Novel solution conformation of DNA observed in d(GAATTCGAATTC) by two-dimensional NMR spectroscopy

International Nuclear Information System (INIS)

Chary, K.V.R.; Hosur, R.V.; Govil, G.; Zu-kun, T.; Miles, H.T.

1987-01-01

Resonance assignments of nonexchangeable base and sugar protons of the self-complementary dodecanucleotide d(GAATTCGAATTC) have been obtained by using the two-dimensional Fourier transform NMR methods correlated spectroscopy and nuclear Overhauser effect spectroscopy. Conformational details about the sugar pucker, the glycosidic dihedral angle, and the overall secondary structure of the molecule has been derived from the relative intensities of cross peaks in the two-dimensional NMR spectra in aqueous solution. It is observed that d(GAATTCGAATTC) assumes a novel double-helical structure. The solution conformations of the two complementary strands are identical, unlike those observed in a related sequence in the solid state. Most of the five-membered sugar rings adopt an unusual O1'-endo geometry. All the glycosidic dihedral angles are in the anti domain. The AATT segments A2-T5 and A8-T11 show better stacking compared to the rest of the molecule. These features fit into a right-handed DNA model for the above two segments, with the sugar geometries different from the conventional ones. There are important structural variations in the central TCG portion, which is known to show preferences for DNase I activity, and between G1-A2 and G7-A8, which are cleavage points in the EcoRI recognition sequence. The sugar puckers for G1 and G7 are significantly different from the rest of the molecule. Further, in the three segments mentioned above, the sugar phosphate geometry is such that the distances between protons on adjacent nucleotides are much larger than those expected for a right-handed DNA. The authors suggest that such crevices in the DNA structure may act as hot points in initiation of protein recognition

Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra

International Nuclear Information System (INIS)

Mercier, Pascal; Lewis, Michael J.; Chang, David; Baker, David; Wishart, David S.

2011-01-01

Nuclear magnetic resonance (NMR) and Mass Spectroscopy (MS) are the two most common spectroscopic analytical techniques employed in metabolomics. The large spectral datasets generated by NMR and MS are often analyzed using data reduction techniques like Principal Component Analysis (PCA). Although rapid, these methods are susceptible to solvent and matrix effects, high rates of false positives, lack of reproducibility and limited data transferability from one platform to the next. Given these limitations, a growing trend in both NMR and MS-based metabolomics is towards targeted profiling or “quantitative” metabolomics, wherein compounds are identified and quantified via spectral fitting prior to any statistical analysis. Despite the obvious advantages of this method, targeted profiling is hindered by the time required to perform manual or computer-assisted spectral fitting. In an effort to increase data analysis throughput for NMR-based metabolomics, we have developed an automatic method for identifying and quantifying metabolites in one-dimensional (1D) proton NMR spectra. This new algorithm is capable of using carefully constructed reference spectra and optimizing thousands of variables to reconstruct experimental NMR spectra of biofluids using rules and concepts derived from physical chemistry and NMR theory. The automated profiling program has been tested against spectra of synthetic mixtures as well as biological spectra of urine, serum and cerebral spinal fluid (CSF). Our results indicate that the algorithm can correctly identify compounds with high fidelity in each biofluid sample (except for urine). Furthermore, the metabolite concentrations exhibit a very high correlation with both simulated and manually-detected values.

Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra

Energy Technology Data Exchange (ETDEWEB)

Mercier, Pascal; Lewis, Michael J.; Chang, David, E-mail: dchang@chenomx.com [Chenomx Inc (Canada); Baker, David [Pfizer Inc (United States); Wishart, David S. [University of Alberta, Department of Computing Science and Biological Sciences (Canada)

