (5a, 5b, 7a, 7b and 10) and 1,5-diaryl pyrazoline (12a and 12b) were prepared as both Cyclooxygenase-2 and 15-lipoxygenase inhibitors. Carrageenan-induced rat paw edema, ulcer index and anti-COX-1/COX-2 and 15-LOX inhibition assays were also included. Cyclization of different pyrazoles was discussed using 2D NMR such as HSQC, HMBC and NOSEY determinations. Compound 5a is more effective with ED50 = 0.98 and 3.98 μM against COX-2 and 15-lipoxygenase respectively, than the references celecoxib (1.54 μM) and meclofenamate sodium (5.64 μM). PMID:27131067
Hines, J.V.; Landry, S.M.; Varani, G.; Tinoco, I. Jr. Lawrence Berkeley Lab., CA )
1994-06-29
Long range carbon-proton scalar couplings were measured for an RNA hairpin of 12 nucleotides using 3D and [sup 13]C-edited 2D NMR. The large one-bond carbon-proton scalar couplings ([sup 1]J[sub CH]) and small n-bond couplings ([sup 1]J[sub CH]) produce ECOSY type cross-peaks, thus facilitating the determination of the sign and magnitude of the smaller [sup 2]J[sub CH] or [sup 3]J[sub CH]. The UUCGRNA hairpin (5[prime]-rGGACUUCGGUCC-3[prime]), whose structure has been determined by our laboratory, was uniformly [sup 13]C-labeled at 30% isotopic enrichment. The observed [sup 1]J[sub CH] couplings were then correlated to the known structure. The signs of [sup 2]J[sub C4[prime]H5[prime
A faster method for 3D/2D medical image registration--a simulation study.
Birkfellner, Wolfgang; Wirth, Joachim; Burgstaller, Wolfgang; Baumann, Bernard; Staedele, Harald; Hammer, Beat; Gellrich, Niels Claudius; Jacob, Augustinus Ludwig; Regazzoni, Pietro; Messmer, Peter
2003-08-21
3D/2D patient-to-computed-tomography (CT) registration is a method to determine a transformation that maps two coordinate systems by comparing a projection image rendered from CT to a real projection image. Iterative variation of the CT's position between rendering steps finally leads to exact registration. Applications include exact patient positioning in radiation therapy, calibration of surgical robots, and pose estimation in computer-aided surgery. One of the problems associated with 3D/2D registration is the fact that finding a registration includes solving a minimization problem in six degrees of freedom (dof) in motion. This results in considerable time requirements since for each iteration step at least one volume rendering has to be computed. We show that by choosing an appropriate world coordinate system and by applying a 2D/2D registration method in each iteration step, the number of iterations can be grossly reduced from n6 to n5. Here, n is the number of discrete variations around a given coordinate. Depending on the configuration of the optimization algorithm, this reduces the total number of iterations necessary to at least 1/3 of it's original value. The method was implemented and extensively tested on simulated x-ray images of a tibia, a pelvis and a skull base. When using one projective image and a discrete full parameter space search for solving the optimization problem, average accuracy was found to be 1.0 +/- 0.6(degrees) and 4.1 +/- 1.9 (mm) for a registration in six parameters, and 1.0 +/- 0.7(degrees) and 4.2 +/- 1.6 (mm) when using the 5 + 1 dof method described in this paper. Time requirements were reduced by a factor 3.1. We conclude that this hardware-independent optimization of 3D/2D registration is a step towards increasing the acceptance of this promising method for a wide number of clinical applications. PMID:12974581
Kumar Pandey, Avadhesh; Rapolu, Ravi; Raju, Ch Krishnam; Sasalamari, Gururaj; Kumar Goud, Sanath; Awasthi, Atul; Navalgund, Sameer G; Surendranath, Koduru V
2016-02-20
Forced degradation of losartan potassium in acidic condition resulted into three potential unknown impurities. These unknown degradation products marked as LD-I, LD-II and LD-III were analyzed using a new reverse-phase high performance liquid chromatography (HPLC), eluting at 3.63, 3.73 and 3.91 relative retention times with respect to losartan potassium (LOS) peak. All three were isolated from reaction mass using preparative HPLC and their structures were elucidated using LC-MS/MS, multidimensional NMR and FTIR spectroscopic techniques, as 5(2),11(2)-dibutyl-5(4),11(4)-dichloro-1(1)H,5(1)H,7(1)H,11(1)H-1(5,1),7(1,5)-ditetrazola-5,11(1,5)-diimidazola-2,8(1,2),3,9(1,4)-tetrabenzenacyclododecaphane,(Z)-5(2),11(2)-dibutyl-5(4),11(4)-dichloro-1(1)H,5(1)H,7(2)H,11(1)H-1(5,1),7(2,5)-ditetrazola-5,11(1,5)-diimidazola-2,8(1,2),3,9(1,4)-tetrabenzenacyclododecaphane, and 5(2),11(2)-dibutyl-5(4),11(4)-dichloro-1(2)H,5(1)H,7(2)H,11(1)H-1(5,2),7(2,5)-ditetrazola-5,11(1,5)-diimidazola-2,8(1,2),3,9(1,4)-tetrabenzenacyclododecaphane, respectively. To best of our knowledge, all three degradation products are novel impurities which are not discussed at any form of publication yet. PMID:26704631
A New Curb Detection Method for Unmanned Ground Vehicles Using 2D Sequential Laser Data
Liu, Zhao; Wang, Jinling; Liu, Daxue
2013-01-01
Curb detection is an important research topic in environment perception, which is an essential part of unmanned ground vehicle (UGV) operations. In this paper, a new curb detection method using a 2D laser range finder in a semi-structured environment is presented. In the proposed method, firstly, a local Digital Elevation Map (DEM) is built using 2D sequential laser rangefinder data and vehicle state data in a dynamic environment and a probabilistic moving object deletion approach is proposed to cope with the effect of moving objects. Secondly, the curb candidate points are extracted based on the moving direction of the vehicle in the local DEM. Finally, the straight and curved curbs are detected by the Hough transform and the multi-model RANSAC algorithm, respectively. The proposed method can detect the curbs robustly in both static and typical dynamic environments. The proposed method has been verified in real vehicle experiments. PMID:23325170
A new curb detection method for unmanned ground vehicles using 2D sequential laser data.
Liu, Zhao; Wang, Jinling; Liu, Daxue
2013-01-01
Curb detection is an important research topic in environment perception, which is an essential part of unmanned ground vehicle (UGV) operations. In this paper, a new curb detection method using a 2D laser range finder in a semi-structured environment is presented. In the proposed method, firstly, a local Digital Elevation Map (DEM) is built using 2D sequential laser rangefinder data and vehicle state data in a dynamic environment and a probabilistic moving object deletion approach is proposed to cope with the effect of moving objects. Secondly, the curb candidate points are extracted based on the moving direction of the vehicle in the local DEM. Finally, the straight and curved curbs are detected by the Hough transform and the multi-model RANSAC algorithm, respectively. The proposed method can detect the curbs robustly in both static and typical dynamic environments. The proposed method has been verified in real vehicle experiments. PMID:23325170
A nearly analytic exponential time difference method for solving 2D seismic wave equations
NASA Astrophysics Data System (ADS)
Zhang, Xiao; Yang, Dinghui; Song, Guojie
2014-02-01
In this paper, we propose a nearly analytic exponential time difference (NETD) method for solving the 2D acoustic and elastic wave equations. In this method, we use the nearly analytic discrete operator to approximate the high-order spatial differential operators and transform the seismic wave equations into semi-discrete ordinary differential equations (ODEs). Then, the converted ODE system is solved by the exponential time difference (ETD) method. We investigate the properties of NETD in detail, including the stability condition for 1-D and 2-D cases, the theoretical and relative errors, the numerical dispersion relation for the 2-D acoustic case, and the computational efficiency. In order to further validate the method, we apply it to simulating acoustic/elastic wave propagation in multilayer models which have strong contrasts and complex heterogeneous media, e.g., the SEG model and the Marmousi model. From our theoretical analyses and numerical results, the NETD can suppress numerical dispersion effectively by using the displacement and gradient to approximate the high-order spatial derivatives. In addition, because NETD is based on the structure of the Lie group method which preserves the quantitative properties of differential equations, it can achieve more accurate results than the classical methods.
Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS
NASA Astrophysics Data System (ADS)
Zhang, Rongchun; Ramamoorthy, Ayyalusamy
2016-01-01
Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D 1H/13C/1H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t1 and t3 periods, respectively. In addition to through-space and through-bond 13C/1H and 13C/13C chemical shift correlations, the 3D 1H/13C/1H experiment also provides a COSY-type 1H/1H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices (1H/1H chemical shift correlation spectrum) at different 13C chemical shift frequencies from the 3D 1H/13C/1H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D 1H/13C/1H experiment would be useful to study the structure and dynamics of a variety of chemical and biological
Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS.
Zhang, Rongchun; Ramamoorthy, Ayyalusamy
2016-01-21
Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D (1)H/(13)C/(1)H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t1 and t3 periods, respectively. In addition to through-space and through-bond (13)C/(1)H and (13)C/(13)C chemical shift correlations, the 3D (1)H/(13)C/(1)H experiment also provides a COSY-type (1)H/(1)H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices ((1)H/(1)H chemical shift correlation spectrum) at different (13)C chemical shift frequencies from the 3D (1)H/(13)C/(1)H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D (1)H/(13)C/(1)H experiment would be useful to study the structure and dynamics of
Galerkin Spectral Method for the 2D Solitary Waves of Boussinesq Paradigm Equation
Christou, M. A.; Christov, C. I.
2009-10-29
We consider the 2D stationary propagating solitary waves of the so-called Boussinesq Paradigm equation. The fourth- order elliptic boundary value problem on infinite interval is solved by a Galerkin spectral method. An iterative procedure based on artificial time ('false transients') and operator splitting is used. Results are obtained for the shapes of the solitary waves for different values of the dispersion parameters for both subcritical and supercritical phase speeds.
Methods for spatial localization in NMR
Rath, A.R.
1985-01-01
Several unique coil configurations were developed that have applications in nuclear magnetic resonance. These include a number of designs appropriate for use as rf surface coils, and two configurations developed as NMR magnets. The magnetic field profiles were calculated for each of these designs, from which field strength and homogeneity information were obtained. The rf coil configurations modelled include the opposed loop, opposed half loop, bicycle wheel, opposed bicycle wheel, and semi-toroid. The opposed loop design was studied in detail in terms of the theoretical spatial sensitivity and selectivity it offers. A number of NMR experiments were performed to test the validity of these theoretical calculations. This configuration produces a field that is substantially reduced near the coil itself, compared with the field produced by a single loop surface coil, but that rises to a maximum along the coil axis yielding a somewhat homogeneous region that may be used to achieve a degree of spatial localization. Several comparison schemes are used to evaluate the relative advantages and disadvantages of both the single loop and the opposed loop coil. The opposed coil concept also has been applied to the design of magnets. The results of calculations on the homogeneity and field strength possible with an opposed solenoid magnet are presented.
Precise and rapid isotopomic analysis by (1)H-(13)C 2D NMR: Application to triacylglycerol matrices.
Merchak, Noelle; Silvestre, Virginie; Rouger, Laetitia; Giraudeau, Patrick; Rizk, Toufic; Bejjani, Joseph; Akoka, Serge
2016-08-15
An optimized HSQC sequence was tested and applied to triacylglycerol matrices to determine their isotopic and metabolomic profiles. Spectral aliasing and non-uniform sampling approaches were used to decrease the experimental time and to improve the resolution, respectively. An excellent long-term repeatability of signal integrals was achieved enabling to perform isotopic measurements. Thirty-two commercial vegetable oils were analyzed by this methodology. The results show that this method can be used to classify oil samples according to their geographical and botanical origins. PMID:27260459
NASA Astrophysics Data System (ADS)
Maximov, Ivan I.; Vinding, Mads S.; Tse, Desmond H. Y.; Nielsen, Niels Chr.; Shah, N. Jon
2015-05-01
There is an increasing need for development of advanced radio-frequency (RF) pulse techniques in modern magnetic resonance imaging (MRI) systems driven by recent advancements in ultra-high magnetic field systems, new parallel transmit/receive coil designs, and accessible powerful computational facilities. 2D spatially selective RF pulses are an example of advanced pulses that have many applications of clinical relevance, e.g., reduced field of view imaging, and MR spectroscopy. The 2D spatially selective RF pulses are mostly generated and optimised with numerical methods that can handle vast controls and multiple constraints. With this study we aim at demonstrating that numerical, optimal control (OC) algorithms are efficient for the design of 2D spatially selective MRI experiments, when robustness towards e.g. field inhomogeneity is in focus. We have chosen three popular OC algorithms; two which are gradient-based, concurrent methods using first- and second-order derivatives, respectively; and a third that belongs to the sequential, monotonically convergent family. We used two experimental models: a water phantom, and an in vivo human head. Taking into consideration the challenging experimental setup, our analysis suggests the use of the sequential, monotonic approach and the second-order gradient-based approach as computational speed, experimental robustness, and image quality is key. All algorithms used in this work were implemented in the MATLAB environment and are freely available to the MRI community.
Maximov, Ivan I; Vinding, Mads S; Tse, Desmond H Y; Nielsen, Niels Chr; Shah, N Jon
2015-05-01
There is an increasing need for development of advanced radio-frequency (RF) pulse techniques in modern magnetic resonance imaging (MRI) systems driven by recent advancements in ultra-high magnetic field systems, new parallel transmit/receive coil designs, and accessible powerful computational facilities. 2D spatially selective RF pulses are an example of advanced pulses that have many applications of clinical relevance, e.g., reduced field of view imaging, and MR spectroscopy. The 2D spatially selective RF pulses are mostly generated and optimised with numerical methods that can handle vast controls and multiple constraints. With this study we aim at demonstrating that numerical, optimal control (OC) algorithms are efficient for the design of 2D spatially selective MRI experiments, when robustness towards e.g. field inhomogeneity is in focus. We have chosen three popular OC algorithms; two which are gradient-based, concurrent methods using first- and second-order derivatives, respectively; and a third that belongs to the sequential, monotonically convergent family. We used two experimental models: a water phantom, and an in vivo human head. Taking into consideration the challenging experimental setup, our analysis suggests the use of the sequential, monotonic approach and the second-order gradient-based approach as computational speed, experimental robustness, and image quality is key. All algorithms used in this work were implemented in the MATLAB environment and are freely available to the MRI community. PMID:25863895
Methods for defect characterisation in thin film materials by depth-selective 2D-ACAR
NASA Astrophysics Data System (ADS)
Eijt, S. W. H.; Falub, C. V.; van Veen, A.; Schut, H.; Mijnarends, P. E.
2002-06-01
The advent of intense positron beams makes it possible to perform depth-selective 2D-ACAR (two-dimensional angular correlation of annihilation radiation) studies. The Delft POSH-ACAR setup employs a strong permanent magnet for focusing of the POSH beam on the sample, which leads to a ˜15% spread in implantation energy. The effects of this spread on positron depth-profiling data are discussed, and are shown to be consistent with Doppler experiments on Si(1 0 0) with a subsurface layer of nanocavities. A method is presented to decompose depth-selective 2D-ACAR spectra reliably into their various (layer) components. This is used to reveal strong positron trapping in the nanocavities in Si(1 0 0).
2D-PCR: a method of mapping DNA in tissue sections†
Armani, Michael; Rodriguez-Canales, Jaime; Gillespie, John; Tangrea, Michael; Erickson, Heidi; Emmert-Buck, Michael R.; Shapiro, Benjamin; Smela, Elisabeth
2010-01-01
A novel approach was developed for mapping the location of target DNA in tissue sections. The method combines a high-density, multi-well plate with an innovative single-tube procedure to directly extract, amplify, and detect the DNA in parallel while maintaining the two-dimensional (2D) architecture of the tissue. A 2D map of the gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was created from a tissue section and shown to correlate with the spatial area of the sample. It is anticipated that this approach may be easily adapted to assess the status of multiple genes within tissue sections, yielding a molecular map that directly correlates with the histology of the sample. This will provide investigators with a new tool to interrogate the molecular heterogeneity of tissue specimens. PMID:20024032
NASA Astrophysics Data System (ADS)
Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy
2014-05-01
Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.
Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy
2014-01-01
Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles. PMID:24657390
Wang, Tuo; Yang, Hui; Kubicki, James D; Hong, Mei
2016-06-13
The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D (13)C-(13)C correlation spectra of uniformly (13)C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose (13)C chemical shifts differ significantly from the (13)C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing, and hydrogen bonding from celluloses of other organisms. 2D (13)C-(13)C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Celluloses f and g are well mixed chains on the microfibril surface, celluloses a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of
Uzawa, Takanori; Nishimura, Chiaki; Akiyama, Shuji; Ishimori, Koichiro; Takahashi, Satoshi; Dyson, H Jane; Wright, Peter E
2008-09-16
The earliest steps in the folding of proteins are complete on an extremely rapid time scale that is difficult to access experimentally. We have used rapid-mixing quench-flow methods to extend the time resolution of folding studies on apomyoglobin and elucidate the structural and dynamic features of members of the ensemble of intermediate states that are populated on a submillisecond time scale during this process. The picture that emerges is of a continuum of rapidly interconverting states. Even after only 0.4 ms of refolding time a compact state is formed that contains major parts of the A, G, and H helices, which are sufficiently well folded to protect amides from exchange. The B, C, and E helix regions fold more slowly and fluctuate rapidly between open and closed states as they search docking sites on this core; the secondary structure in these regions becomes stabilized as the refolding time is increased from 0.4 to 6 ms. No further stabilization occurs in the A, G, H core at 6 ms of folding time. These studies begin to time-resolve a progression of compact states between the fully unfolded and native folded states and confirm the presence an ensemble of intermediates that interconvert in a hierarchical sequence as the protein searches conformational space on its folding trajectory. PMID:18779573
A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows
NASA Astrophysics Data System (ADS)
Bijleveld, H. A.; Veldman, A. E. P.