2011-04-15

Nuclear magnetic resonance (NMR) and Mass Spectroscopy (MS) are the two most common spectroscopic analytical techniques employed in metabolomics. The large spectral datasets generated by NMR and MS are often analyzed using data reduction techniques like Principal Component Analysis (PCA). Although rapid, these methods are susceptible to solvent and matrix effects, high rates of false positives, lack of reproducibility and limited data transferability from one platform to the next. Given these limitations, a growing trend in both NMR and MS-based metabolomics is towards targeted profiling or 'quantitative' metabolomics, wherein compounds are identified and quantified via spectral fitting prior to any statistical analysis. Despite the obvious advantages of this method, targeted profiling is hindered by the time required to perform manual or computer-assisted spectral fitting. In an effort to increase data analysis throughput for NMR-based metabolomics, we have developed an automatic method for identifying and quantifying metabolites in one-dimensional (1D) proton NMR spectra. This new algorithm is capable of using carefully constructed reference spectra and optimizing thousands of variables to reconstruct experimental NMR spectra of biofluids using rules and concepts derived from physical chemistry and NMR theory. The automated profiling program has been tested against spectra of synthetic mixtures as well as biological spectra of urine, serum and cerebral spinal fluid (CSF). Our results indicate that the algorithm can correctly identify compounds with high fidelity in each biofluid sample (except for urine). Furthermore, the metabolite concentrations exhibit a very high correlation with both simulated and manually-detected values.

Investigation of the spatial structure of des-Gly9-[Arg8]vasopressin by the methods of two-dimensional NMR spectroscopy and theoretical conformational analysis

International Nuclear Information System (INIS)

Shenderovich, M.D.; Sekatsis, I.P.; Liepin'sh, E.E.; Nikiforovich, G.V.; Papsuevich, O.S.

1986-01-01

An assignment of the 1 H NMR signals of des-Gly 9 -[Arg 8 ]vasopressin in dimethyl sulfoxide has been made by 2D spectroscopy. The SSCCs and temperature coefficients Δδ/Δ T have been obtained for the amide protons and the system of NOE cross-peaks in the two-dimensional NOESY spectrum has been analyzed. The most important information on the spatial structure of des-Gly 9 -[Arg 8 ]vasopressin is given by the low value of the temperature coefficient Δδ/Δ T of the Asn 5 amide proton and the NOE between the α-protons of Cys 1 and Cys 6 . It is assumed that the screening of the NH proton of the Asn 5 residue from the solvent is connected with a β-bend of the backbone in the 2-5 sequence, and the distance between the C/sup α/H atoms of the Cys 1 and Cys 6 residues does not exceed 4 A. Bearing these limitations in mind, a theoretical conformational analysis of the molecule has been made. The group of low-energy conformations of the backbone obtained has been compared with the complete set of NMR characteristics

Metabolic profiling based on two-dimensional J-resolved 1H NMR data and parallel factor analysis

DEFF Research Database (Denmark)

Yilmaz, Ali; Nyberg, Nils T; Jaroszewski, Jerzy W.

2011-01-01

the intensity variances along the chemical shift axis are taken into account. Here, we describe the use of parallel factor analysis (PARAFAC) as a tool to preprocess a set of two-dimensional J-resolved spectra with the aim of keeping the J-coupling information intact. PARAFAC is a mathematical decomposition......-model was done automatically by evaluating amount of explained variance and core consistency values. Score plots showing the distribution of objects in relation to each other, and loading plots in the form of two-dimensional pseudo-spectra with the same appearance as the original J-resolved spectra...

Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy.

Directory of Open Access Journals (Sweden)

Young Kee Chae

Full Text Available Escherichia coli has been the most widely used host to produce large amounts of heterologous proteins. However, given an input plasmid DNA, E. coli may produce soluble protein, produce only inclusion bodies, or yield little or no protein at all. Many efforts have been made to surmount these problems, but most of them have involved time-consuming and labor-intensive trial-and-error. We hypothesized that different metabolomic fingerprints might be associated with different protein production outcomes. If so, then it might be possible to change the expression pattern by manipulating the metabolite environment. As a first step in testing this hypothesis, we probed a subset of the intracellular metabolites by partially labeling it with 13C-glucose. We tested 71 genes and identified 17 metabolites by employing the two-dimensional NMR spectroscopy. The statistical analysis showed that there existed the metabolite compositions favoring protein production. We hope that this work would help devise a systematic and predictive approach to the recombinant protein production.

Fast multi-dimensional NMR by minimal sampling

Science.gov (United States)

Kupče, Ēriks; Freeman, Ray

2008-03-01

A new scheme is proposed for very fast acquisition of three-dimensional NMR spectra based on minimal sampling, instead of the customary step-wise exploration of all of evolution space. The method relies on prior experiments to determine accurate values for the evolving frequencies and intensities from the two-dimensional 'first planes' recorded by setting t1 = 0 or t2 = 0. With this prior knowledge, the entire three-dimensional spectrum can be reconstructed by an additional measurement of the response at a single location (t1∗,t2∗) where t1∗ and t2∗ are fixed values of the evolution times. A key feature is the ability to resolve problems of overlap in the acquisition dimension. Applied to a small protein, agitoxin, the three-dimensional HNCO spectrum is obtained 35 times faster than systematic Cartesian sampling of the evolution domain. The extension to multi-dimensional spectroscopy is outlined.

Uniform and selective deuteration in two-dimensional NMR of proteins

International Nuclear Information System (INIS)

LeMaster, D.M.

1990-01-01

This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Gronenborn, A.M.; Clore, G.M. [National Institutes of Health, Bethesda, MD (United States)

1994-12-01

Complete understanding of a protein`s function and mechanism of action can only be achieved with a knowledge of its three-dimensional structure at atomic resolution. At present, there are two methods available for determining such structures. The first method, which has been established for many years, is x-ray diffraction of protein single crystals. The second method has blossomed only in the last 5 years and is based on the application of nuclear magnetic resonance (NMR) spectroscopy to proteins in solution. This review paper describes three- and four-dimensional NMR methods applied to protein structure determination and was adapted from Clore and Gronenborn. The review focuses on the underlying principals and practice of multidimensional NMR and the structural information obtained.

NMR experiments on a three-dimensional vibrofluidized granular medium

Science.gov (United States)

Huan, Chao; Yang, Xiaoyu; Candela, D.; Mair, R. W.; Walsworth, R. L.

2004-04-01

A three-dimensional granular system fluidized by vertical container vibrations was studied using pulsed field gradient NMR coupled with one-dimensional magnetic resonance imaging. The system consisted of mustard seeds vibrated vertically at 50 Hz, and the number of layers Nl⩽4 was sufficiently low to achieve a nearly time-independent granular fluid. Using NMR, the vertical profiles of density and granular temperature were directly measured, along with the distributions of vertical and horizontal grain velocities. The velocity distributions showed modest deviations from Maxwell-Boltzmann statistics, except for the vertical velocity distribution near the sample bottom, which was highly skewed and non-Gaussian. Data taken for three values of Nl and two dimensionless accelerations Γ=15,18 were fitted to a hydrodynamic theory, which successfully models the density and temperature profiles away from the vibrating container bottom. A temperature inversion near the free upper surface is observed, in agreement with predictions based on the hydrodynamic parameter μ which is nonzero only in inelastic systems.

Two approaches to 3D reconstruction in NMR zeugmatography

International Nuclear Information System (INIS)

Marr, R.B.; Chen, C.N.; Lauterbur, P.C.

1980-01-01

In nuclear magnetic resonance (NMR) zeugmatography, the primary data pertain to integrals of the unknown nuclear spin density f(x,y,z) over planes instead of lines in R 3 . Two natural approaches to reconstructing f from such data are: (1) By numerical implementation of the inverse Radon transform in three dimensions (the direct approach), and (2) by application, in two successive stages, of existing well-known algorithms for inverting the two-dimensional Radon transform (the two-stage approach). These two approaches are discussed and compared, both from a theoretical standpoint and through computer results obtained with real NMR data. For the cases studied to date the two methods appear to produce qualitatively similar results