2014-12-01
A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.
NASA Astrophysics Data System (ADS)
Martel, Dimitri; Tse Ve Koon, K.; Le Fur, Yann; Ratiney, Hélène
2015-11-01
Two-dimensional spectroscopy offers the possibility to unambiguously distinguish metabolites by spreading out the multiplet structure of J-coupled spin systems into a second dimension. Quantification methods that perform parametric fitting of the 2D MRS signal have recently been proposed for resolved PRESS (JPRESS) but not explicitly for Localized Correlation Spectroscopy (LCOSY). Here, through a whole metabolite quantification approach, correlation spectroscopy quantification performances are studied. The ability to quantify metabolite relaxation constant times is studied for three localized 2D MRS sequences (LCOSY, LCTCOSY and the JPRESS) in vitro on preclinical MR systems. The issues encountered during implementation and quantification strategies are discussed with the help of the Fisher matrix formalism. The described parameterized models enable the computation of the lower bound for error variance - generally known as the Cramér Rao bounds (CRBs), a standard of precision - on the parameters estimated from these 2D MRS signal fittings. LCOSY has a theoretical net signal loss of two per unit of acquisition time compared to JPRESS. A rapid analysis could point that the relative CRBs of LCOSY compared to JPRESS (expressed as a percentage of the concentration values) should be doubled but we show that this is not necessarily true. Finally, the LCOSY quantification procedure has been applied on data acquired in vivo on a mouse brain.
Comparison of lifetime-based methods for 2D phosphor thermometry in high-temperature environment
NASA Astrophysics Data System (ADS)
Peng, Di; Liu, Yingzheng; Zhao, Xiaofeng; Kim, Kyung Chun
2016-09-01
This paper discusses the currently available techniques for 2D phosphor thermometry, and compares the performance of two lifetime-based methods: high-speed imaging and the dual-gate. High-speed imaging resolves luminescent decay with a fast frame rate, and has become a popular method for phosphor thermometry in recent years. But it has disadvantages such as high equipment cost and long data processing time, and it would fail at sufficiently high temperature due to a low signal-to-noise ratio and short lifetime. The dual-gate method only requires two images on the decay curve and therefore greatly reduces cost in hardware and processing time. A dual-gate method for phosphor thermometry has been developed and compared with the high-speed imaging method through both calibration and a jet impingement experiment. Measurement uncertainty has been evaluated for a temperature range of 473–833 K. The effects of several key factors on uncertainty have been discussed, including the luminescent signal level, the decay lifetime and temperature sensitivity. The results show that both methods are valid for 2D temperature sensing within the given range. The high-speed imaging method shows less uncertainty at low temperatures where the signal level and the lifetime are both sufficient, but its performance is degraded at higher temperatures due to a rapidly reduced signal and lifetime. For T > 750 K, the dual-gate method outperforms the high-speed imaging method thanks to its superiority in signal-to-noise ratio and temperature sensitivity. The dual-gate method has great potential for applications in high-temperature environments where the high-speed imaging method is not applicable.
Scattering of elastic waves by a 2-D crack using the Indirect Boundary Element Method (IBEM)
NASA Astrophysics Data System (ADS)
Iturrarán-Viveros, Ursula; Vai, Rossana; Sánchez-Sesma, Francisco J.
2005-09-01
The scattering of elastic waves by cracks is an old problem and various ways to solve it have been proposed in the last decades. One approach is using dual integral equations, another useful and common formulation is the Boundary Element Method (BEM). With the last one, the boundary conditions of the crack lead to hyper-singularities and particular care should be taken to regularize and solve the resulting integral equations. In this work, instead, the Indirect Boundary Element Method (IBEM) is applied to study problems of zero-thickness 2-D cracks. The IBEM yields the Crack Opening Displacement (COD) which is used to evaluate the solution away from the crack. We use a multiregional approach which consists of splitting a boundary S into two identical boundaries S+ and S- chosen such that the cracks lie in the interface. The resulting integral equations are not hyper-singular and wave propagation within media that contain zero-thickness cracks can be rigorously solved. In order to validate the method, we deal with the scalar case, namely the scattering of antiplane SH waves by a 2-D crack. We compare results against a recently published analytic solution, obtaining an excellent agreement. This comparison gives us confidence to study cases where no analytic solutions exist. Some examples of incidence of P- or SV waves are depicted and the salient aspects of the method are also discussed.
A new stationary gridline artifact suppression method based on the 2D discrete wavelet transform
Tang, Hui; Tong, Dan; Dong Bao, Xu; Dillenseger, Jean-Louis
2015-04-15
Purpose: In digital x-ray radiography, an antiscatter grid is inserted between the patient and the image receptor to reduce scattered radiation. If the antiscatter grid is used in a stationary way, gridline artifacts will appear in the final image. In most of the gridline removal image processing methods, the useful information with spatial frequencies close to that of the gridline is usually lost or degraded. In this study, a new stationary gridline suppression method is designed to preserve more of the useful information. Methods: The method is as follows. The input image is first recursively decomposed into several smaller subimages using a multiscale 2D discrete wavelet transform. The decomposition process stops when the gridline signal is found to be greater than a threshold in one or several of these subimages using a gridline detection module. An automatic Gaussian band-stop filter is then applied to the detected subimages to remove the gridline signal. Finally, the restored image is achieved using the corresponding 2D inverse discrete wavelet transform. Results: The processed images show that the proposed method can remove the gridline signal efficiently while maintaining the image details. The spectra of a 1D Fourier transform of the processed images demonstrate that, compared with some existing gridline removal methods, the proposed method has better information preservation after the removal of the gridline artifacts. Additionally, the performance speed is relatively high. Conclusions: The experimental results demonstrate the efficiency of the proposed method. Compared with some existing gridline removal methods, the proposed method can preserve more information within an acceptable execution time.
Canonical vs. micro-canonical sampling methods in a 2D Ising model
Kepner, J.
1990-12-01
Canonical and micro-canonical Monte Carlo algorithms were implemented on a 2D Ising model. Expressions for the internal energy, U, inverse temperature, Z, and specific heat, C, are given. These quantities were calculated over a range of temperature, lattice sizes, and time steps. Both algorithms accurately simulate the Ising model. To obtain greater than three decimal accuracy from the micro-canonical method requires that the more complicated expression for Z be used. The overall difference between the algorithms is small. The physics of the problem under study should be the deciding factor in determining which algorithm to use. 13 refs., 6 figs., 2 tabs.
Pulse methods in 1D and 2D liquid-phase NMR
Brey, W.S.
1988-01-01
State-of-the-art nuclear magnetic resonance spectrometers are capable of performing an array of multiple-pulse one-dimensional and two-dimensional experiments. These experiments can provide detailed information about the structure, dynamics, and reactions of molecules. However, their successful application to chemical problems requires that the chemist have some knowledge of the various experiments and the information they can provide. This book, written by authorities in the field, provides such information for both the specialist and the nonspecialist.
NASA Astrophysics Data System (ADS)
Li, Jinghe; Song, Linping; Liu, Qing Huo
2016-02-01
A simultaneous multiple frequency contrast source inversion (CSI) method is applied to reconstructing hydrocarbon reservoir targets in a complex multilayered medium in two dimensions. It simulates the effects of a salt dome sedimentary formation in the context of reservoir monitoring. In this method, the stabilized biconjugate-gradient fast Fourier transform (BCGS-FFT) algorithm is applied as a fast solver for the 2D volume integral equation for the forward computation. The inversion technique with CSI combines the efficient FFT algorithm to speed up the matrix-vector multiplication and the stable convergence of the simultaneous multiple frequency CSI in the iteration process. As a result, this method is capable of making quantitative conductivity image reconstruction effectively for large-scale electromagnetic oil exploration problems, including the vertical electromagnetic profiling (VEP) survey investigated here. A number of numerical examples have been demonstrated to validate the effectiveness and capacity of the simultaneous multiple frequency CSI method for a limited array view in VEP.
Comparison of 2D transmon coherence for different capacitive shunt fabrication methods
NASA Astrophysics Data System (ADS)
Yoder, Jonilyn; Kamal, Archana; Yan, Fei; Gudmundsen, Theodore; Welander, Paul; Gustavsson, Simon; Hover, David; Kerman, Andrew; Sears, Adam; Oliver, William
2015-03-01
Improvements in superconducting qubit coherence times and reproducibility have been demonstrated using capacitive shunting. In this study, we present a side-by-side comparison of two distinct methods for preparing the aluminum shunt capacitor material for 2D transmon superconducting qubit devices. The first method involved in situ wafer outgassing prior to molecular beam epitaxy aluminum evaporation. The second method involved ex situ wafer annealing prior to electron gun aluminum evaporation. Materials analysis for each process will be detailed. Experimental results, including qubit coherence times and superconducting coplanar waveguide resonator internal quality factors, will be presented for representative devices prepared using both methods. This work is sponsored by the Assistant Secretary of Defense for Research and Engineering under Air Force Contract FA8721-05-0002. Opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by the United States Government.
A Novel Crosstalk Suppression Method of the 2-D Networked Resistive Sensor Array
Wu, Jianfeng; Wang, Lei; Li, Jianqing; Song, Aiguo
2014-01-01
The 2-D resistive sensor array in the row–column fashion suffered from the crosstalk problem for parasitic parallel paths. Firstly, we proposed an Improved Isolated Drive Feedback Circuit with Compensation (IIDFCC) based on the voltage feedback method to suppress the crosstalk. In this method, a compensated resistor was specially used to reduce the crosstalk caused by the column multiplexer resistors and the adjacent row elements. Then, a mathematical equivalent resistance expression of the element being tested (EBT) of this circuit was analytically derived and verified by the circuit simulations. The simulation results show that the measurement method can greatly reduce the influence on the EBT caused by parasitic parallel paths for the multiplexers' channel resistor and the adjacent elements. PMID:25046011
Fast 2D DOA Estimation Algorithm by an Array Manifold Matching Method with Parallel Linear Arrays.
Yang, Lisheng; Liu, Sheng; Li, Dong; Jiang, Qingping; Cao, Hailin
2016-01-01
In this paper, the problem of two-dimensional (2D) direction-of-arrival (DOA) estimation with parallel linear arrays is addressed. Two array manifold matching (AMM) approaches, in this work, are developed for the incoherent and coherent signals, respectively. The proposed AMM methods estimate the azimuth angle only with the assumption that the elevation angles are known or estimated. The proposed methods are time efficient since they do not require eigenvalue decomposition (EVD) or peak searching. In addition, the complexity analysis shows the proposed AMM approaches have lower computational complexity than many current state-of-the-art algorithms. The estimated azimuth angles produced by the AMM approaches are automatically paired with the elevation angles. More importantly, for estimating the azimuth angles of coherent signals, the aperture loss issue is avoided since a decorrelation procedure is not required for the proposed AMM method. Numerical studies demonstrate the effectiveness of the proposed approaches. PMID:26907301
Fast 2D DOA Estimation Algorithm by an Array Manifold Matching Method with Parallel Linear Arrays
Yang, Lisheng; Liu, Sheng; Li, Dong; Jiang, Qingping; Cao, Hailin
2016-01-01
In this paper, the problem of two-dimensional (2D) direction-of-arrival (DOA) estimation with parallel linear arrays is addressed. Two array manifold matching (AMM) approaches, in this work, are developed for the incoherent and coherent signals, respectively. The proposed AMM methods estimate the azimuth angle only with the assumption that the elevation angles are known or estimated. The proposed methods are time efficient since they do not require eigenvalue decomposition (EVD) or peak searching. In addition, the complexity analysis shows the proposed AMM approaches have lower computational complexity than many current state-of-the-art algorithms. The estimated azimuth angles produced by the AMM approaches are automatically paired with the elevation angles. More importantly, for estimating the azimuth angles of coherent signals, the aperture loss issue is avoided since a decorrelation procedure is not required for the proposed AMM method. Numerical studies demonstrate the effectiveness of the proposed approaches. PMID:26907301
A linear analytical boundary element method (BEM) for 2D homogeneous potential problems
NASA Astrophysics Data System (ADS)
Friedrich, Jürgen
2002-06-01
The solution of potential problems is not only fundamental for geosciences, but also an essential part of related subjects like electro- and fluid-mechanics. In all fields, solution algorithms are needed that should be as accurate as possible, robust, simple to program, easy to use, fast and small in computer memory. An ideal technique to fulfill these criteria is the boundary element method (BEM) which applies Green's identities to transform volume integrals into boundary integrals. This work describes a linear analytical BEM for 2D homogeneous potential problems that is more robust and precise than numerical methods because it avoids numerical schemes and coordinate transformations. After deriving the solution algorithm, the introduced approach is tested against different benchmarks. Finally, the gained method was incorporated into an existing software program described before in this journal by the same author.
Observation of 2D Ising criticality of liquid-gas transition by the flowgram method
NASA Astrophysics Data System (ADS)
Yarmolinsky, Max; Kuklov, Anatoly
We study the critical properties of the transition in 2D liquid-gas system with the square-well potential interaction by Monte Carlo simulations in the grand canonical ensemble. Due to lack of the underlying Ising symmetry, the analysis cannot be done reliably by the standard methods applicable to lattice systems. In contrast, the analysis based on the flowgram method allowed us to find the critical point to significantly higher (and controllable) accuracy than in previous studies by other authors. Simulations were performed in a progression of sizes L up to size L = 84 , with the particle numbers varying over 3 orders of magnitude and the subcritical behavior not extending beyond L = 10 - 15 . The finite size scaling analysis of the critical exponents and their ratio, μ and γ / ν , gives values consistent with the 2D Ising universality class within 1-2% of errors. Our result essentially closes proposals that the nature of the liquid-gas transition might be different from the Ising model in systems with short-range interactions. This work was supported by the NSF Grant PHY1314469.
ARC2D - EFFICIENT SOLUTION METHODS FOR THE NAVIER-STOKES EQUATIONS (DEC RISC ULTRIX VERSION)
NASA Technical Reports Server (NTRS)
Biyabani, S. R.
1994-01-01
ARC2D is a computational fluid dynamics program developed at the NASA Ames Research Center specifically for airfoil computations. The program uses implicit finite-difference techniques to solve two-dimensional Euler equations and thin layer Navier-Stokes equations. It is based on the Beam and Warming implicit approximate factorization algorithm in generalized coordinates. The methods are either time accurate or accelerated non-time accurate steady state schemes. The evolution of the solution through time is physically realistic; good solution accuracy is dependent on mesh spacing and boundary conditions. The mathematical development of ARC2D begins with the strong conservation law form of the two-dimensional Navier-Stokes equations in Cartesian coordinates, which admits shock capturing. The Navier-Stokes equations can be transformed from Cartesian coordinates to generalized curvilinear coordinates in a manner that permits one computational code to serve a wide variety of physical geometries and grid systems. ARC2D includes an algebraic mixing length model to approximate the effect of turbulence. In cases of high Reynolds number viscous flows, thin layer approximation can be applied. ARC2D allows for a variety of solutions to stability boundaries, such as those encountered in flows with shocks. The user has considerable flexibility in assigning geometry and developing grid patterns, as well as in assigning boundary conditions. However, the ARC2D model is most appropriate for attached and mildly separated boundary layers; no attempt is made to model wake regions and widely separated flows. The techniques have been successfully used for a variety of inviscid and viscous flowfield calculations. The Cray version of ARC2D is written in FORTRAN 77 for use on Cray series computers and requires approximately 5Mb memory. The program is fully vectorized. The tape includes variations for the COS and UNICOS operating systems. Also included is a sample routine for CONVEX
ARC2D - EFFICIENT SOLUTION METHODS FOR THE NAVIER-STOKES EQUATIONS (CRAY VERSION)
NASA Technical Reports Server (NTRS)
Pulliam, T. H.
1994-01-01
ARC2D is a computational fluid dynamics program developed at the NASA Ames Research Center specifically for airfoil computations. The program uses implicit finite-difference techniques to solve two-dimensional Euler equations and thin layer Navier-Stokes equations. It is based on the Beam and Warming implicit approximate factorization algorithm in generalized coordinates. The methods are either time accurate or accelerated non-time accurate steady state schemes. The evolution of the solution through time is physically realistic; good solution accuracy is dependent on mesh spacing and boundary conditions. The mathematical development of ARC2D begins with the strong conservation law form of the two-dimensional Navier-Stokes equations in Cartesian coordinates, which admits shock capturing. The Navier-Stokes equations can be transformed from Cartesian coordinates to generalized curvilinear coordinates in a manner that permits one computational code to serve a wide variety of physical geometries and grid systems. ARC2D includes an algebraic mixing length model to approximate the effect of turbulence. In cases of high Reynolds number viscous flows, thin layer approximation can be applied. ARC2D allows for a variety of solutions to stability boundaries, such as those encountered in flows with shocks. The user has considerable flexibility in assigning geometry and developing grid patterns, as well as in assigning boundary conditions. However, the ARC2D model is most appropriate for attached and mildly separated boundary layers; no attempt is made to model wake regions and widely separated flows. The techniques have been successfully used for a variety of inviscid and viscous flowfield calculations. The Cray version of ARC2D is written in FORTRAN 77 for use on Cray series computers and requires approximately 5Mb memory. The program is fully vectorized. The tape includes variations for the COS and UNICOS operating systems. Also included is a sample routine for CONVEX
A two-step Hilbert transform method for 2D image reconstruction.
Noo, Frédéric; Clackdoyle, Rolf; Pack, Jed D
2004-09-01
The paper describes a new accurate two-dimensional (2D) image reconstruction method consisting of two steps. In the first step, the backprojected image is formed after taking the derivative of the parallel projection data. In the second step, a Hilbert filtering is applied along certain lines in the differentiated backprojection (DBP) image. Formulae for performing the DBP step in fanbeam geometry are also presented. The advantage of this two-step Hilbert transform approach is that in certain situations, regions of interest (ROIs) can be reconstructed from truncated projection data. Simulation results are presented that illustrate very similar reconstructed image quality using the new method compared to standard filtered backprojection, and that show the capability to correctly handle truncated projections. In particular, a simulation is presented of a wide patient whose projections are truncated laterally yet for which highly accurate ROI reconstruction is obtained. PMID:15470913
Total Protein Extraction and 2-D Gel Electrophoresis Methods for Burkholderia Species
Velapatiño, Billie; Zlosnik, James E. A.; Hird, Trevor J.; Speert, David P.