Two-dimensional nuclear magnetic resonance of quadrupolar systems

Energy Technology Data Exchange (ETDEWEB)

Wang, Shuanhu [Univ. of California, Berkeley, CA (United States)

1997-09-01

This dissertation describes two-dimensional nuclear magnetic resonance theory and experiments which have been developed to study quadruples in the solid state. The technique of multiple-quantum magic-angle spinning (MQMAS) is extensively reviewed and expanded upon in this thesis. Specifically, MQMAS is first compared with another technique, dynamic-angle spinning (DAS). The similarity between the two techniques allows us to extend much of the DAS work to the MQMAS case. Application of MQMAS to a series of aluminum containing materials is then presented. The superior resolution enhancement through MQMAS is exploited to detect the five- and six-coordinated aluminum in many aluminosilicate glasses. Combining the MQMAS method with other experiments, such as HETCOR, greatly expands the possibility of the use of MQMAS to study a large range of problems and is demonstrated in Chapter 5. Finally, the technique switching-angle spinning (SAS) is applied to quadrupolar nuclei to fully characterize a quadrupolar spin system in which all of the 8 NMR parameters are accurately determined. This dissertation is meant to demonstrate that with the combination of two-dimensional NMR concepts and new advanced spinning technologies, a series of multiple-dimensional NMR techniques can be designed to allow a detailed study of quadrupolar nuclei in the solid state.

Characterization of pH titration shifts for all the nonlabile proton resonances in a protein by two-dimensional NMR: The case of mouse epidermal growth factor

International Nuclear Information System (INIS)

Kohda, Daisuke; Sawada, Toshie; Inagaki, Fuyuhiko

1991-01-01

The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p 2 H range 1.5-9 with two-dimensional (2D) 1 H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable group which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups (α-amino group, four Asp, two Glu, one His, and α-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal α-amino group induced a widespread conformational change over the β-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. The authors found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins

Two-dimensional NMR spectroscopy links structural moieties of soil organic matter to the temperature sensitivity of its decomposition

Science.gov (United States)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Schleucher, Jürgen

2015-04-01

Soil organic matter (SOM) represents a huge carbon pool, specifically in boreal ecosystems. Warming-induced release of large amounts of CO2 from the soil carbon pool might become a significant exacerbating feedback to global warming, if decomposition rates of boreal soils were more sensitive to increased temperatures. Despite a large number of studies dedicated to the topic, it has proven difficult to elucidate how the organo-chemical composition of SOM influences its decomposition, or its quality as a substrate for microbial metabolism. A great part of this challenge results from our inability to achieve a detailed characterization of the complex composition of SOM on the level of molecular structural moieties. 13C nuclear magnetic resonance (NMR) spectroscopy is a common tool to characterize SOM. However, SOM is a very complex mixture and the chemical shift regions distinguished in the 13C NMR spectra often represent many different molecular fragments. For example, in the carbohydrates region, signals of all monosaccharides present in many different polymers overlap. This overlap thwarts attempts to identify molecular moieties, resulting in insufficient information to characterize SOM composition. We applied two-dimensional (2D) NMR to characterize SOM with highly increased resolution. We directly dissolved finely ground litters and forest floors'fibric and humic horizons'of both coniferous and deciduous boreal forests in dimethyl sulfoxide and analyzed the resulting solution with a 2D 1H-13C NMR experiment. In the 2D planes of these spectra, signals of CH groups can be resolved based on their 13C and 1H chemical shifts, hence the resolving power and information content of these NMR spectra is hugely increased. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra, so that hundreds of distinct CH groups could be observed and many molecular fragments could be identified. For instance, in the aromatics region, signals from individual lignin units could

Three-dimensional absorbed dose determinations by N.M.R. analysis of phantom-dosemeters

International Nuclear Information System (INIS)

Gambarini, G.; Birattari, C.; Fumagalli, M.L.; Vai, A.; Monti, D.; Salvadori, P.; Facchielli, L.; Sichirollo, A.E.