2013-01-01
The investigation of the intracellular protein levels of bacterial species is of importance to understanding the pathogenic mechanisms of diseases caused by these organisms. Here we describe a procedure for protein extraction from Burkholderia species based on mechanical lysis using glass beads in the presence of ethylenediamine tetraacetic acid and phenylmethylsulfonyl fluoride in phosphate buffered saline. This method can be used for different Burkholderia species, for different growth conditions, and it is likely suitable for the use in proteomic studies of other bacteria. Following protein extraction, a two-dimensional (2-D) gel electrophoresis proteomic technique is described to study global changes in the proteomes of these organisms. This method consists of the separation of proteins according to their isoelectric point by isoelectric focusing in the first dimension, followed by separation on the basis of molecular weight by acrylamide gel electrophoresis in the second dimension. Visualization of separated proteins is carried out by silver staining. PMID:24192802
Eulerian and Lagrangian methods for vortex tracking in 2D and 3D flows
NASA Astrophysics Data System (ADS)
Huang, Yangzi; Green, Melissa
2014-11-01
Coherent structures are a key component of unsteady flows in shear layers. Improvement of experimental techniques has led to larger amounts of data and requires of automated procedures for vortex tracking. Many vortex criteria are Eulerian, and identify the structures by an instantaneous local swirling motion in the field, which are indicated by closed or spiral streamlines or pathlines in a reference frame. Alternatively, a Lagrangian Coherent Structures (LCS) analysis is a Lagrangian method based on the quantities calculated along fluid particle trajectories. In the current work, vortex detection is demonstrated on data from the simulation of two cases: a 2D flow with a flat plate undergoing a 45 ° pitch-up maneuver and a 3D wall-bounded turbulence channel flow. Vortices are visualized and tracked by their centers and boundaries using Γ1, the Q criterion, and LCS saddle points. In the cases of 2D flow, saddle points trace showed a rapid acceleration of the structure which indicates the shedding from the plate. For channel flow, saddle points trace shows that average structure convection speed exhibits a similar trend as a function of wall-normal distance as the mean velocity profile, and leads to statistical quantities of vortex dynamics. Dr. Jeff Eldredge and his research group at UCLA are gratefully acknowledged for sharing the database of simulation for the current research. This work was supported by the Air Force Office of Scientific Research under AFOSR Award No. FA9550-14-1-0210.
High Pressure NMR Methods for Characterizing Functional Substates of Proteins.
Kalbitzer, Hans Robert
2015-01-01
Proteins usually exist in multiple conformational states in solution. High pressure NMR spectroscopy is a well-suited method to identify these states. In addition, these states can be characterized by their thermodynamic parameters, the free enthalpies at ambient pressure, the partial molar volumes, and the partial molar compressibility that can be obtained from the analysis of the high pressure NMR data. Two main types of states of proteins exist, functional states and folding states. There is a strong link between these two types, the functional states represent essential folding states (intermediates), other folding states may have no functional meaning (optional folding states). In this chapter, this concept is tested on the Ras protein, an important proto-oncogen in humans where all substates required by theory can be identified experimentally by high pressure NMR spectroscopy. Finally, we show how these data can be used to develop allosteric inhibitors of proteins. PMID:26174382
Inversion Method for Evapotranspiration from 2D Measurements of Water Vapor Concentration
NASA Astrophysics Data System (ADS)
Eichinger, W. E.; Barnhart, B. L.; Plenner, S.; Thompson, A.; Winsky, B.
2011-12-01
A method has been developed to use 2D measurements of water vapor concentration to make spatial estimates of evapotranspiration. The method is based on theoretical solutions to the conservation of water vapor equation (similar to Sutton, Sienfeld) and is related to methods used to generate footprints. The method uses a diffusion coefficient to close the conservation equation and assumes uniformity of the surface with respect to turbulent processes. This solution allows the development of a transfer coefficient between each location at the surface and each of the water vapor measurements. The problem has been constrained to two dimensions for development, but is easily expanded to three. The method assumes water vapor concentration measurements in a plane at arbitrary positions above the field. Evapotranspiration is allowed to vary in increments across the field. This geometry and the transfer coefficients allow the water vapor concentration at each of the measured locations to be expressed as the sum of the contributions from the entire surface. A least squares solution is found that estimates the evapotranspiration across the field as a function of position. To evaluate the accuracy of the approach in solving for evaporation rates two artificial data sets of water vapor concentration (with varying amounts of artificial noise added) for known evaporation rates were generated and used to estimate the surface evaporation. The method is sensitive to the assumptions made near the edges of field. Results and details of the methods used to resolve edge effects will be shown.
Efficiency of Pareto joint inversion of 2D geophysical data using global optimization methods
NASA Astrophysics Data System (ADS)
Miernik, Katarzyna; Bogacz, Adrian; Kozubal, Adam; Danek, Tomasz; Wojdyła, Marek
2016-04-01
Pareto joint inversion of two or more sets of data is a promising new tool of modern geophysical exploration. In the first stage of our investigation we created software enabling execution of forward solvers of two geophysical methods (2D magnetotelluric and gravity) as well as inversion with possibility of constraining solution with seismic data. In the algorithm solving MT forward solver Helmholtz's equations, finite element method and Dirichlet's boundary conditions were applied. Gravity forward solver was based on Talwani's algorithm. To limit dimensionality of solution space we decided to describe model as sets of polygons, using Sharp Boundary Interface (SBI) approach. The main inversion engine was created using Particle Swarm Optimization (PSO) algorithm adapted to handle two or more target functions and to prevent acceptance of solutions which are non - realistic or incompatible with Pareto scheme. Each inversion run generates single Pareto solution, which can be added to Pareto Front. The PSO inversion engine was parallelized using OpenMP standard, what enabled execution code for practically unlimited amount of threads at once. Thereby computing time of inversion process was significantly decreased. Furthermore, computing efficiency increases with number of PSO iterations. In this contribution we analyze the efficiency of created software solution taking under consideration details of chosen global optimization engine used as a main joint minimization engine. Additionally we study the scale of possible decrease of computational time caused by different methods of parallelization applied for both forward solvers and inversion algorithm. All tests were done for 2D magnetotelluric and gravity data based on real geological media. Obtained results show that even for relatively simple mid end computational infrastructure proposed solution of inversion problem can be applied in practice and used for real life problems of geophysical inversion and interpretation.
Holographic method for site-resolved detection of a 2D array of ultracold atoms
NASA Astrophysics Data System (ADS)
Hoffmann, Daniel Kai; Deissler, Benjamin; Limmer, Wolfgang; Hecker Denschlag, Johannes
2016-08-01
We propose a novel approach to site-resolved detection of a 2D gas of ultracold atoms in an optical lattice. A near-resonant laser beam is coherently scattered by the atomic array, and after passing a lens its interference pattern is holographically recorded by superimposing it with a reference laser beam on a CCD chip. Fourier transformation of the recorded intensity pattern reconstructs the atomic distribution in the lattice with single-site resolution. The holographic detection method requires only about two hundred scattered photons per atom in order to achieve a high reconstruction fidelity of 99.9 %. Therefore, additional cooling during detection might not be necessary even for light atomic elements such as lithium. Furthermore, first investigations suggest that small aberrations of the lens can be post-corrected in imaging processing.
Numerical method of crack analysis in 2D finite magnetoelectroelastic media
NASA Astrophysics Data System (ADS)
Zhao, Minghao; Xu, Guangtao; Fan, Cuiying
2010-04-01
The present paper extends the hybrid extended displacement discontinuity fundamental solution method (HEDD-FSM) (Eng Anal Bound Elem 33:592-600, 2009) to analysis of cracks in 2D finite magnetoelectroelastic media. The solution of the crack is expressed approximately by a linear combination of fundamental solutions of the governing equations, which includes the extended point force fundamental solutions with sources placed at chosen points outside the domain of the problem under consideration, and the extended Crouch fundamental solutions with extended displacement discontinuities placed on the crack. The coefficients of the fundamental solutions are determined by letting the approximated solution satisfy the prescribed boundary conditions on the boundary of the domain and on the crack face. The Crouch fundamental solution for a parabolic element at the crack tip is derived to model the square root variations of near tip fields. The extended stress intensity factors are calculated under different electric and magnetic boundary conditions.
A framework for grand scale parallelization of the combined finite discrete element method in 2d
NASA Astrophysics Data System (ADS)
Lei, Z.; Rougier, E.; Knight, E. E.; Munjiza, A.
2014-09-01
Within the context of rock mechanics, the Combined Finite-Discrete Element Method (FDEM) has been applied to many complex industrial problems such as block caving, deep mining techniques (tunneling, pillar strength, etc.), rock blasting, seismic wave propagation, packing problems, dam stability, rock slope stability, rock mass strength characterization problems, etc. The reality is that most of these were accomplished in a 2D and/or single processor realm. In this work a hardware independent FDEM parallelization framework has been developed using the Virtual Parallel Machine for FDEM, (V-FDEM). With V-FDEM, a parallel FDEM software can be adapted to different parallel architecture systems ranging from just a few to thousands of cores.
The Wavelet Element Method. Part 2; Realization and Additional Features in 2D and 3D
NASA Technical Reports Server (NTRS)
Canuto, Claudio; Tabacco, Anita; Urban, Karsten
1998-01-01
The Wavelet Element Method (WEM) provides a construction of multiresolution systems and biorthogonal wavelets on fairly general domains. These are split into subdomains that are mapped to a single reference hypercube. Tensor products of scaling functions and wavelets defined on the unit interval are used on the reference domain. By introducing appropriate matching conditions across the interelement boundaries, a globally continuous biorthogonal wavelet basis on the general domain is obtained. This construction does not uniquely define the basis functions but rather leaves some freedom for fulfilling additional features. In this paper we detail the general construction principle of the WEM to the 1D, 2D and 3D cases. We address additional features such as symmetry, vanishing moments and minimal support of the wavelet functions in each particular dimension. The construction is illustrated by using biorthogonal spline wavelets on the interval.
A 2-D Implicit, Energy and Charge Conserving Particle In Cell Method
McPherson, Allen L.; Knoll, Dana A.; Cieren, Emmanuel B.; Feltman, Nicolas; Leibs, Christopher A.; McCarthy, Colleen; Murthy, Karthik S.; Wang, Yijie
2012-09-10
Recently, a fully implicit electrostatic 1D charge- and energy-conserving particle-in-cell algorithm was proposed and implemented by Chen et al ([2],[3]). Central to the algorithm is an advanced particle pusher. Particles are moved using an energy conserving scheme and are forced to stop at cell faces to conserve charge. Moreover, a time estimator is used to control errors in momentum. Here we implement and extend this advanced particle pusher to include 2D and electromagnetic fields. Derivations of all modifications made are presented in full. Special consideration is taken to ensure easy coupling into the implicit moment based method proposed by Taitano et al [19]. Focus is then given to optimizing the presented particle pusher on emerging architectures. Two multicore implementations, and one GPU (Graphics Processing Unit) implementation are discussed and analyzed.
A New Method for Detecting Goaf Area of Coal Mine :2D Microtremor Profiling Technique
NASA Astrophysics Data System (ADS)
Xu, P.; Ling, S.; Guo, H.; Shi, W.; Li, S.; Tian, B.
2012-12-01
A goaf area is referred to as a cavity where coal has been removed or mined out. These cavities will change the original geostress equilibrium of stratigraphic system and cause local geostress focusing or concentration. Consequently, the surrounding rock of a goaf may be deformed, fractured, displaced and caved resulting from the combined effect of gravity and geostress. In the cases of little or no effective mining control, widespread cracks, fractures and even subsidence of the rock mass above the goaf will not only lead to groundwater depletion, farmland destruction and deterioration of ecological environment, but also present a serious threat to the mining safety, engineering construction, and even people's lives and property. So, it is important to locate the boundary of the goaf and to evaluate its stability in order to provide the basis for comprehensive control in the latter period of mining. This article attempts to explore a new geophysical method - 2D microtremor profiling technique for goaf detection and mapping. 2D microtremor profiling technique is based on the microtremor array theory (Aki, 1957; Ling, 1994; Okada, 2003) utilizing spatial autocorrelation analysis to obtain Rayleigh-wave dispersion curves for apparent S-wave velocity (Vx) calculation (Ling & Miwa, 2006;Xu et al.,2012). A laterally continuous S-wave velocity section can then be obtained through data interpolation. The final result will be used for interpreting lateral changes in lithology and geological structures. Let's take a case study in Henan Province of China as an example. The coal seams in the survey area were about 150 ~ 250m deep. A triple-circular array was adopted for acquiring microtremor data, with the observation radius in 20, 40 and 80m, respectively, and a sampling the interval of 50m. We observed the following characteristics of the goaf area from the microtremor Vx section: (1) obvious low pseudo velocity anomaly corresponding to limestone layer below the goaf; (2
NASA Astrophysics Data System (ADS)
Mikulka, J.; Gescheidtova, E.; Bartusek, K.
2012-01-01
The paper deals with modern methods of image processing, especially image segmentation, classification and evaluation of parameters. It focuses primarily on processing medical images of soft tissues obtained by magnetic resonance tomography (MR). It is easy to describe edges of the sought objects using segmented images. The edges found can be useful for further processing of monitored object such as calculating the perimeter, surface and volume evaluation or even three-dimensional shape reconstruction. The proposed solutions can be used for the classification of healthy/unhealthy tissues in MR or other imaging. Application examples of the proposed segmentation methods are shown. Research in the area of image segmentation focuses on methods based on solving partial differential equations. This is a modern method for image processing, often called the active contour method. It is of great advantage in the segmentation of real images degraded by noise with fuzzy edges and transitions between objects. In the paper, results of the segmentation of medical images by the active contour method are compared with results of the segmentation by other existing methods. Experimental applications which demonstrate the very good properties of the active contour method are given.
A comparative study for 2D and 3D computer-aided diagnosis methods for solitary pulmonary nodules.
Yeh, Chinson; Wang, Jen-Feng; Wu, Ming-Ting; Yen, Chen-Wen; Nagurka, Mark L; Lin, Chen-Liang
2008-06-01
Many computer-aided diagnosis (CAD) methods, including 2D and 3D approaches, have been proposed for solitary pulmonary nodules (SPNs). However, the detection and diagnosis of SPNs remain challenging in many clinical circumstances. One goal of this work is to investigate the relative diagnostic accuracy of 2D and 3D methods. An additional goal is to develop a two-stage approach that combines the simplicity of 2D and the accuracy of 3D methods. The experimental results show statistically significant differences between the diagnostic accuracy of 2D and 3D methods. The results also show that with a very minor drop in diagnostic performance the two-stage approach can significantly reduce the number of nodules needed to be processed by the 3D method, streamlining the computational demand. PMID:18313899
Structural NMR of Protein Oligomers using Hybrid Methods
Wang, Xu; Lee, Hsiau-Wei; Liu, Yizhou; Prestegard, James H.
2010-01-01
Solving structures of native oligomeric protein complexes using traditional high resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of NMR-applicable targets. This article reviews several of the techniques capable of providing less traditional and complementary structural information. In particular, the use of orientational constraints coming from residual dipolar couplings and residual chemical shift anisotropy offsets are shown to simplify the construction of models for oligomeric complexes, especially in cases of weak homo-dimers. Combining this orientational information with interaction site information supplied by computation, chemical shift perturbation, paramagnetic surface perturbation, cross-saturation and mass spectrometry allows high resolution models of the complexes to be constructed with relative ease. Non-NMR techniques, such as mass spectrometry, EPR and small angle X-ray scattering, are also expected to play increasingly important roles by offering alternative methods of probing the overall shape of the complex. Computational platforms capable of integrating information from multiple sources in the modeling process are also discussed in the article. And finally a new, detailed example on the determination of a chemokine tetramer structure will be used to illustrate how a non-traditional approach to oligomeric structure determination works in practice. PMID:21074622
Quasi-simultaneous interaction method for solving 2D boundary layer flows over plates and airfoils
NASA Astrophysics Data System (ADS)
Bijleveld, H. A.; Veldman, A. E. P.
2012-11-01
This paper studies unsteady 2D boundary layer flows over dented plates and a NACA 0012 airfoil. An inviscid flow is assumed to exist outside the boundary layer and is solved iteratively with the boundary layer flow together with the interaction method until a matching solution is achieved. Hereto a quasi-simultaneous interaction method is applied, in which the integral boundary layer equations are solved together with an interaction-law equation. The interaction-law equation is an approximation of the external flow and based on thin-airfoil theory. It is an algebraic relation between the velocity and displacement thickness. The interaction-law equation ensures that the eigenvalues of the system of equations do not have a sign change and that no singularities occur. Three numerical schemes are used to solve the boundary layer flow with the interaction method. These are: a standard scheme, a splitting method and a characteristics solver. All schemes use a finite difference discretization. The three schemes yield comparable results for the simulations carried out. The standard scheme is deviating most from the splitting and characteristics solvers. The results show that the eigenvalues remain positive, even in separation. As expected, the addition of the interaction-law equation prevents a sign change of the eigenvalues. The quasi-simultaneous interaction scheme is applicable to the three numerical schemes tested.
Simulations of SH wave scattering due to cracks by the 2-D finite difference method
NASA Astrophysics Data System (ADS)
Suzuki, Y.; Kawahara, J.; Okamoto, T.; Miyashita, K.