1996-01-01

Magnetic resonance imaging of a tissue-equivalent phantom is a promising technique for three-dimensional determination of absorbed dose from ionizing radiation. A reliable method of determining the spatial distribution of absorbed dose is indispensable for the planning of treatment in the presently developed radiotherapy techniques aimed at obtaining high energy selectively delivered to cancerous tissues, with low dose delivered to the surrounding healthy tissue. Aqueous gels infused with the Fricke dosemeter (i.e. with a ferrous sulphate solution), as proposed in 1984 by Gore et al., have shown interesting characteristics and, in spite of some drawbacks that cause a few limitations to their utilisation, they have shown the feasibility of three-dimensional dose determinations by nuclear magnetic resonance (NMR) imaging. Fricke-infused agarose gels with various compositions have been analysed, considering the requirements of the new radiotherapy techniques, in particular Boron Neutron Capture Therapy (B.N.C.T.) and proton therapy. Special attention was paid to obtain good tissue equivalence for every radiation type of interest. In particular, the tissue equivalence for thermal neutrons, which is a not simple problem, has also been satisfactorily attained. The responses of gel-dosemeters having the various chosen compositions have been analysed, by mean of NMR instrumentation. Spectrophotometric measurements have also been performed, to verify the consistence of the results. (author)

Rapid prediction of multi-dimensional NMR data sets

International Nuclear Information System (INIS)

Gradmann, Sabine; Ader, Christian; Heinrich, Ines; Nand, Deepak; Dittmann, Marc; Cukkemane, Abhishek; Dijk, Marc van; Bonvin, Alexandre M. J. J.; Engelhard, Martin; Baldus, Marc

2012-01-01

We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such “in silico” data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAShttp://www.wenmr.eu/services/FANDAS).

Rapid prediction of multi-dimensional NMR data sets

Energy Technology Data Exchange (ETDEWEB)

Gradmann, Sabine; Ader, Christian [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Heinrich, Ines [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Nand, Deepak [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Dittmann, Marc [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Cukkemane, Abhishek; Dijk, Marc van; Bonvin, Alexandre M. J. J. [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Engelhard, Martin [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

2012-12-15

We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such 'in silico' data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAShttp://www.wenmr.eu/services/FANDAS).

Two dimensional NMR studies of polysaccharides

International Nuclear Information System (INIS)

Byrd, R.A.; Egan, W.; Summers, M.F.

1987-01-01

Polysaccharides are very important components in the immune response system. Capsular polysaccharides and lipopolysaccharides occupy cell surface sites of bacteria, play key roles in recognition and some have been used to develop vaccines. Consequently, the ability to determine chemical structures of these systems is vital to an understanding of their immunogenic action. The authors have been utilizing recently developed two-dimensional homonuclear and heteronuclear correlation spectroscopy for unambiguous assignment and structure determination of a number of polysaccharides. In particular, the 1 H-detected heteronuclear correlation experiments are essential to the rapid and sensitive determination of these structures. Linkage sites are determined by independent polarization transfer experiments and multiple quantum correlation experiments. These methods permit the complete structure determination on very small amounts of the polysaccharides. They present the results of a number of structural determinations and discuss the limits of these experiments in terms of their applications to polysaccharides

Application of two-dimensional J-resolved nuclear magnetic resonance spectroscopy to differentiation of beer

International Nuclear Information System (INIS)

Khatib, Alfi; Wilson, Erica G.; Kim, Hye Kyong; Lefeber, Alfons W.M.; Erkelens, Cornelis; Choi, Young Hae; Verpoorte, Robert