2006-05-01
We simulate SH wave scattering by 2-D parallel cracks using the finite difference method (FDM), instead of the popularly used boundary integral equation method (BIEM). Here special emphasis is put on simplicity; we apply a standard FDM (fourth-order velocity-stress scheme with a staggered grid) to media in cluding traction-freecracks, which are expressed by arrays of grid points with zero traction. Two types of accuracy tests based oncomparison with a reliable BIEM, suggest that the present method gives practically sufficient accuracy, except for the wavefields in the vicinity of cracks, which can be well handled if the second-order FDM is used instead. As an application of this method, we also simulate wave propagation in media with randomly distributed cracks of the same length. We experimentally determine the attenuation and velocity dispersion induced by scattering from the synthetic seismograms, using a waveform averaging technique. It is shown that the results are well explained by a theory based on the Foldy approximation for crack densities of up to about 01. The presence of a free surface does not affect the validity of the theory. A preliminary experiment also suggests that the validity will not change even for multi-scale cracks.
Methods to determine the Orientation and Velocity of 2-D structures based on multi- spacecraft data
NASA Astrophysics Data System (ADS)
Zhang, X.; Pu, Z.; Zhou, X.; Wang, J.; Zong, Q.; Shi, Q.
2006-12-01
Many techniques have been developed to study the axial orientation and/or velocity of 2-D structures (flux ropes), by analyzing in situ data from single or multiple spacecraft. To obtain the axial orientation, there are magnetic based MVA (BMVA), current based MVA (CMVA), Minimum Direction Derivative (MDD) and Multiple Triangulation Analysis (MTA) as a modified version of timing method. To further calculate the velocity, we have DeHoffmann-Teller analysis, Spatio-Temporal Difference (STD) and several version of timing method including MTA. After a brief introduction on the principle of these methods, we theoretically estimate their error ranges based on modeled structures to examine the validity of these techniques. Because of their different principles, their error bars are shown to be distinct, depending on the parameters (such as radius, model selected and even the satellite crossing path) of the certain structure. The error estimation thus provides us some clue on the selection of methods under different conditions. Some real events are further analyzed using these techniques as the example.
Identification of olive pollen allergens using a fluorescence-based 2D multiplex method.
Zienkiewicz, Krzysztof; Alché, Juan de Dios; Zienkiewicz, Agnieszka; Tormo, Alejandro; Castro, Antonio Jesús
2015-04-01
Olive (Olea europaea L.) pollen is a major health concern in the Mediterranean countries and some olive growing regions in America and Australia. The molecular variability of pollen allergens constitutes a handicap for commercial extract standardization, which is the base of current diagnosis and vaccination procedures. In this paper, we report a time-saving and plant material saving multiplex detection method for the rapid and simultaneous analysis of Ole e 1, Ole e 2, and Ole e 5 allergen polymorphism on a single blot. This method combines high-resolution 2DE techniques with high-sensitive fluorescence-based detection methods. Using this strategy, we were capable to identify a higher number of allergen forms compared with classical 1D approach. The use of fluorescent probes and the increased resolution of 2D blots avoided overlapping effects, and allow estimating the amount of individual allergen forms. In addition, the pattern and identity of the IgE-reactive proteins of either a population or individual patients allergic to olive pollen was also effortlessly determined in a single additional step. This flexible method might be extended to a higher number of olive allergens and cultivars, and is also applicable to other allergogenic plant species and sources. PMID:25640071
A 2D/1D coupling neutron transport method based on the matrix MOC and NEM methods
Zhang, H.; Zheng, Y.; Wu, H.; Cao, L.
2013-07-01
A new 2D/1D coupling method based on the matrix MOC method (MMOC) and nodal expansion method (NEM) is proposed for solving the three-dimensional heterogeneous neutron transport problem. The MMOC method, used for radial two-dimensional calculation, constructs a response matrix between source and flux with only one sweep and then solves the linear system by using the restarted GMRES algorithm instead of the traditional trajectory sweeping process during within-group iteration for angular flux update. Long characteristics are generated by using the customization of commercial software AutoCAD. A one-dimensional diffusion calculation is carried out in the axial direction by employing the NEM method. The 2D and ID solutions are coupled through the transverse leakage items. The 3D CMFD method is used to ensure the global neutron balance and adjust the different convergence properties of the radial and axial solvers. A computational code is developed based on these theories. Two benchmarks are calculated to verify the coupling method and the code. It is observed that the corresponding numerical results agree well with references, which indicates that the new method is capable of solving the 3D heterogeneous neutron transport problem directly. (authors)
SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism
2010-01-01
SMARTCyp is an in silico method that predicts the sites of cytochrome P450-mediated metabolism of druglike molecules. The method is foremost a reactivity model, and as such, it shows a preference for predicting sites that are metabolized by the cytochrome P450 3A4 isoform. SMARTCyp predicts the site of metabolism directly from the 2D structure of a molecule, without requiring calculation of electronic properties or generation of 3D structures. This is a major advantage, because it makes SMARTCyp very fast. Other advantages are that experimental data are not a prerequisite to create the model, and it can easily be integrated with other methods to create models for other cytochrome P450 isoforms. Benchmarking tests on a database of 394 3A4 substrates show that SMARTCyp successfully identifies at least one metabolic site in the top two ranked positions 76% of the time. SMARTCyp is available for download at http://www.farma.ku.dk/p450. PMID:24936230
NMR method for accurate quantification of polysorbate 80 copolymer composition.
Zhang, Qi; Wang, Aifa; Meng, Yang; Ning, Tingting; Yang, Huaxin; Ding, Lixia; Xiao, Xinyue; Li, Xiaodong
2015-10-01
(13)C NMR spectroscopic integration employing short relaxation delays and a 30° pulse width was evaluated as a quantitative tool for analyzing the components of polysorbate 80. (13)C NMR analysis revealed that commercial polysorbate 80 formulations are a complex oligomeric mixture of sorbitan polyethoxylate esters and other intermediates, such as isosorbide polyethoxylate esters and poly(ethylene glycol) (PEG) esters. This novel approach facilitates the quantification of the component ratios. In this study, the ratios of the three major oligomers in polysorbate 80 were measured and the PEG series was found to be the major component of commercial polysorbate 80. The degree of polymerization of -CH2CH2O- groups and the ratio of free to bonded -CH2CH2O- end groups, which correlate with the hydrophilic/hydrophobic nature of the polymer, were analyzed, and were suggested to be key factors for assessing the likelihood of adverse biological reactions to polysorbate 80. The (13)C NMR data suggest that the feed ratio of raw materials and reaction conditions in the production of polysorbate 80 are not well controlled. Our results demonstrate that (13)C NMR is a universal, powerful tool for polysorbate analysis. Such analysis is crucial for the synthesis of a high-quality product, and is difficult to obtain by other methods. PMID:26356097
NMR Shielding in Metals Using the Augmented Plane Wave Method
2015-01-01
We present calculations of solid state NMR magnetic shielding in metals, which includes both the orbital and the complete spin response of the system in a consistent way. The latter contains an induced spin-polarization of the core states and needs an all-electron self-consistent treatment. In particular, for transition metals, the spin hyperfine field originates not only from the polarization of the valence s-electrons, but the induced magnetic moment of the d-electrons polarizes the core s-states in opposite direction. The method is based on DFT and the augmented plane wave approach as implemented in the WIEN2k code. A comparison between calculated and measured NMR shifts indicates that first-principle calculations can obtain converged results and are more reliable than initially concluded based on previous publications. Nevertheless large k-meshes (up to 2 000 000 k-points in the full Brillouin-zone) and some Fermi-broadening are necessary. Our results show that, in general, both spin and orbital components of the NMR shielding must be evaluated in order to reproduce experimental shifts, because the orbital part cancels the shift of the usually highly ionic reference compound only for simple sp-elements but not for transition metals. This development paves the way for routine NMR calculations of metallic systems. PMID:26322148
ERIC Educational Resources Information Center
Mak, Kendrew K. W.
2004-01-01
NMR spectroscopy is presented. It is seen that the experiment regarding the synthesis and resolution of 1,1'-Bi-2-naphtol presents a good experiment for teaching organic synthesis and NMR spectroscopy and provides a strategy for obtaining enantiopure compounds from achiral starting materials.
A 2D Electromechanical Model of Human Atrial Tissue Using the Discrete Element Method
Brocklehurst, Paul; Adeniran, Ismail; Yang, Dongmin; Sheng, Yong; Zhang, Henggui; Ye, Jianqiao
2015-01-01
Cardiac tissue is a syncytium of coupled cells with pronounced intrinsic discrete nature. Previous models of cardiac electromechanics often ignore such discrete properties and treat cardiac tissue as a continuous medium, which has fundamental limitations. In the present study, we introduce a 2D electromechanical model for human atrial tissue based on the discrete element method (DEM). In the model, single-cell dynamics are governed by strongly coupling the electrophysiological model of Courtemanche et al. to the myofilament model of Rice et al. with two-way feedbacks. Each cell is treated as a viscoelastic body, which is physically represented by a clump of nine particles. Cell aggregations are arranged so that the anisotropic nature of cardiac tissue due to fibre orientations can be modelled. Each cell is electrically coupled to neighbouring cells, allowing excitation waves to propagate through the tissue. Cell-to-cell mechanical interactions are modelled using a linear contact bond model in DEM. By coupling cardiac electrophysiology with mechanics via the intracellular Ca2+ concentration, the DEM model successfully simulates the conduction of cardiac electrical waves and the tissue's corresponding mechanical contractions. The developed DEM model is numerically stable and provides a powerful method for studying the electromechanical coupling problem in the heart. PMID:26583141
NASA Astrophysics Data System (ADS)
Ali, Nisa'; Saad, Rosli; Muztaza, Nordiana M.; Ismail, Noer E. H.
2013-05-01
The purpose of this study was to locate the geological contact using 2D resistivity method for Light Rail Transit (LRT) track alignment. The resistivity method was conducted on eight survey lines with the length of line 1 was 600m. The length of line 2, 3, 4, 5, 6, and 7 were 200m each while line 8 is 115m. All the survey used minimum electrode spacing of 5m and using Pole-dipole array with minimum current is 2mA and maximum was 20mA. The result obtained from the pseudosection showed that the area generally divided into three main zones, fill materials/residual soil with a resistivity value of <500 Ωm, saturated zone with a resistivity value of 30-100 Ωm and bedrock with a resistivity value of >2000 Ωm. Three fractured zones were detected along line L1 and a lot of boulders were detected at L1, L3, L4, L5 and L6. The geological contact was between the residual soil and granite bedrock.
Chen, Mingqing; Bai, Junjie; Siochi, R Alfredo C
2013-02-01
To present a new method of estimating 3D positions of the ipsi-lateral hemi-diaphragm apex (IHDA) from 2D projection images of mega-voltage cone beam CT (MVCBCT). The detection framework reconstructs a 3D volume from all the 2D projection images. An initial estimated 3D IHDA position is determined in this volume based on an imaging processing pipeline, including Otsu thresholding, connected component labeling and template matching. This initial position is then projected onto each 2D projection image to create a region of interest (ROI). To accurately detect the IHDA position in 2D projection space, two methods, dynamic Hough transform (DHT) and a tracking approach based on a joint probability density function (PDF) are developed. Both methods utilize a double-parabola model to fit the 2D diaphragm boundary. The 3D IHDA motion in the superior-inferior (SI) direction is estimated from the initial static 3D position and the detected 2D positions in projection space. The two Hough-based detection methods are tested on 35 MVCBCT scans from 15 patients. The detection is compared to manually identified IHDA positions in 2D projection space by three clinicians. An average and standard deviation of 4.252 ± 3.354 and 2.485 ± 1.750 mm was achieved for DHT and tracking-based approaches respectively, compared with the inter-expert variance among three experts of 1.822 ± 1.106 mm. Based on the results of the scans, the PDF tracking-based approach appears more robust than the DHT. The combination of the automatic ROI localization and the tracking-based approach is a quicker and more accurate method of extracting 3D IHDA motion from 2D projection images. PMID:23321998
2D Distinct Element Method (DEM) models of the initiation, propagation and saturation of rock joints
NASA Astrophysics Data System (ADS)
Arslan, A.; Schöpfer, M. P.; Walsh, J. J.; Childs, C.
2009-12-01
In layered sequences, rock joints usually best develop within the more brittle layers and commonly display a regular spacing that scales with layer thickness. A variety of conceptual and mechanical models have been developed for these observations. A limitation of previous approaches, however, is that fracture initiation and associated interface slip are not explicitly simulated; instead, fractures were predefined and interfaces were welded. To surmount this problem, we have modelled the formation and growth of joints in layered sequences by using the two-dimensional Distinct Element Method (DEM) as implemented in the Particle Flow Code (PFC-2D). In PFC-2D, rock is represented by an assemblage of circular particles that are bonded at particle-particle contacts. Failure occurs if either the tensile or shear strength of a bond is exceeded. The models comprise a central brittle layer with high Young’s modulus, which is embedded in a low Young’s modulus matrix. The interfaces between the layers are defined by ‘smooth joint’ contacts, a modelling feature that eliminates interparticle bumpiness and associated interlocking friction. Consequently, this feature allows the user to assign macroscopic properties such as friction and cohesion along layer interfaces in a controlled manner. Layer parallel extension is applied by assigning a velocity to particles at the lateral boundaries of the model while maintaining a constant vertical confining pressure. Models were extended until joint saturation in the central layer was reached. We thereby explored the impact of confining pressure and interface properties (friction, cohesion) on joint spacing. A number of important conclusions can be drawn from our models: (i) The distributions of average horizontal normal stress within the layer and of shear stress at the interface are consistent with analytical solutions (stress-transfer theory). (ii) At low interfacial shear strength, new joints form preferentially midway between
The method of polarized traces for the 2D Helmholtz equation
NASA Astrophysics Data System (ADS)
Zepeda-Núñez, Leonardo; Demanet, Laurent
2016-03-01
We present a solver for the 2D high-frequency Helmholtz equation in heterogeneous acoustic media, with online parallel complexity that scales optimally as O (N/L), where N is the number of volume unknowns, and L is the number of processors, as long as L grows at most like a small fractional power of N. The solver decomposes the domain into layers, and uses transmission conditions in boundary integral form to explicitly define "polarized traces", i.e., up- and down-going waves sampled at interfaces. Local direct solvers are used in each layer to precompute traces of local Green's functions in an embarrassingly parallel way (the offline part), and incomplete Green's formulas are used to propagate interface data in a sweeping fashion, as a preconditioner inside a GMRES loop (the online part). Adaptive low-rank partitioning of the integral kernels is used to speed up their application to interface data. The method uses second-order finite differences. The complexity scalings are empirical but motivated by an analysis of ranks of off-diagonal blocks of oscillatory integrals. They continue to hold in the context of standard geophysical community models such as BP and Marmousi 2, where convergence occurs in 5 to 10 GMRES iterations. While the parallelism in this paper stems from decomposing the domain, we do not explore the alternative of parallelizing the systems solves with distributed linear algebra routines.
Identification of histidine tautomers in proteins by 2D 1H/13C(delta2) one-bond correlated NMR.
Sudmeier, James L; Bradshaw, Elizabeth M; Haddad, Kristin E Coffman; Day, Regina M; Thalhauser, Craig J; Bullock, Peter A; Bachovchin, William W
2003-07-16
If the 13Cdelta2 chemical shift of neutral ("high pH") histidine is >122 ppm, primarily Ndelta1-H tautomer (2) is indicated; if it is <122 ppm, primarily Nepsilon2-H tautomer (1) is indicated. His resonances from the catalytic triad of active serine proteases, for example, are readily distinguished from those of denatured enzyme. The 13Cdelta2 chemical shifts increased by 6.2 ppm for the catalytic histidines in both alpha-lytic protease and subtilisin BPN' in raising the pH from that of imidazolium cation to that of tautomer 2. This tautomer identification method is easy to implement, requiring only bioincorporation of [U-13C] (or the more readily available [U-13C,15N])-histidine. Standard 1H/13C correlation HMQC or HSQC NMR pulse programs then yield the 13Cdelta2 chemical shifts with the benefit of high 1H sensitivity. Because of large one-bond spin-couplings (1JCH approximately 200 Hz), the method should extend to proteins having large 1H and 13C line widths, including very high molecular weights. PMID:12848537
Wan, Yong; Otsuna, Hideo; Chien, Chi-Bin; Hansen, Charles
2013-01-01
2D image space methods are processing methods applied after the volumetric data are projected and rendered into the 2D image space, such as 2D filtering, tone mapping and compositing. In the application domain of volume visualization, most 2D image space methods can be carried out more efficiently than their 3D counterparts. Most importantly, 2D image space methods can be used to enhance volume visualization quality when applied together with volume rendering methods. In this paper, we present and discuss the applications of a series of 2D image space methods as enhancements to confocal microscopy visualizations, including 2D tone mapping, 2D compositing, and 2D color mapping. These methods are easily integrated with our existing confocal visualization tool, FluoRender, and the outcome is a full-featured visualization system that meets neurobiologists’ demands for qualitative analysis of confocal microscopy data. PMID:23584131
A Novel 2D-to-3D Video Conversion Method Using Time-Coherent Depth Maps
Yin, Shouyi; Dong, Hao; Jiang, Guangli; Liu, Leibo; Wei, Shaojun
2015-01-01
In this paper, we propose a novel 2D-to-3D video conversion method for 3D entertainment applications. 3D entertainment is getting more and more popular and can be found in many contexts, such as TV and home gaming equipment. 3D image sensors are a new method to produce stereoscopic video content conveniently and at a low cost, and can thus meet the urgent demand for 3D videos in the 3D entertaiment market. Generally, 2D image sensor and 2D-to-3D conversion chip can compose a 3D image sensor. Our study presents a novel 2D-to-3D video conversion algorithm which can be adopted in a 3D image sensor. In our algorithm, a depth map is generated by combining global depth gradient and local depth refinement for each frame of 2D video input. Global depth gradient is computed according to image type while local depth refinement is related to color information. As input 2D video content consists of a number of video shots, the proposed algorithm reuses the global depth gradient of frames within the same video shot to generate time-coherent depth maps. The experimental results prove that this novel method can adapt to different image types, reduce computational complexity and improve the temporal smoothness of generated 3D video. PMID:26131674
A Novel 2D-to-3D Video Conversion Method Using Time-Coherent Depth Maps.
Yin, Shouyi; Dong, Hao; Jiang, Guangli; Liu, Leibo; Wei, Shaojun
2015-01-01
In this paper, we propose a novel 2D-to-3D video conversion method for 3D entertainment applications. 3D entertainment is getting more and more popular and can be found in many contexts, such as TV and home gaming equipment. 3D image sensors are a new method to produce stereoscopic video content conveniently and at a low cost, and can thus meet the urgent demand for 3D videos in the 3D entertaiment market. Generally, 2D image sensor and 2D-to-3D conversion chip can compose a 3D image sensor. Our study presents a novel 2D-to-3D video conversion algorithm which can be adopted in a 3D image sensor. In our algorithm, a depth map is generated by combining global depth gradient and local depth refinement for each frame of 2D video input. Global depth gradient is computed according to image type while local depth refinement is related to color information. As input 2D video content consists of a number of video shots, the proposed algorithm reuses the global depth gradient of frames within the same video shot to generate time-coherent depth maps. The experimental results prove that this novel method can adapt to different image types, reduce computational complexity and improve the temporal smoothness of generated 3D video. PMID:26131674
Gao, Ling; Cui, Weina; Zhang, Pengyuan; Jang, Albert; Zhu, Wuqiang; Zhang, Jianyi
2016-01-01
Utilizing a fast 31P magnetic resonance spectroscopy (MRS) 2-dimensional chemical shift imaging (2D-CSI) method, this study examined the heterogeneity of creatine kinase (CK) forward flux rate of hearts with postinfarction left ventricular (LV) remodeling. Immunosuppressed Yorkshire pigs were assigned to 4 groups: 1) A sham-operated normal group (SHAM, n = 6); 2) A 60 minutes distal left anterior descending coronary artery ligation and reperfusion (MI, n = 6); 3) Open patch group; ligation injury plus open fibrin patch over the site of injury (Patch, n = 6); and 4) Cell group, hiPSCs-cardiomyocytes, -endothelial cells, and -smooth muscle cells (2 million, each) were injected into the injured myocardium pass through a fibrin patch (Cell+Patch, n = 5). At 4 weeks, the creatine phosphate (PCr)/ATP ratio, CK forward flux rate (Flux PCr→ATP), and k constant of CK forward flux rate (kPCr→ATP) were severely decreased at border zone myocardium (BZ) adjacent to MI. Cell treatment results in significantly increase of PCr/ATP ratio and improve the value of kPCr→ATP and Flux PCr→ATP in BZ myocardium. Moreover, the BZ myocardial CK total activity and protein expression of CK mitochondria isozyme and CK myocardial isozyme were significantly reduced, but recovered in response to cell treatment. Thus, cell therapy results in improvement of BZ bioenergetic abnormality in hearts with postinfarction LV remodeling, which is accompanied by significantly improvements in BZ CK activity and CK isozyme expression. The fast 2D 31P MR CSI mapping can reliably measure the heterogeneity of bioenergetics in hearts with post infarction LV remodeling. PMID:27606901
Calculating tissue shear modulus and pressure by 2D Log-Elastographic methods
McLaughlin, Joyce R; Zhang, Ning; Manduca, Armando
2010-01-01
Shear modulus imaging, often called elastography, enables detection and characterization of tissue abnormalities. In this paper the data is two displacement components obtained from successive MR or ultrasound data sets acquired while the tissue is excited mechanically. A 2D plane strain elastic model is assumed to govern the 2D displacement, u. The shear modulus, μ, is unknown and whether or not the first Lamé parameter, λ, is known the pressure p = λ∇ · u which is present in the plane strain model cannot be measured and is unreliably computed from measured data and can be shown to be an order one quantity in the units kPa. So here we present a 2D Log-Elastographic inverse algorithm that: (1) simultaneously reconstructs the shear modulus, μ, and p, which together satisfy a first order partial differential equation system, with the goal of imaging μ; (2) controls potential exponential growth in the numerical error; and (3) reliably reconstructs the quantity p in the inverse algorithm as compared to the same quantity computed with a forward algorithm. This work generalizes the Log-Elastographic algorithm in [20] which uses one displacement component, is derived assuming the component satisfies the wave equation, and is tested on synthetic data computed with the wave equation model. The 2D Log-Elastographic algorithm is tested on 2D synthetic data and 2D in-vivo data from Mayo Clinic. We also exhibit examples to show that the 2D Log-Elastographic algorithm improves the quality of the recovered images as compared to the Log-Elastographic and Direct Inversion algorithms. PMID:21822349
2D and 3D visualization methods of endoscopic panoramic bladder images
NASA Astrophysics Data System (ADS)
Behrens, Alexander; Heisterklaus, Iris; Müller, Yannick; Stehle, Thomas; Gross, Sebastian; Aach, Til
2011-03-01
While several mosaicking algorithms have been developed to compose endoscopic images of the internal urinary bladder wall into panoramic images, the quantitative evaluation of these output images in terms of geometrical distortions have often not been discussed. However, the visualization of the distortion level is highly desired for an objective image-based medical diagnosis. Thus, we present in this paper a method to create quality maps from the characteristics of transformation parameters, which were applied to the endoscopic images during the registration process of the mosaicking algorithm. For a global first view impression, the quality maps are laid over the panoramic image and highlight image regions in pseudo-colors according to their local distortions. This illustration supports then surgeons to identify geometrically distorted structures easily in the panoramic image, which allow more objective medical interpretations of tumor tissue in shape and size. Aside from introducing quality maps in 2-D, we also discuss a visualization method to map panoramic images onto a 3-D spherical bladder model. Reference points are manually selected by the surgeon in the panoramic image and the 3-D model. Then the panoramic image is mapped by the Hammer-Aitoff equal-area projection onto the 3-D surface using texture mapping. Finally the textured bladder model can be freely moved in a virtual environment for inspection. Using a two-hemisphere bladder representation, references between panoramic image regions and their corresponding space coordinates within the bladder model are reconstructed. This additional spatial 3-D information thus assists the surgeon in navigation, documentation, as well as surgical planning.
Development of an ab-initio calculation method for 2D layered materials-based optoelectronic devices
NASA Astrophysics Data System (ADS)
Kim, Han Seul; Kim, Yong-Hoon
We report on the development of a novel first-principles method for the calculation of non-equilibrium nanoscale device operation process. Based on region-dependent Δ self-consistent field method beyond the standard density functional theory (DFT), we will introduce a novel method to describe non-equilibrium situations such as external bias and simultaneous optical excitations. In particular, we will discuss the limitation of conventional method and advantage of our scheme in describing 2D layered materials-based devices operations. Then, we investigate atomistic mechanism of optoelectronic effects from 2D layered materials-based devices and suggest the optimal material and architecture for such devices.
Simple fully reflective method of scatter reduction in 2D-IR spectroscopy.
Spector, Ivan C; Olson, Courtney M; Huber, Christopher J; Massari, Aaron M
2015-04-15
A fully reflective two-dimensional IR (2D-IR) setup is described that enables efficient cancellation of scattered light from multiple pulses in the phase-matched direction. The local oscillator pulse and the pulse that stimulates the vibrational echo signal are synchronously modulated (or fibrillated) in time maintaining their phase relationships with the echo wavepacket. The modification is cost-effective and can be easily implemented on existing 2D-IR instruments, and it avoids the addition of dispersive elements into the beam paths. The fibrillation results in a decrease of waiting-time resolution of only tens of femtoseconds and has no impact on the spectral lineshape, making it a general improvement for 2D-IR spectrometers even for weakly or non-scattering samples. PMID:25872090
Calculating tissue shear modulus and pressure by 2D Log-Elastographic methods.
McLaughlin, Joyce R; Zhang, Ning; Manduca, Armando
2010-01-01
Shear modulus imaging, often called elastography, enables detection and characterization of tissue abnormalities. In this paper the data is two displacement components obtained from successive MR or ultrasound data sets acquired while the tissue is excited mechanically. A 2D plane strain elastic model is assumed to govern the 2D displacement, u. The shear modulus, μ, is unknown and whether or not the first Lamé parameter, λ, is known the pressure p = λ∇ · u which is present in the plane strain model cannot be measured and is unreliably computed from measured data and can be shown to be an order one quantity in the units kPa. So here we present a 2D Log-Elastographic inverse algorithm that: (1) simultaneously reconstructs the shear modulus, μ, and p, which together satisfy a first order partial differential equation system, with the goal of imaging μ; (2) controls potential exponential growth in the numerical error; and (3) reliably reconstructs the quantity p in the inverse algorithm as compared to the same quantity computed with a forward algorithm. This work generalizes the Log-Elastographic algorithm in [20] which uses one displacement component, is derived assuming the component satisfies the wave equation, and is tested on synthetic data computed with the wave equation model. The 2D Log-Elastographic algorithm is tested on 2D synthetic data and 2Din-vivo data from Mayo Clinic. We also exhibit examples to show that the 2D Log-Elastographic algorithm improves the quality of the recovered images as compared to the Log-Elastographic and Direct Inversion algorithms. PMID:21822349
Effects of Training Method and Gender on Learning 2D/3D Geometry
ERIC Educational Resources Information Center
Khairulanuar, Samsudin; Nazre, Abd Rashid; Jamilah, H.; Sairabanu, Omar Khan; Norasikin, Fabil
2010-01-01
This article reports the findings of an experimental study involving 36 primary school students (16 girls, 20 boys, Mean age = 9.5 years, age range: 8-10 years) in geometrical understanding of 2D and 3D objects. Students were assigned into two experimental groups and one control group based on a stratified random sampling procedure. The first…
SIMULATIONS OF 2D AND 3D THERMOCAPILLARY FLOWS BY A LEAST-SQUARES FINITE ELEMENT METHOD. (R825200)
Numerical results for time-dependent 2D and 3D thermocapillary flows are presented in this work. The numerical algorithm is based on the Crank-Nicolson scheme for time integration, Newton's method for linearization, and a least-squares finite element method, together with a matri...
Mach number validation of a new zonal CFD method (ZAP2D) for airfoil simulations
NASA Technical Reports Server (NTRS)
Strash, Daniel J.; Summa, Michael; Yoo, Sungyul
1991-01-01
A closed-loop overlapped velocity coupling procedure has been utilized to combine a two-dimensional potential-flow panel code and a Navier-Stokes code. The fully coupled two-zone code (ZAP2D) has been used to compute the flow past a NACA 0012 airfoil at Mach numbers ranging from 0.3 to 0.84 near the two-dimensional airfoil C(lmax) point for a Reynolds number of 3 million. For these cases, the grid domain size can be reduced to 3 chord lengths with less than 3-percent loss in accuracy for freestream Mach numbers through 0.8. Earlier validation work with ZAP2D has demonstrated a reduction in the required Navier-Stokes computation time by a factor of 4 for subsonic Mach numbers. For this more challenging condition of high lift and Mach number, the saving in CPU time is reduced to a factor of 2.
Application of a generalized minimal residual method to 2D unsteady flows
NASA Technical Reports Server (NTRS)
Hixon, Ray; Sankar, L. N.
1992-01-01
A generalized minimum residual scheme (GMRES), previously developed for solving nonlinear and linear systems of equations, has been applied to the numerical solution of 2D unsteady compressible flows. It is found that the use of GMRES significantly increases the time step that may be used, compared to noniterative implicit schemes. The feasibility of reducing the memory requirements of the GMRES scheme using a multigrid strategy has also been explored. Several sample steady and unsteady viscous flow applications are presented.
Multi-method determination of continuous 2D velocity profiles from the surface to 1 km
NASA Astrophysics Data System (ADS)
Peterie, S.; Miller, R. D.; Ivanov, J.; Schwenk, J.; Bailey, B. L.; Schwarzer, J.; Markiewicz, R.
2012-12-01
Compressional and shear reflection data provide critical measurements of velocity and attenuation that are necessary for numerical simulations of site response from earthquake energy and seismic investigations to lithologic and pore characterizations. Imperative for accurate site response models is a seismic velocity model extending from the surface to the depth of interest that is representative of the true subsurface. In general, no seismic method can be used to characterize the shallowest (< 30 m) and deepest (30 m to 1 km) portions of the subsurface in a single pass with a consistent set of equipment and acquisition parameters. With four unique seismic surveys targeting different portions of the subsurface and different components of the seismic wavefield, we were able to build a comprehensive dataset that facilitated continuous 2D velocity profiles. The upper kilometer underlying our study site consists of Lake Bonneville lucustrine sediments and post-Bonneville alluvium and colluvium from the nearby Wasatch Front in north central Utah (Eardley, 1938; Hintze, 2005). Four unique seismic surveys were acquired along each of two 1.5 km lines located approximately 3 km apart. Data for tomography and multi-channel analysis of surface waves (MASW) were acquired with a bungee accelerated weight drop and 4.5 Hz compressional geophones. P-wave and S-wave reflection data were acquired with an IVI minivib 1 and 28 Hz compressional and 14 Hz SH geophones, respectively. P-wave and S-wave velocities from the surface to 30 m were determined using tomography and MASW, respectively. Stacking velocities of reflections on common midpoint gathers from the vibroseis data were used to determine Vp and Vs from approximately 30 m to nearly 1 km below ground surface. Each Vp and Vs dataset were merged to generate continuous interval and average velocity profiles. The sutured velocity cross-sections were produced for both P- and S-waves in a fashion not previously described in the
Komatsu, Takanori; Ohishi, Risa; Shino, Amiu; Kikuchi, Jun
2016-05-10
Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant. PMID:27060701
NASA Astrophysics Data System (ADS)
Pahomov, Valery I.; Rogova, Olga V.; Volynkin, Vladimir S.; Veselkov, Kyrill A.; Hernandez Santiago, Adrian A.; Semanin, Alexander V.; Djimant, Leonid N.; Veselkov, Alexei N.
2004-07-01
Complexation of anthracycline antibiotic daunomycin (DAU) with self-complementary deoxyhexanucleotide d(GCATGC) in aqueous solution has been investigated by one-dimensional and two-dimensional homonuclear 'H NMR spectroscopy (TOCSY and NOESY) and heteronuclear 'H-31P NMR spectroscopy (HMBC). Quantitative determination of parameters of oligonucleotide self-association and its complexation with DAU was based on the analysis of the dependences of proton chemical shifts on concentration and temperature. Experimental results were analysed in terms of the equilibrium reaction constants, limiting proton chemical shifts and thermodynamical parameters (enthalpies AN, entropies AS) of the formation of hexamer duplex and different drug-DNA complexes. The most favourable structures of the single-stranded form of d(GCATGC) and the intercalated DAU-hexamer complex have been determined using X-PLOR software taking into consideration both intra- and intermolecular NOE contacts.
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
Sen, Sabyasachi; Kaseman, Derrick C; Colas, Bruno; Jacob, Dorrit E; Clark, Simon M
2016-07-27
Systematic correlation in alkaline-earth carbonate compounds between the deviation of the CO3 units from the perfect D3h symmetry and their (13)C nuclear magnetic resonance (NMR) chemical shift anisotropy (CSA) parameters is established. The (13)C NMR CSA parameters of amorphous calcium carbonate (ACC) are measured using two-dimensional (13)C phase adjusted spinning sidebands (PASS) NMR spectroscopy and are analyzed on the basis of this correlation. The results indicate a distortion of the CO3 units in ACC in the form of an in-plane displacement of the C atom away from the centroid of the O3 triangle, resulting from hydrogen bonding with the surrounding H2O molecules, without significant out-of-plane displacement. Similar distortion for all C atoms in the structure of ACC suggests a uniform spatial disposition of H2O molecules around the CO3 units forming a hydrogen-bonded amorphous network. This amorphous network is stabilized against crystallization by steric frustration, while additives such as Mg presumably provide further stabilization by increasing the energy of dehydration. PMID:27276013
Xia, Yong-Gang; Liang, Jun; Yang, Bing-You; Wang, Qiu-Hong; Kuang, Hai-Xue
2015-05-01
Plant arabinan has important biological activity. In this study, a water-soluble arabinan (Mw∼6.15kDa) isolated from the stems of Ephedra sinica was found to consist of (1→5)-Araƒ, (1→3,5)-Araƒ, T-Araƒ, (1→3)-Araƒ and (1→2,5)-Araƒ residues at proportions of 10:2:3:2:1. A tentative structure was proposed by methylation analysis, nuclear magnetic resonance (NMR) spectroscopy ((1)H NMR, (13)C NMR, DEPT-135, (1)H-(1)H COSY, HSQC, HMBC and ROESY) and literature. The structure proposed includes a branched (1→5)-α-Araf backbone where branching occurs at the O-2 and O-3 positions of the residues with 7.7% and 15.4% of the 1,5-linked α-Araf substituted at the O-2 and O-3 positions. The presence of a branched structure was further observed by atomic force microscopy. This polymer was characterized as having a much longer linear (1→5)-α-Araf backbone as a repeating unit. In particular, the presence of α-Araf→3)-α-Araf-(1→3)-α-Araf-(1→ attached at the O-2 is a new finding. This study may facilitate a deeper understanding of structure-activity relationships of biological polysaccharides from the stems of E. sinica. PMID:25659720
NASA Astrophysics Data System (ADS)
Stevens, E. W.; Sumner, D. Y.