2006-01-01

A number of ingredients in beer that directly or indirectly affect its quality require an unbiased wide-spectrum analytical method that allows for the determination of a wide array of compounds for its efficient control. 1 H nuclear magnetic resonance (NMR) spectroscopy is a method that clearly meets this description as the broad range of compounds in beer is detectable. However, the resulting congestion of signals added to the low resolution of 1 H NMR spectra makes the identification of individual components very difficult. Among two-dimensional (2D) NMR techniques that increase the resolution, J-resolved NMR spectra were successfully applied to the analysis of 2-butanol extracts of beer as overlapping signals in 1 H NMR spectra were fully resolved by the additional axis of the coupling constant. Principal component analysis based on the projected J-resolved NMR spectra showed a clear separation between all of the six brands of pilsner beer evaluated in this study. The compounds responsible for the differentiation were identified by 2D NMR spectra including correlated spectroscopy and heteronuclear multiple bond correlation spectra together with J-resolved spectra. They were identified as nucleic acid derivatives (adenine, uridine and xanthine), amino acids (tyrosine and proline), organic acid (succinic and lactic acid), alcohol (tyrosol and isopropanol), cholines and carbohydrates

NMR analysis of male fathead minnow urinary metabolites: A potential approach for studying impacts of chemical exposures

Energy Technology Data Exchange (ETDEWEB)

Ekman, D.R. [Ecosystems Research Division, U.S. EPA, 960 College Station Road, Athens, GA 30605 (United States)], E-mail: ekman.drew@epa.gov; Teng, Q. [Ecosystems Research Division, U.S. EPA, 960 College Station Road, Athens, GA 30605 (United States); Jensen, K.M.; Martinovic, D.; Villeneuve, D.L.; Ankley, G.T. [Mid-Continent Ecology Division, U.S. EPA, 6201 Congdon Boulevard, Duluth, MN 55804 (United States); Collette, T.W. [Ecosystems Research Division, U.S. EPA, 960 College Station Road, Athens, GA 30605 (United States)

2007-11-30

The potential for profiling metabolites in urine from male fathead minnows (Pimephales promelas) to assess chemical exposures was explored using nuclear magnetic resonance (NMR) spectroscopy. Both one-dimensional (1D) and two-dimensional (2D) NMR spectroscopy was used for the assignment of metabolites in urine from unexposed fish. Because fathead minnow urine is dilute, we lyophilized these samples prior to analysis. Furthermore, 1D {sup 1}H NMR spectra of unlyophilized urine from unexposed male fathead minnow and Sprague-Dawley rat were acquired to qualitatively compare rat and fish metabolite profiles and to provide an estimate of the total urinary metabolite pool concentration difference. As a small proof-of-concept study, lyophilized urine samples from male fathead minnows exposed to three different concentrations of the antiandrogen vinclozolin were analyzed by 1D {sup 1}H NMR to assess exposure-induced changes. Through a combination of principal components analysis (PCA) and measurements of {sup 1}H NMR peak intensities, several metabolites were identified as changing with statistical significance in response to exposure. Among those changes occurring in response to exposure to the highest concentration (450 {mu}g/L) of vinclozolin were large increases in taurine, lactate, acetate, and formate. These increases coincided with a marked decrease in hippurate, a combination potentially indicative of hepatotoxicity. The results of these investigations clearly demonstrate the potential utility of an NMR-based approach for assessing chemical exposures in male fathead minnow, using urine collected from individual fish.

NMR analysis of male fathead minnow urinary metabolites: A potential approach for studying impacts of chemical exposures

International Nuclear Information System (INIS)

Ekman, D.R.; Teng, Q.; Jensen, K.M.; Martinovic, D.; Villeneuve, D.L.; Ankley, G.T.; Collette, T.W.