2009-12-01
Microbialites in the 2521 ± 3 Ma Gamohaan Formation, South Africa, have several different end-member morphologies which show distinct growth structures and spatial relationships. We characterized several growth structures and spatial relationships in two samples (DK20 and 2_06) using a combination of 2D and 3D analytical techniques. There are two main goals in studying complicated microbialites with a combination of 2D and 3D methods. First, one can better understand microbialite growth by identifying important structures and structural relationships. Once structures are identified, the order in which the structures formed and how they are related can be inferred from observations of crosscutting relationships. Second, it is important to use both 2D and 3D methods to correlate 3D observations with those in 2D that are more common in the field. Combining analysis provides significantly more insight into the 3D morphology of microbial structures. In our studies, 2D analysis consisted of describing polished slabs and serial sections created by grinding down the rock 100 microns at a time. 3D analysis was performed on serial sections visualized in 3D using Vrui and 3DVisualizer software developed at KeckCAVES, UCD (http://keckcaves.org). Data were visualized on a laptop and in an immersive cave system. Both samples contain microbial laminae and more vertically orients microbial "walls" called supports. The relationships between these features created voids now filled with herringbone and blocky calcite crystals. DK20, a classic plumose structure, contains two types of support structures. Both are 1st order structures (1st order structures with organic inclusions and 1st without organic inclusions) interpreted as planar features based on 2D analysis. In the 2D analysis the 1st order structures show v branching relationships as well as single cuspate relationships (two 1st order structures with inclusions merging upward), and single tented relationships (three supports
Application of the 2-D discrete-ordinates method to multiple scattering of laser radiation
Zardecki, A.; Gerstl, S.A.W.; Embury, J.F.
1983-05-01
The discrete-ordinates finite-element radiation transport code twotran is applied to describe the multiple scattering of a laser beam from a reflecting target. For a model scenario involving a 99% relative humidity rural aerosol we compute the average intensity of the scattered radiation and correction factors to the Beer-Lambert law arising from multiple scattering. As our results indicate, 2-D x-y and r-z geometry modeling can reliably describe a realistic 3-D scenario. Specific results are presented for the two visual ranges of 1.52 and 0.76 km which show that, for sufficiently high aerosol concentrations (e.g., equivalent to V = 0.76 km), the target signature in a distant detector becomes dominated by multiply scattered radiation from interactions of the laser light with the aerosol environment. The merits of the scaling group and the delta-M approximation for the transfer equation are also explored.
NASA Astrophysics Data System (ADS)
Senthilkumar, R.; Gnanamurthy, R. K.
2015-07-01
In this paper, two-dimensional principal component analysis (2D PCA) is compared with other algorithms like 1D PCA, Fisher discriminant analysis (FDA), independent component analysis (ICA) and Kernel PCA (KPCA) which are used for image representation and face recognition. As opposed to PCA, 2D PCA is based on 2D image matrices rather than 1D vectors, so the image matrix does not need to be transformed into a vector prior to feature extraction. Instead, an image covariance matrix is constructed directly using the original image matrices and its Eigen vectors are derived for image feature extraction. To test 2D PCA and evaluate its performance, a series of experiments are performed on three face image databases: ORL, Senthil, and Yale face databases. The recognition rate across all trials higher using 2D PCA than PCA, FDA, ICA and KPCA. The experimental results also indicated that the extraction of image features is computationally more efficient using 2D PCA than PCA.
Veijola, Timo; Råback, Peter
2007-01-01
We present a straightforward method to solve gas damping problems for perforated structures in two dimensions (2D) utilising a Perforation Profile Reynolds (PPR) solver. The PPR equation is an extended Reynolds equation that includes additional terms modelling the leakage flow through the perforations, and variable diffusivity and compressibility profiles. The solution method consists of two phases: 1) determination of the specific admittance profile and relative diffusivity (and relative compressibility) profiles due to the perforation, and 2) solution of the PPR equation with a FEM solver in 2D. Rarefied gas corrections in the slip-flow region are also included. Analytic profiles for circular and square holes with slip conditions are presented in the paper. To verify the method, square perforated dampers with 16–64 holes were simulated with a three-dimensional (3D) Navier-Stokes solver, a homogenised extended Reynolds solver, and a 2D PPR solver. Cases for both translational (in normal to the surfaces) and torsional motion were simulated. The presented method extends the region of accurate simulation of perforated structures to cases where the homogenisation method is inaccurate and the full 3D Navier-Stokes simulation is too time-consuming.
Keum, Sam-Rok; Lim, Hyun-Woo
2016-02-01
We report the synthesis of a series of novel stilbene-based (St) Fischer base analogs of leuco-triarylmethane (LTAM) dyes by treating Fischer base with (E)-4-styrylbenzaldehyde derivatives. All St-LTAM molecules examined herein are characterized by 1D and 2D NMR. They were found to exhibit ZE configuration and isomerize to their diastereomers EE and ZZ in 2-3 h. They exhibit type I behavior of diastereomeric isomerization. PMID:26448377
NASA Astrophysics Data System (ADS)
Aspers, Ruud L. E. G.; Ampt, Kirsten A. M.; Dvortsak, Peter; Jaeger, Martin; Wijmenga, Sybren S.
2013-06-01
The use of fluorine in molecules obtained from chemical synthesis has become increasingly important within the pharmaceutical and agricultural industry. NMR characterization of these compounds is of great value with respect to their structure elucidation, their screening in metabolomics investigations and binding studies. The favorable NMR properties of the fluorine nucleus make NMR with fluorine detection of great value in this respect. A suite of NMR 2D F-F- and F-C-correlation experiments with fluorine detection was applied to the assignment of resonances, nJCF- and nJFF-couplings as well as the determination of their size and sign. The utilization of this experiment suite was exemplarily demonstrated for a highly fluorinated vinyl alkyl ether. Especially F-C HSQC and J-scaled F-C HMBC experiments allowed determining the size of the J-couplings of this compound. The relative sign of its homo- and heteronuclear couplings was achieved by different combinations of 2D NMR experiments, including non-selective and F2-selective F-C XLOC, F2-selective F-C HMQC, and F-F COSY. The F2-one/two-site selective F-C XLOC versions were found highly useful, as they led to simplifications of the common E.COSY patterns and resulted in a higher confidence level of the assignment by using selective excitation. The combination of F2-one/two-site selective F-C XLOC experiments with a F2-one-site selective F-C HMQC experiment provided the signs of all nJCF- and nJFF-couplings in the vinyl moiety of the test compound. Other combinations of experiments were found useful as well for special purposes when focusing for example on homonuclear couplings a combination of F-F COSY-10 with a F2-one-site selective F-C HMQC could be used. The E.COSY patterns in the spectra demonstrated were analyzed by use of the spin-selective displacement vectors, and in case of the XLOC also by use of the DQ- and ZQ-displacement vectors. The variety of experiments presented shall contribute to facilitate the
Laskowski, Tomasz; Czub, Jacek; Sowiński, Paweł; Mazerski, Jan
2016-03-01
Imidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311 intercalation complex has been studied by means of two-dimensional NMR spectroscopy, yielding a full assignment of the resonance lines observed in (1)H NMR spectra. The observation of the intermolecular NOE contacts between C-1311 and DNA allowed locating the ligand between the guanine and adenine moieties. Formation of a symmetric complex was pointed out on the basis of the lack of a second set of the (1)H resonances. The resulting stereostructure of the complex was then improved by means of molecular dynamics, using the CHARMM force field and GROMACS software. To this end, distance restraints derived from the NOESY cross-peak volumes were applied to the atomistic model of the d(CGATCG)2:C-1311 complex. Obtained results are in full agreement with biochemical data on the mechanism of action of C-1311, in particular with the previously postulated post-intercalation enzymatic activation of the studied drug. PMID:26211888
Generation and Radiation of Acoustic Waves from a 2-D Shear Layer using the CE/SE Method
NASA Technical Reports Server (NTRS)
Loh, Ching Y.; Wang, Xiao Y.; Chang, Sin-Chung; Jorgenson, Philip C. E.
2000-01-01
In the present work, the generation and radiation of acoustic waves from a 2-D shear layer problem is considered. An acoustic source inside of a 2-D jet excites an instability wave in the shear layer, resulting in sound Mach radiation. The numerical solution is obtained by solving the Euler equations using the space time conservation element and solution element (CE/SE) method. Linearization is achieved through choosing a small acoustic source amplitude. The Euler equations are nondimensionalized as instructed in the problem statement. All other conditions are the same except that the Crocco's relation has a slightly different form. In the following, after a brief sketch of the CE/SE method, the numerical results for this problem are presented.
Andersen, N.H.; Eaton, H.L.; Nguyen, K.T.; Hartzell, C.; Nelson, R.J.; Priest, J.H.
1988-04-19
Phase-sensitive 2D /sup 1/H//sup 1/H COSY spectra can be used to identify the structures of individual pure specimens of the aminoglycoside antibiotic amikacin and its N-hemisuccinyl derivatives. However, even at 500 MHz the 2D chemical shift dispersion does not allow for unambiguous assignment of all cross-peaks. By use of 2D relayed coherence transfer experiments (RELAY) optimized to detect two-step /sup 1/H//sup 1/H scalar interactions in which one of the J-values is small, sufficient additional correlations can be obtained from the frequency-isolated resonances to allow facile tracing of all scalar connectivities. Complete assignments of the /sup 1/H NMR spectra of amikacin, its 6'-N-hemisuccinamide, and a novel bis(acylate) (..gamma..-N-(p-vinylbenzoyl)amikacin 6'-N-hemisuccinamide) were obtained for aqueous media. The NMR spectrum of amikacin free base was also assigned in dimethyl sulfoxide solution. The RELAY experiment can be extended to the analysis of reaction mixtures, which allows for the identification and resonance assignment of regioisomeric amikacin haptens in the mixture state. All of the N-monohemisuccinyl isomers of amikacin have been identified in reaction mixtures through the RELAY experiment. The relative reactivities of the amino functions of amikacin toward acylating agents were found to be 6'-N > 3-N greater than or equal to 3''-N greater than or equal to ..gamma..-N. However, this reactivity order is altered after the initial acylation event.
NMR Wool Tube: a novel method for NMR solution analysis of derivatized glass surfaces.
Cholewa, Olivia Maria
2004-08-13
Glass wool was placed within an NMR tube as a solid support for the covalent attachment of a molecule to allow for a simple one-dimensional 1H FT NMR solution analysis. This novel procedure avoids the use of expensive sample tubes or platforms, as required for magic angle or fast spinning, exotic pulse sequences, isotopic labeling or the use of a large number of scans to provide the ability to analyze the structure, mobility, ligand binding, and solvent interactions of the surface bound molecule. PMID:15387199
NASA Astrophysics Data System (ADS)
Antzutkin, Oleg N.; Lee, Young K.; Levitt, Malcolm H.
1998-11-01
The principal values of the chemical shift tensors of all13C and15N sites in two antibiotics, ampicillin and penicillin-V, were determined by 2-dimensionalphaseadjustedspinningsideband (2D-PASS) and conventional CP/MAS experiments. The13C and15N chemical shift anisotropies (CSA), and their confidence limits, were evaluated using a Mathematica program. The CSA values suggest a revised assignment of the 2-methyl13C sites in the case of ampicillin. We speculate on a relationship between the chemical shift principal values of many of the13C and15N sites and the β-lactam ring conformation.
NASA Astrophysics Data System (ADS)
Tanaka, Satoyuki; Suzuki, Hirotaka; Sadamoto, Shota; Sannomaru, Shogo; Yu, Tiantang; Bui, Tinh Quoc
2016-08-01
Two-dimensional (2D) in-plane mixed-mode fracture mechanics problems are analyzed employing an efficient meshfree Galerkin method based on stabilized conforming nodal integration (SCNI). In this setting, the reproducing kernel function as meshfree interpolant is taken, while employing the SCNI for numerical integration of stiffness matrix in the Galerkin formulation. The strain components are smoothed and stabilized employing Gauss divergence theorem. The path-independent integral ( J-integral) is solved based on the nodal integration by summing the smoothed physical quantities and the segments of the contour integrals. In addition, mixed-mode stress intensity factors (SIFs) are extracted from the J-integral by decomposing the displacement and stress fields into symmetric and antisymmetric parts. The advantages and features of the present formulation and discretization in evaluation of the J-integral of in-plane 2D fracture problems are demonstrated through several representative numerical examples. The mixed-mode SIFs are evaluated and compared with reference solutions. The obtained results reveal high accuracy and good performance of the proposed meshfree method in the analysis of 2D fracture problems.
An experimental method for eliminating effect of rigid out-of-plane motion on 2D-DIC
NASA Astrophysics Data System (ADS)
Zhiqiang, Wang; Fengzhou, Fang; Bing, Liu; Zhiyong, Wang
2015-10-01
The out-of-plane motion is one of the most important factors that affect the precision of two-dimensional digital image correlation (2D-DIC). In this paper, a novel solution is presented to improve conventional 2D-DIC by eliminating the effect of out-of-plane motion, including translation and rotation. Firstly, an experimental technique using two projected laser strips is proposed to measure the out-of-plane motion of a planar specimen. A theoretical model is then established to predict the pseudostrains caused by out-of-plane motion based on the pin-hole imaging model. Using the measured out-of-plane displacement, the captured deformed images used in 2D-DIC are amended to eliminate the effect of out-of-plane motion by the theoretical model. Finally, two experiments were conducted to validate the effectiveness of the proposed method. Results indicate that application of the proposed method can effectively eliminate the errors caused by out-of-plane motion.
Study of colloidal quantum dot surfaces using an innovative thin-film positron 2D-ACAR method
NASA Astrophysics Data System (ADS)
Barbiellini, B.; Bansil, A.; Eijt, S. W. H.; Schut, H.; Mijnarends, P. E.; Denison, A. B.
2006-03-01
Despite a wealth of information, many fundamental questions regarding the nature of the surface of nanosized inorganic particles and its relationship with the electronic structure remain unsolved. We have investigated the electron momentum density (EMD) of colloidal CdSe quantum-dots via depth-resolved positron 2D angular correlation of annihilation (2D-ACAR) spectroscopy at the Delft intense variable-energy positron beam. This method, in combination with first-principles calculations of the EMD, shows that implanted positrons are trapped at the surface of CdSe nanocrystals. They annihilate mostly with the Se electrons and monitor changes in composition and structure of the surface while hardly sensing the ligand molecules. We thus unambiguously confirm [1] the strong surface relaxation predicted by first-principles calculations [2]. Work supported by the USDOE.[1] S.W.H. Eijt et al., Nature Materials (in press).[2] A. Puzder, et al., Phys. Rev. Lett. 92, 217401 (2004).
Mao, Jingdong; Kong, Xueqian; Schmidt-Rohr, Klaus; Pignatello, Joseph J; Perdue, E Michael
2012-06-01
Advanced (13)C solid-state techniques were employed to investigate the major structural characteristics of two surface-seawater dissolved organic matter (DOM) samples isolated using the novel coupled reverse osmosis/electrodialysis method. The NMR techniques included quantitative (13)C direct polarization/magic angle spinning (DP/MAS) and DP/MAS with recoupled dipolar dephasing, (13)C cross-polarization/total sideband suppression (CP/TOSS), (13)C chemical shift anisotropy filter, CH, CH(2), and CH(n) selection, two-dimensional (1)H-(13)C heteronuclear correlation NMR (2D HETCOR), 2D HETCOR combined with dipolar dephasing, and (15)N cross-polarization/magic angle spinning (CP/MAS). The two samples (Coastal and Marine DOM) were collected at the mouth of the Ogeechee River and in the Gulf Stream, respectively. The NMR results indicated that they were structurally distinct. Coastal DOM contained significantly more aromatic and carbonyl carbons whereas Marine DOM was markedly enriched in alkoxy carbon (e.g., carbohydrate-like moieties). Both samples contained significant amide N, but Coastal DOM had nitrogen bonded to aromatic carbons. Our dipolar-dephased spectra indicated that a large fraction of alkoxy carbons were not protonated. For Coastal DOM, our NMR results were consistent with the presence of the major structural units of (1) carbohydrate-like moieties, (2) lignin residues, (3) peptides or amino sugars, and (4) COO-bonded alkyls. For Marine DOM, they were (1) carbohydrate-like moieties, (2) peptides or amino sugars, and (3) COO-bonded alkyls. In addition, both samples contained significant amounts of nonpolar alkyl groups. The potential sources of the major structural units of DOM were discussed in detail. Nonprotonated O-alkyl carbon content was proposed as a possible index of humification. PMID:22553962
NASA Astrophysics Data System (ADS)
van der Bom, I. M. J.; Klein, S.; Staring, M.; Homan, R.; Bartels, L. W.; Pluim, J. P. W.
2011-03-01
The advantage of 2D-3D image registration methods versus direct image-to-patient registration, is that these methods generally do not require user interaction (such as manual annotations), additional machinery or additional acquisition of 3D data. A variety of intensity-based similarity measures has been proposed and evaluated for different applications. These studies showed that the registration accuracy and capture range are influenced by the choice of similarity measure. However, the influence of the optimization method on intensity-based 2D-3D image registration has not been investigated. We have compared the registration performance of seven optimization methods in combination with three similarity measures: gradient difference, gradient correlation, and pattern intensity. Optimization methods included in this study were: regular step gradient descent, Nelder-Mead, Powell-Brent, Quasi-Newton, nonlinear conjugate gradient, simultaneous perturbation stochastic approximation, and evolution strategy. Registration experiments were performed on multiple patient data sets that were obtained during cerebral interventions. Various component combinations were evaluated on registration accuracy, capture range, and registration time. The results showed that for the same similarity measure, different registration accuracies and capture ranges were obtained when different optimization methods were used. For gradient difference, largest capture ranges were obtained with Powell-Brent and simultaneous perturbation stochastic approximation. Gradient correlation and pattern intensity had the largest capture ranges in combination with Powell-Brent, Nelder-Mead, nonlinear conjugate gradient, and Quasi-Newton. Average registration time, expressed in the number of DRRs required for convergence, was the lowest for Powell-Brent. Based on these results, we conclude that Powell-Brent is a reliable optimization method for intensity-based 2D-3D registration of x-ray images to CBCT
Iterative and FEM methods to solve the 2-D Radiative Transfer Equation with specular reflexion
NASA Astrophysics Data System (ADS)
Le Hardy, David; Favennec, Yann; Rousseau, Benoît
2016-01-01
The present paper deals with iterative algorithms coupled with finite element methods (FEM) to solve the Radiative Transfer Equation (RTE) within semi-transparent heterogenous materials where specular reflexions occur on their boundaries. As our intention is to use such solution for inversion, the forward model should be solved as fastly as possible. This communication compares, in terms of both accuracy and CPU, the Discontinuous Galerkin (DG) method with the Streamline Upwind Petrov-Galerkin (SUPG) method, both being coupled with the Discrete Ordinate Method. Next, several iteratives methods used to accelerate the convergence are compared. These methods are the Gauss-Siedel (GS), the Source-Iteration (SI) and the Successive Over-Relaxation (SOR) methods.
Mixed-RKDG Finite Element Methods for the 2-D Hydrodynamic Model for Semiconductor Device Simulation
Chen, Zhangxin; Cockburn, Bernardo; Jerome, Joseph W.; Shu, Chi-Wang
1995-01-01
In this paper we introduce a new method for numerically solving the equations of the hydrodynamic model for semiconductor devices in two space dimensions. The method combines a standard mixed finite element method, used to obtain directly an approximation to the electric field, with the so-called Runge-Kutta Discontinuous Galerkin (RKDG) method, originally devised for numerically solving multi-dimensional hyperbolic systems of conservation laws, which is applied here to the convective part of the equations. Numerical simulations showing the performance of the new method are displayed, and the results compared with those obtained by using Essentially Nonoscillatory (ENO) finite difference schemes. Frommore » the perspective of device modeling, these methods are robust, since they are capable of encompassing broad parameter ranges, including those for which shock formation is possible. The simulations presented here are for Gallium Arsenide at room temperature, but we have tested them much more generally with considerable success.« less
Proteus-MOC: A 3D deterministic solver incorporating 2D method of characteristics
Marin-Lafleche, A.; Smith, M. A.; Lee, C.
2013-07-01
A new transport solution methodology was developed by combining the two-dimensional method of characteristics with the discontinuous Galerkin method for the treatment of the axial variable. The method, which can be applied to arbitrary extruded geometries, was implemented in PROTEUS-MOC and includes parallelization in group, angle, plane, and space using a top level GMRES linear algebra solver. Verification tests were performed to show accuracy and stability of the method with the increased number of angular directions and mesh elements. Good scalability with parallelism in angle and axial planes is displayed. (authors)
Coupling finite and boundary element methods for 2-D elasticity problems
NASA Technical Reports Server (NTRS)
Krishnamurthy, T.; Raju, I. S.; Sistla, R.
1993-01-01
A finite element-boundary element (FE-BE) coupling method for two-dimensional elasticity problems is developed based on a weighted residual variational method in which a portion of the domain of interest is modeled by FEs and the remainder of the region by BEs. The performance of the FE-BE coupling method is demonstrated via applications to a simple 'patch test' problem and three-crack problems. The method passed the patch tests for various modeling configurations and yielded accurate strain energy release rates for the crack problems studied.
NASA Astrophysics Data System (ADS)
Pylak, M.; Kontrym-Sznajd, G.; Dobrzyński, L.
2011-08-01
A successful application of the Maximum Entropy Method (MEM) to the reconstruction of electron-positron momentum density distribution in gadolinium out of the experimental of 2D ACAR data is presented. Formally, the algorithm used was prepared for two-dimensional reconstructions from line integrals. For the first time the results of MEM, applied to such data, are compared in detail with the ones obtained by means of Cormack's method. It is also shown how the experimental uncertainties may influence the results of the latter analysis. Preliminary calculations, using WIEN2k code, of band structure and Fermi surface have been done as well.
Numerical solution of 2D-vector tomography problem using the method of approximate inverse
NASA Astrophysics Data System (ADS)
Svetov, Ivan; Maltseva, Svetlana; Polyakova, Anna
2016-08-01
We propose a numerical solution of reconstruction problem of a two-dimensional vector field in a unit disk from the known values of the longitudinal and transverse ray transforms. The algorithm is based on the method of approximate inverse. Numerical simulations confirm that the proposed method yields good results of reconstruction of vector fields.
2D Quantum Simulation of MOSFET Using the Non Equilibrium Green's Function Method
NASA Technical Reports Server (NTRS)
Svizhenko, Alexel; Anantram, M. P.; Govindan, T. R.; Yan, Jerry (Technical Monitor)
2000-01-01
The objectives this viewgraph presentation summarizes include: (1) the development of a quantum mechanical simulator for ultra short channel MOSFET simulation, including theory, physical approximations, and computer code; (2) explore physics that is not accessible by semiclassical methods; (3) benchmarking of semiclassical and classical methods; and (4) study other two-dimensional devices and molecular structure, from discretized Hamiltonian to tight-binding Hamiltonian.
NASA Astrophysics Data System (ADS)
Zheng, Hui; Zhang, Chuanzeng; Wang, Yuesheng; Sladek, Jan; Sladek, Vladimir
2016-01-01
In this paper, a meshfree or meshless local radial basis function (RBF) collocation method is proposed to calculate the band structures of two-dimensional (2D) anti-plane transverse elastic waves in phononic crystals. Three new techniques are developed for calculating the normal derivative of the field quantity required by the treatment of the boundary conditions, which improve the stability of the local RBF collocation method significantly. The general form of the local RBF collocation method for a unit-cell with periodic boundary conditions is proposed, where the continuity conditions on the interface between the matrix and the scatterer are taken into account. The band structures or dispersion relations can be obtained by solving the eigenvalue problem and sweeping the boundary of the irreducible first Brillouin zone. The proposed local RBF collocation method is verified by using the corresponding results obtained with the finite element method. For different acoustic impedance ratios, various scatterer shapes, scatterer arrangements (lattice forms) and material properties, numerical examples are presented and discussed to show the performance and the efficiency of the developed local RBF collocation method compared to the FEM for computing the band structures of 2D phononic crystals.
Sakhratov, Yu. A.; Svistov, L. E.; Kuhns, P. L.; Zhou, H. D.; Reyes, A. P.
2014-11-15
We have carried out {sup 63,65}Cu NMR spectra measurements in a magnetic field up to about 15.5 T on a single crystal of the multiferroic triangular-lattice antiferromagnet CuCrO{sub 2}. The measurements were performed for perpendicular and parallel orientations of the magnetic field with respect to the c axis of the crystal, and the detailed angle dependence of the spectra on the magnetic field direction in the ab plane was studied. The shape of the spectra can be well described in the model of spiral spin structure proposed by recent neutron diffraction experiments. When the field is rotated perpendicular to the crystal c axis, we observed, directly for the first time, a remarkable reorientation of the spin plane simultaneous with rotation of the incommensurate wavevector, by quantitatively deducing the conversion of the energetically less favorable domain to a more favorable one. At high enough fields parallel to the c axis, the data are consistent with either a field-induced commensurate spiral magnetic structure or an incommensurate spiral magnetic structure with a disorder in the c direction, suggesting that high fields may have influence on interplanar ordering.
The 2-D and 3-D time marching transonic potential flow method for propfans
NASA Technical Reports Server (NTRS)
Williams, Marc H.
1988-01-01
Recent efforts concentrated on the development of aerodynamic tools for the analysis of rotors at transonic speeds and of configurations involving relative rotation. Three distinct approaches were taken: (1) extension of the lifting surface method of Williams and Hwang (1986) to relative rotation; (2) development of a time marching linear potential method for counter rotation; and (3) development of 2 and 3 dimensional finite volume potential flow schemes for single rotation. Results from each of these approaches are described.
Lattice Boltzmann methods for some 2-D nonlinear diffusion equations:Computational results
Elton, B.H.; Rodrigue, G.H. . Dept. of Applied Science Lawrence Livermore National Lab., CA ); Levermore, C.D. . Dept. of Mathematics)
1990-01-01
In this paper we examine two lattice Boltzmann methods (that are a derivative of lattice gas methods) for computing solutions to two two-dimensional nonlinear diffusion equations of the form {partial derivative}/{partial derivative}t u = v ({partial derivative}/{partial derivative}x D(u){partial derivative}/{partial derivative}x u + {partial derivative}/{partial derivative}y D(u){partial derivative}/{partial derivative}y u), where u = u({rvec x},t), {rvec x} {element of} R{sup 2}, v is a constant, and D(u) is a nonlinear term that arises from a Chapman-Enskog asymptotic expansion. In particular, we provide computational evidence supporting recent results showing that the methods are second order convergent (in the L{sub 1}-norm), conservative, conditionally monotone finite difference methods. Solutions computed via the lattice Boltzmann methods are compared with those computed by other explicit, second order, conservative, monotone finite difference methods. Results are reported for both the L{sub 1}- and L{sub {infinity}}-norms.
NASA Technical Reports Server (NTRS)
Gardner, J. P.; Straughn, Amber N.; Meurer, Gerhardt R.; Pirzkal, Norbert; Cohen, Seth H.; Malhotra, Sangeeta; Rhoads, james; Windhorst, Rogier A.; Gardner, Jonathan P.; Hathi, Nimish P.; Xu, Chun; Gronwall, Caryl; Koekemoer, Anton M.; Walsh, Jeremy; diSeregoAlighieri, Sperello
2007-01-01
The Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) grism PEARS (Probing Evolution And Reionization Spectroscopically) survey provides a large dataset of low-resolution spectra from thousands of galaxies in the GOODS North and South fields. One important subset of objects in these data are emission-line galaxies (ELGs), and we have investigated several different methods aimed at systematically selecting these galaxies. Here we present a new methodology and results of a search for these ELGs in the PEARS observations of the Hubble Ultra Deep Field (HUDF) using a 2D detection method that utilizes the observation that many emission lines originate from clumpy knots within galaxies. This 2D line-finding method proves to be useful in detecting emission lines from compact knots within galaxies that might not otherwise be detected using more traditional 1D line-finding techniques. We find in total 96 emission lines in the HUDF, originating from 81 distinct "knots" within 63 individual galaxies. We find in general that [0 1111 emitters are the most common, comprising 44% of the sample, and on average have high equivalent widths (70% of [0 1111 emitters having rest-frame EW> 100A). There are 12 galaxies with multiple emitting knots; several show evidence of variations in H-alpha flux in the knots, suggesting that the differing star formation properties across a single galaxy can in general be probed at redshifts approximately greater than 0.2 - 0.4. The most prevalent morphologies are large face-on spirals and clumpy interacting systems, many being unique detections owing to the 2D method described here, thus highlighting the strength of this technique.
Hyun, Eugin; Jin, Young-Seok; Lee, Jong-Hun
2016-01-01
For an automotive pedestrian detection radar system, fast-ramp based 2D range-Doppler Frequency Modulated Continuous Wave (FMCW) radar is effective for distinguishing between moving targets and unwanted clutter. However, when a weak moving target such as a pedestrian exists together with strong clutter, the pedestrian may be masked by the side-lobe of the clutter even though they are notably separated in the Doppler dimension. To prevent this problem, one popular solution is the use of a windowing scheme with a weighting function. However, this method leads to a spread spectrum, so the pedestrian with weak signal power and slow Doppler may also be masked by the main-lobe of clutter. With a fast-ramp based FMCW radar, if the target is moving, the complex spectrum of the range- Fast Fourier Transform (FFT) is changed with a constant phase difference over ramps. In contrast, the clutter exhibits constant phase irrespective of the ramps. Based on this fact, in this paper we propose a pedestrian detection for highly cluttered environments using a coherent phase difference method. By detecting the coherent phase difference from the complex spectrum of the range-FFT, we first extract the range profile of the moving pedestrians. Then, through the Doppler FFT, we obtain the 2D range-Doppler map for only the pedestrian. To test the proposed detection scheme, we have developed a real-time data logging system with a 24 GHz FMCW transceiver. In laboratory tests, we verified that the signal processing results from the proposed method were much better than those expected from the conventional 2D FFT-based detection method. PMID:26805835
Hyun, Eugin; Jin, Young-Seok; Lee, Jong-Hun
2016-01-01
For an automotive pedestrian detection radar system, fast-ramp based 2D range-Doppler Frequency Modulated Continuous Wave (FMCW) radar is effective for distinguishing between moving targets and unwanted clutter. However, when a weak moving target such as a pedestrian exists together with strong clutter, the pedestrian may be masked by the side-lobe of the clutter even though they are notably separated in the Doppler dimension. To prevent this problem, one popular solution is the use of a windowing scheme with a weighting function. However, this method leads to a spread spectrum, so the pedestrian with weak signal power and slow Doppler may also be masked by the main-lobe of clutter. With a fast-ramp based FMCW radar, if the target is moving, the complex spectrum of the range- Fast Fourier Transform (FFT) is changed with a constant phase difference over ramps. In contrast, the clutter exhibits constant phase irrespective of the ramps. Based on this fact, in this paper we propose a pedestrian detection for highly cluttered environments using a coherent phase difference method. By detecting the coherent phase difference from the complex spectrum of the range-FFT, we first extract the range profile of the moving pedestrians. Then, through the Doppler FFT, we obtain the 2D range-Doppler map for only the pedestrian. To test the proposed detection scheme, we have developed a real-time data logging system with a 24 GHz FMCW transceiver. In laboratory tests, we verified that the signal processing results from the proposed method were much better than those expected from the conventional 2D FFT-based detection method. PMID:26805835
Habibi, Ehsanollah; Soury, Shiva; Zadeh, Akbar Hasan
2013-10-01
Various studies carried out on different photo anthropometry, but each one had some deficiencies which during the years they have been resolved. The objective of this paper is to test the efficiency of two-dimensional image processing software in photo anthropometry of hand. In this applied research, 204 office workers and industrial workers were selected. Their hands were measured by manual with photo anthropometric methods. In this study, designing the "Hand Photo Anthropometry Set," we tried to fix the angle and distance of the camera in all of the photos. Thus, some of the common mistakes in photo anthropometric method got controlled. The taken photos were analyzed by Digimizer software, version 4.1.1.0 and Digital Caliper (Model: Mitutoyo Corp., Tokyo, Japan) was used via manual method. t-test statistical test on data revealed that there is no significant difference between the manual and photo anthropometric results (P > 0.05) and the correlation coefficients for hand dimensions are similar in both methods illustrated in the range of 0.71-0.95. The statistical analyses showed that photo anthropometry can be replaced with manual methods. Furthermore, it can provide a great help to develop an anthropometric database for work gloves manufacturers. Since the hand anthropometry is a necessary input for tool design, this survey can be used to determine the percentiles of workers' hands. PMID:24696802
Body edge delineation in 2D DC resistivity imaging using differential method
NASA Astrophysics Data System (ADS)
Susanto, Kusnahadi; Fitrah Bahari, Mohammad
2016-01-01
DC resistivity is widely used to identify the kind of rock and the lithology contact. However, the image resulting from resistivity processing is shown in a contour image. There is be a problem to interpret where the edge of body location is. This study uses differential method to delineate the edge of body in DC resistivity contour. This method was applied to the boundary between gravel and underlying clay layer. The first and the second order differential method is applied to the delineation of lithology contact. The profiling curve has to be sliced and extracted from the resistivity contour before the differential method can be used. The spectral analysis shows the frequency and wavenumber of the profiling curve used to make gridding. The slicing process was conducted horizontally and vertically in order to get the mesh size which will be used in the differential method. The second order differential, the Laplace operator, is able to show the edge of body more clearly than the first order differential and shows the contact between gravel and clay.
Precise Evaluation of Anthropometric 2D Software Processing of Hand in Comparison with Direct Method
Habibi, Ehsanollah; Soury, Shiva; Zadeh, Akbar Hasan
2013-01-01
Various studies carried out on different photo anthropometry, but each one had some deficiencies which during the years they have been resolved. The objective of this paper is to test the efficiency of two-dimensional image processing software in photo anthropometry of hand. In this applied research, 204 office workers and industrial workers were selected. Their hands were measured by manual with photo anthropometric methods. In this study, designing the “Hand Photo Anthropometry Set,” we tried to fix the angle and distance of the camera in all of the photos. Thus, some of the common mistakes in photo anthropometric method got controlled. The taken photos were analyzed by Digimizer software, version 4.1.1.0 and Digital Caliper (Model: Mitutoyo Corp., Tokyo, Japan) was used via manual method. t-test statistical test on data revealed that there is no significant difference between the manual and photo anthropometric results (P > 0.05) and the correlation coefficients for hand dimensions are similar in both methods illustrated in the range of 0.71-0.95. The statistical analyses showed that photo anthropometry can be replaced with manual methods. Furthermore, it can provide a great help to develop an anthropometric database for work gloves manufacturers. Since the hand anthropometry is a necessary input for tool design, this survey can be used to determine the percentiles of workers’ hands. PMID:24696802
NASA Astrophysics Data System (ADS)
Rabahi, Amal; Hamdi, Safouane M.; Rachedi, Yahia; Hamdi, Maamar; Talhi, Oualid; Almeida Paz, Filipe A.; Silva, Artur S. M.; Fadila, Balegroune; Malika, Hamadène; Kamel, Taïbi
2014-03-01
The synthesis of 1,5-benzodiazepines by the reaction of o-phenylenediamines (o-PDAs) with dehydroacetic acid DHAA [3-acetyl-4-hydroxy-6-methyl-2H-pyran-2-one] or conjugate analogues is largely reported in the literature, but still with uncontrolled stereochemistry. In this work, a comprehensive mechanistic study on the formation of some synthesized 1,5-benzodiazepine models following different organic routes is established based on liquid-state 2D NMR, single-crystal X-ray diffraction and theoretical calculations allowing the classification of two prototropic forms A (enaminopyran-2,4-dione) and B (imino-4-hydroxypyran-2-one). Evidences are presented to show that most of the reported 1,5-benzodiazepine structures arising from DHAA and derivatives preferentially adopt the (E)-enaminopyran-2,4-diones A.