2007-01-01

The potential for profiling metabolites in urine from male fathead minnows (Pimephales promelas) to assess chemical exposures was explored using nuclear magnetic resonance (NMR) spectroscopy. Both one-dimensional (1D) and two-dimensional (2D) NMR spectroscopy was used for the assignment of metabolites in urine from unexposed fish. Because fathead minnow urine is dilute, we lyophilized these samples prior to analysis. Furthermore, 1D 1 H NMR spectra of unlyophilized urine from unexposed male fathead minnow and Sprague-Dawley rat were acquired to qualitatively compare rat and fish metabolite profiles and to provide an estimate of the total urinary metabolite pool concentration difference. As a small proof-of-concept study, lyophilized urine samples from male fathead minnows exposed to three different concentrations of the antiandrogen vinclozolin were analyzed by 1D 1 H NMR to assess exposure-induced changes. Through a combination of principal components analysis (PCA) and measurements of 1 H NMR peak intensities, several metabolites were identified as changing with statistical significance in response to exposure. Among those changes occurring in response to exposure to the highest concentration (450 μg/L) of vinclozolin were large increases in taurine, lactate, acetate, and formate. These increases coincided with a marked decrease in hippurate, a combination potentially indicative of hepatotoxicity. The results of these investigations clearly demonstrate the potential utility of an NMR-based approach for assessing chemical exposures in male fathead minnow, using urine collected from individual fish

Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition.

Science.gov (United States)

Rajan, Arunkumar Chitteth; Rezapour, Mohammad Reza; Yun, Jeonghun; Cho, Yeonchoo; Cho, Woo Jong; Min, Seung Kyu; Lee, Geunsik; Kim, Kwang S

2014-02-25

Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

Applications of NMR spectroscopy to xenobiotic metabolism

International Nuclear Information System (INIS)

Harris, T.M.

1989-01-01

Recent years have seen high field NMR spectrometers become commonplace in research laboratories. At the same time, major advances in methodology for structural analysis have occurred, particularly notable among these being the development of two-dimensional spectroscopic techniques. Many applications have been made of NMR spectroscopy in the study of xenobiotic metabolic processes. This deals with two specific applications which have been made in the author's laboratory and involve mechanistic studies of the reactions of the carcinogens ethylene dibromide and aflatoxin with DNA

Complex Mixture Analysis of Organic Compounds in Yogurt by NMR Spectroscopy

Science.gov (United States)

Lu, Yi; Hu, Fangyu; Miyakawa, Takuya; Tanokura, Masaru

2016-01-01

NMR measurements do not require separation and chemical modification of samples and therefore rapidly and directly provide non-targeted information on chemical components in complex mixtures. In this study, one-dimensional (1H, 13C, and 31P) and two-dimensional (1H-13C and 1H-31P) NMR spectroscopy were conducted to analyze yogurt without any pretreatment. 1H, 13C, and 31P NMR signals were assigned to 10 types of compounds. The signals of α/β-lactose and α/β-galactose were separately observed in the 1H NMR spectra. In addition, the signals from the acyl chains of milk fats were also successfully identified but overlapped with many other signals. Quantitative difference spectra were obtained by subtracting the diffusion ordered spectroscopy (DOSY) spectra from the quantitative 1H NMR spectra. This method allowed us to eliminate interference on the overlaps; therefore, the correct intensities of signals overlapped with those from the acyl chains of milk fat could be determined directly without separation. Moreover, the 1H-31P HMBC spectra revealed for the first time that N-acetyl-d-glucosamine-1-phosphate is contained in yogurt. PMID:27322339

Two-dimensional NMR measurement and point dipole model prediction of paramagnetic shift tensors in solids

Energy Technology Data Exchange (ETDEWEB)

Walder, Brennan J.; Davis, Michael C.; Grandinetti, Philip J. [Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210 (United States); Dey, Krishna K. [Department of Physics, Dr. H. S. Gour University, Sagar, Madhya Pradesh 470003 (India); Baltisberger, Jay H. [Division of Natural Science, Mathematics, and Nursing, Berea College, Berea, Kentucky 40403 (United States)