A numerical method for computing unsteady 2-D boundary layer flows
NASA Technical Reports Server (NTRS)
Krainer, Andreas
1988-01-01
A numerical method for computing unsteady two-dimensional boundary layers in incompressible laminar and turbulent flows is described and applied to a single airfoil changing its incidence angle in time. The solution procedure adopts a first order panel method with a simple wake model to solve for the inviscid part of the flow, and an implicit finite difference method for the viscous part of the flow. Both procedures integrate in time in a step-by-step fashion, in the course of which each step involves the solution of the elliptic Laplace equation and the solution of the parabolic boundary layer equations. The Reynolds shear stress term of the boundary layer equations is modeled by an algebraic eddy viscosity closure. The location of transition is predicted by an empirical data correlation originating from Michel. Since transition and turbulence modeling are key factors in the prediction of viscous flows, their accuracy will be of dominant influence to the overall results.
A High Order Discontinuous Galerkin Method for 2D Incompressible Flows
NASA Technical Reports Server (NTRS)
Liu, Jia-Guo; Shu, Chi-Wang
1999-01-01
In this paper we introduce a high order discontinuous Galerkin method for two dimensional incompressible flow in vorticity streamfunction formulation. The momentum equation is treated explicitly, utilizing the efficiency of the discontinuous Galerkin method The streamfunction is obtained by a standard Poisson solver using continuous finite elements. There is a natural matching between these two finite element spaces, since the normal component of the velocity field is continuous across element boundaries. This allows for a correct upwinding gluing in the discontinuous Galerkin framework, while still maintaining total energy conservation with no numerical dissipation and total enstrophy stability The method is suitable for inviscid or high Reynolds number flows. Optimal error estimates are proven and verified by numerical experiments.
Edge gradients evaluation for 2D hybrid finite volume method model
Technology Transfer Automated Retrieval System (TEKTRAN)
In this study, a two-dimensional depth-integrated hydrodynamic model was developed using FVM on a hybrid unstructured collocated mesh system. To alleviate the negative effects of mesh irregularity and non-uniformity, a conservative evaluation method for edge gradients based on the second-order Tayl...
A spectral boundary integral equation method for the 2-D Helmholtz equation
NASA Technical Reports Server (NTRS)
Hu, Fang Q.
1994-01-01
In this paper, we present a new numerical formulation of solving the boundary integral equations reformulated from the Helmholtz equation. The boundaries of the problems are assumed to be smooth closed contours. The solution on the boundary is treated as a periodic function, which is in turn approximated by a truncated Fourier series. A Fourier collocation method is followed in which the boundary integral equation is transformed into a system of algebraic equations. It is shown that in order to achieve spectral accuracy for the numerical formulation, the nonsmoothness of the integral kernels, associated with the Helmholtz equation, must be carefully removed. The emphasis of the paper is on investigating the essential elements of removing the nonsmoothness of the integral kernels in the spectral implementation. The present method is robust for a general boundary contour. Aspects of efficient implementation of the method using FFT are also discussed. A numerical example of wave scattering is given in which the exponential accuracy of the present numerical method is demonstrated.
Toward a 2D vector map with a feature nodes-based watermarking method
NASA Astrophysics Data System (ADS)
Zhang, Hongsheng; Li, Yan
2009-10-01
With a wide use of vector maps, the copyright issue is educing an increasing importance and attracting focus on the transmission and the exchange of the vector maps through a network environment. This paper discusses a feature nodes based watermarking method (FNBW) towards keeping robustness and high accuracy of digital map based on SVG and GML format. The digital map treats as a set of curves in the embedding algorithm, and each curve was divided up into several shorter curves under two given thresholds. And then a watermark bit combined with user certificate was embedded into each segment around the feature nodes with the maximum curvature in the segment series nodes. To extract the watermark, all watermark nodes were calculated and searched for in the watermarked map with the Watermark node Searching Algorithm by using the original map. Finally the method calculates the similarity between the original watermark bits and the extracted ones, and determines whether the watermark exists or not. As the experiment result shown, the method not only guarantees the accuracy of vector map but also possesses the good robustness, such as it gives 1.00 similarity under no attack or only geometric transformation with the map; And the anticopping ability is also good enough to give a more than 0.87 similarity for the map cropped 80%. In addition, the method has the full ability of anti-compression lossless methods and good ability to the loss approaches. And an experiment curve of the similarity threshold was given in the paper, which helped to control the anti-attack ability of the watermark and set parameters for an automatic procedure of watermark detection.
2-D transmitral flows simulation by means of the immersed boundary method on unstructured grids
NASA Astrophysics Data System (ADS)
Denaro, F. M.; Sarghini, F.
2002-04-01
Interaction between computational fluid dynamics and clinical researches recently allowed a deeper understanding of the physiology of complex phenomena involving cardio-vascular mechanisms. The aim of this paper is to develop a simplified numerical model based on the Immersed Boundary Method and to perform numerical simulations in order to study the cardiac diastolic phase during which the left ventricle is filled with blood flowing from the atrium throughout the mitral valve. As one of the diagnostic problems to be faced by clinicians is the lack of a univocal definition of the diastolic performance from the velocity measurements obtained by Eco-Doppler techniques, numerical simulations are supposed to provide an insight both into the physics of the diastole and into the interpretation of experimental data. An innovative application of the Immersed Boundary Method on unstructured grids is presented, fulfilling accuracy requirements related to the development of a thin boundary layer along the moving immersed boundary. It appears that this coupling between unstructured meshes and the Immersed Boundary Method is a promising technique when a wide range of spatial scales is involved together with a moving boundary. Numerical simulations are performed in a range of physiological parameters and a qualitative comparison with experimental data is presented, in order to demonstrate that, despite the simplified model, the main physiological characteristics of the diastole are well represented. Copyright
A wideband FMBEM for 2D acoustic design sensitivity analysis based on direct differentiation method
NASA Astrophysics Data System (ADS)
Chen, Leilei; Zheng, Changjun; Chen, Haibo
2013-09-01
This paper presents a wideband fast multipole boundary element method (FMBEM) for two dimensional acoustic design sensitivity analysis based on the direct differentiation method. The wideband fast multipole method (FMM) formed by combining the original FMM and the diagonal form FMM is used to accelerate the matrix-vector products in the boundary element analysis. The Burton-Miller formulation is used to overcome the fictitious frequency problem when using a single Helmholtz boundary integral equation for exterior boundary-value problems. The strongly singular and hypersingular integrals in the sensitivity equations can be evaluated explicitly and directly by using the piecewise constant discretization. The iterative solver GMRES is applied to accelerate the solution of the linear system of equations. A set of optimal parameters for the wideband FMBEM design sensitivity analysis are obtained by observing the performances of the wideband FMM algorithm in terms of computing time and memory usage. Numerical examples are presented to demonstrate the efficiency and validity of the proposed algorithm.
Gradient ROtating Outer Volume Excitation (GROOVE): A Novel Method for Single-Shot 2-D OVS
Powell, Nathaniel J.; Jang, Albert; Park, Jang-Yeon; Valette, Julien; Garwood, Michael; Marjańska, Małgorzata
2014-01-01
Purpose A new outer volume suppression (OVS) technique is introduced that uses a single pulse and rotating gradients to accomplish frequency-swept excitation. This new technique, which is called Gradient ROtating Outer Volume Excitation (GROOVE), produces a circular or elliptical suppression band rather than suppressing the entire outer volume. Methods Theoretical and k-space descriptions of GROOVE are provided. The properties of GROOVE were investigated with simulations, phantom, and human experiments performed using a 4 T horizontal bore magnet equipped with a TEM coil. Results Similar suppression performance was obtained in phantom and human brain using GROOVE with circular and elliptical shapes. Simulations indicate that GROOVE requires less SAR and time than traditional OVS schemes, but traditional schemes provide a sharper transition zone and less residual signal. Conclusion GROOVE represents a new way of performing OVS in which spins are excited temporally in space on a trajectory which can be tailored to fit the shape of the suppression region. In addition, GROOVE is capable of suppressing tailored regions of space with more flexibility and in a shorter period of time than conventional methods. GROOVE provides a fast, low SAR alternative to conventional OVS methods in some applications (e.g., scalp suppression). PMID:24478130
Development for 2D pattern quantification method on mask and wafer
NASA Astrophysics Data System (ADS)
Matsuoka, Ryoichi; Mito, Hiroaki; Toyoda, Yasutaka; Wang, Zhigang
2010-03-01
We have developed the effective method of mask and silicon 2-dimensional metrology. The aim of this method is evaluating the performance of the silicon corresponding to Hotspot on a mask. The method adopts a metrology management system based on DBM (Design Based Metrology). This is the high accurate contouring created by an edge detection algorithm used in mask CD-SEM and silicon CD-SEM. Currently, as semiconductor manufacture moves towards even smaller feature size, this necessitates more aggressive optical proximity correction (OPC) to drive the super-resolution technology (RET). In other words, there is a trade-off between highly precise RET and mask manufacture, and this has a big impact on the semiconductor market that centers on the mask business. 2-dimensional Shape quantification is important as optimal solution over these problems. Although 1-dimensional shape measurement has been performed by the conventional technique, 2-dimensional shape management is needed in the mass production line under the influence of RET. We developed the technique of analyzing distribution of shape edge performance as the shape management technique. On the other hand, there is roughness in the silicon shape made from a mass-production line. Moreover, there is variation in the silicon shape. For this reason, quantification of silicon shape is important, in order to estimate the performance of a pattern. In order to quantify, the same shape is equalized in two dimensions. And the method of evaluating based on the shape is popular. In this study, we conducted experiments for averaging method of the pattern (Measurement Based Contouring) as two-dimensional mask and silicon evaluation technique. That is, observation of the identical position of a mask and a silicon was considered. It is possible to analyze variability of the edge of the same position with high precision. The result proved its detection accuracy and reliability of variability on two-dimensional pattern (mask and
Application of 2D-Nonlinear Shallow Water Model of Tsunami by using Adomian Decomposition Method
Waewcharoen, Sribudh; Boonyapibanwong, Supachai; Koonprasert, Sanoe
2008-09-01
One of the most important questions in tsunami modeling is the estimation of tsunami run-up heights at different points along a coastline. Methods for numerical simulation of tsunami wave propagation in deep and shallow seas are well developed and have been widely used by many scientists (2001-2008). In this paper, we consider a two-dimensional nonlinear shallow water model of tsunami given by Tivon Jacobson is work [1]. u{sub t}+uu{sub x}+{nu}u{sub y} -c{sup 2}(h{sub x}+(h{sub b}){sub x}) {nu}{sub t}+u{nu}{sub x}+{nu}{nu}{sub y} = -c{sup 2}(h{sub y}+(h{sub b}){sub y}) h{sub t}+(hu){sub x}+(h{nu}){sub y} = 0 g-shore, h is surface elevation and s, t is time, u is velocity of cross-shore, {nu} is velocity of along-shore, h is surface elevation and h{sub b} is function of shore. This is a nondimensionalized model with the gravity g and constant reference depth H factored into c = {radical}(gH). We apply the Adomian Decompostion Method (ADM) to solve the tsunami model. This powerful method has been used to obtain explicit and numerical solutions of three types of diffusion-convection-reaction (DECR) equations. The ADM results for the tsunami model yield analytical solutions in terms of a rapidly convergent infinite power series. Symbolic computation, numerical results and graphs of solutions are obtained by Maple program.
An IPOT meshless method using DC PSE approximation for fluid flow equations in 2D and 3D geometries
NASA Astrophysics Data System (ADS)
Bourantas, G. C.; Loukopoulos, V. C.; Skouras, E. D.; Burganos, V. N.; Nikiforidis, G. C.
2016-06-01
Navier-Stokes (N-S) equations, in their primitive variable (u-v-p) formulation, are numerically solved using the Implicit Potential (IPOT) numerical scheme in the context of strong form Meshless Point Collocation (MPC) method. The unknown field functions are computed using the Discretization Correction Particle Strength Exchange (DC PSE) approximation method. The latter makes use of discrete moment conditions to derive the operator kernels, which leads to low condition number for the moment matrix compared to other meshless interpolation methods and increased stability for the numerical solution. The proposed meshless scheme is applied on 2D and 3D spatial domains, using uniform or irregular set of nodes to represent the domain. The numerical results obtained are compared against those obtained using well-established methods.
[Novel methods for studies of testicular development and spermatogenesis: From 2D to 3D culture].
Zhang, Lian-dong; Li, He-cheng; Zhang, Tong-dian; Wang, Zi-ming
2016-03-01
The two-dimensional model of cell culture is an important method in the study of testicular development and spermatogenesis but can not effectively mimic and regulate the testicular microenvironment and the whole process of spermatogenesis due to the lack of relevant cell factors and the disruption of a three-dimensional spatial structure. In the past 20 years, the development and optimization of the in vitro model such as testis organotypic culture and in vivo model such as testis transplantation achieved a transformation from two- to three-dimension. The maintenance and optimization of the testicular niche structure could mimic the testicular microenvironment and cell types including Leydig, Sertoli and germ cells, which showed similar biological behaviors to those in vivo. Besides, the cell suspension or tissue fragment floats in the gas-liquid interface so that the development of somatic and germ cells is well maintained in vitro whilst the feedback linkage between grafted testis tissue and hypothalamus-pituitary of the host rebuilt in the in vitro model provides an endocrinological basis for spermatogenesis, which serves as an effective methodology to better understand the organogenesis and development of the testis as well as testicular function regulation, advancing the concept of treatment of male infertility. Al- though each of the methods may have its limitations, the progress in the processing, freezing, thawing, and transplantation of cells and tissues will surely promote their clinical application and present their value in translational medicine. PMID:27172668
A quasi-spectral method for Cauchy problem of 2/D Laplace equation on an annulus
NASA Astrophysics Data System (ADS)
Saito, Katsuyoshi; Nakada, Manabu; Iijima, Kentaro; Onishi, Kazuei
2005-01-01
Real numbers are usually represented in the computer as a finite number of digits hexa-decimal floating point numbers. Accordingly the numerical analysis is often suffered from rounding errors. The rounding errors particularly deteriorate the precision of numerical solution in inverse and ill-posed problems. We attempt to use a multi-precision arithmetic for reducing the rounding error evil. The use of the multi-precision arithmetic system is by the courtesy of Dr Fujiwara of Kyoto University. In this paper we try to show effectiveness of the multi-precision arithmetic by taking two typical examples; the Cauchy problem of the Laplace equation in two dimensions and the shape identification problem by inverse scattering in three dimensions. It is concluded from a few numerical examples that the multi-precision arithmetic works well on the resolution of those numerical solutions, as it is combined with the high order finite difference method for the Cauchy problem and with the eigenfunction expansion method for the inverse scattering problem.
Sastry, Madhavi; Lowrie, Jeffrey F; Dixon, Steven L; Sherman, Woody
2010-05-24
A systematic virtual screening study on 11 pharmaceutically relevant targets has been conducted to investigate the interrelation between 8 two-dimensional (2D) fingerprinting methods, 13 atom-typing schemes, 13 bit scaling rules, and 12 similarity metrics using the new cheminformatics package Canvas. In total, 157 872 virtual screens were performed to assess the ability of each combination of parameters to identify actives in a database screen. In general, fingerprint methods, such as MOLPRINT2D, Radial, and Dendritic that encode information about local environment beyond simple linear paths outperformed other fingerprint methods. Atom-typing schemes with more specific information, such as Daylight, Mol2, and Carhart were generally superior to more generic atom-typing schemes. Enrichment factors across all targets were improved considerably with the best settings, although no single set of parameters performed optimally on all targets. The size of the addressable bit space for the fingerprints was also explored, and it was found to have a substantial impact on enrichments. Small bit spaces, such as 1024, resulted in many collisions and in a significant degradation in enrichments compared to larger bit spaces that avoid collisions. PMID:20450209
A Monte Carlo Method for Projecting Uncertainty in 2D Lagrangian Trajectories
NASA Astrophysics Data System (ADS)
Robel, A.; Lozier, S.; Gary, S. F.
2009-12-01
In this study, a novel method is proposed for modeling the propagation of uncertainty due to subgrid-scale processes through a Lagrangian trajectory advected by ocean surface velocities. The primary motivation and application is differentiating between active and passive trajectories for sea turtles as observed through satellite telemetry. A spatiotemporal launch box is centered on the time and place of actual launch and populated with launch points. Synthetic drifters are launched at each of these locations, adding, at each time step along the trajectory, Monte Carlo perturbations in velocity scaled to the natural variability of the velocity field. The resulting trajectory cloud provides a dynamically evolving density field of synthetic drifter locations that represent the projection of subgrid-scale uncertainty out in time. Subsequently, by relaunching synthetic drifters at points along the trajectory, plots are generated in a daisy chain configuration of the “most likely passive pathways” for the drifter.
Detecting 2D symmetry-protected topological phases with the tensor-network method
NASA Astrophysics Data System (ADS)
Huang, Ching-Yu; Wei, Tzu-Chieh
Symmetry-protected topological (SPT) phases exhibit nontrivial order if symmetry is respected but are adiabatically connected to the trivial product phase if symmetry is not respected. However, unlike the symmetry breaking phase, there is no local order parameter for SPT phases. Here we employ a tensor-network method to compute the topological invariants characterized by the simulated modular S and T matrices proposed by Hung and Wen to study a transition in a one-parameter family of wavefunctions which are Z2 symmetric. The studied wavefunctions are in some sense the SPT analog of Z2 topological states under a string tension. The numerically obtained S and T matrices are able to characterize the two different phases and identify the transition point.
NMR system and method having a permanent magnet providing a rotating magnetic field
Schlueter, Ross D [Berkeley, CA; Budinger, Thomas F [Berkeley, CA
2009-05-19
Disclosed herein are systems and methods for generating a rotating magnetic field. The rotating magnetic field can be used to obtain rotating-field NMR spectra, such as magic angle spinning spectra, without having to physically rotate the sample. This result allows magic angle spinning NMR to be conducted on biological samples such as live animals, including humans.