2015-01-07

A new two-dimensional Nuclear Magnetic Resonance (NMR) experiment to separate and correlate the first-order quadrupolar and chemical/paramagnetic shift interactions is described. This experiment, which we call the shifting-d echo experiment, allows a more precise determination of tensor principal components values and their relative orientation. It is designed using the recently introduced symmetry pathway concept. A comparison of the shifting-d experiment with earlier proposed methods is presented and experimentally illustrated in the case of {sup 2}H (I = 1) paramagnetic shift and quadrupolar tensors of CuCl{sub 2}⋅2D{sub 2}O. The benefits of the shifting-d echo experiment over other methods are a factor of two improvement in sensitivity and the suppression of major artifacts. From the 2D lineshape analysis of the shifting-d spectrum, the {sup 2}H quadrupolar coupling parameters are 〈C{sub q}〉 = 118.1 kHz and 〈η{sub q}〉 = 0.88, and the {sup 2}H paramagnetic shift tensor anisotropy parameters are 〈ζ{sub P}〉 = − 152.5 ppm and 〈η{sub P}〉 = 0.91. The orientation of the quadrupolar coupling principal axis system (PAS) relative to the paramagnetic shift anisotropy principal axis system is given by (α,β,γ)=((π)/2 ,(π)/2 ,0). Using a simple ligand hopping model, the tensor parameters in the absence of exchange are estimated. On the basis of this analysis, the instantaneous principal components and orientation of the quadrupolar coupling are found to be in excellent agreement with previous measurements. A new point dipole model for predicting the paramagnetic shift tensor is proposed yielding significantly better agreement than previously used models. In the new model, the dipoles are displaced from nuclei at positions associated with high electron density in the singly occupied molecular orbital predicted from ligand field theory.

Two-dimensional NMR data of a water-soluble β-(1→3, 1→6-glucan from Aureobasidium pullulans and schizophyllan from Schizophyllum commune

Directory of Open Access Journals (Sweden)

Hiroyuki Kono

2017-12-01

Full Text Available This article contains two-dimensional (2D NMR experimental data, obtained by the Bruker BioSpin 500 MHz NMR spectrometer (Germany which can used for the determination of primary structures of schizophyllan from Schizophyllum commune (SPG and a water-soluble β-(1→3, 1→6-glucan from Aureobasidium pullulans. Data include analyzed the 2D NMR spectra of these β-glucans, which are related to the subject of an article in Carbohydrate Polymers, entitled “NMR spectroscopic structural characterization of a water-soluble β-(1→3, 1→6-glucan from A. pullulans” (Kono et al., 2017 [1]. Data can help to assign the 1H and 13C chemical shifts of the structurally complex polysaccharides. Keywords: NMR, β-(1→3, 1→6-glucan, Aureobasidium pullulans, Schizophyllan, Spectral data

Two-dimensional NMR spectroscopy: correlated, homonuclear-correlated, and nuclear Overhauser spectroscopy. January 1975-December 1988 (Citations from the INSPEC: Information Services for the Physics and Engineering Communities data base). Report for January 1975-December 1988

International Nuclear Information System (INIS)

1988-12-01

This bibliography contains citations concerning the enhanced analytical techniques of two-dimensional nuclear magnetic resonance (2-D NMR). Applications to specific molecules, biomolecules, and compounds as well as comparisons of three 2-D NMR techniques: correlated spectroscopy (COSY), nuclear Overhauser (NOSEY), and homonuclear-correlated spectroscopy (HOMCOR). (Contains 190 citations fully indexed and including a title list.)

Complete 1H and 13C NMR assignments and anti fungal activity of two 8-hydroxy flavonoids in mixture

International Nuclear Information System (INIS)

Johann, Susana; Smania Junior, Artur; Branco, Alexsandro

2007-01-01

A mixture of the two new flavonols 8-hydroxy-3, 4', 5, 6, 7-pentamethoxyflavone (1) and 8-hydroxy-3, 3', 4', 5, 6, 7-hexamethoxyflavone (2) was isolated from a commercial sample of Citrus aurantifolia. An array of one- ( 1 H NMR, { 1 H} -13 C NMR, and APT -13 C NMR) and two-dimensional NMR techniques (COSY, NOESY, HMQC and HMBC) was used to achieve the structural elucidation and the complete 1 H and 13 C chemical shift assignments of these natural compounds. In addition, the antifungal activity of these compounds against phytopathogenic and human pathogenic fungi was investigated. (author)

CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis

International Nuclear Information System (INIS)

Skinner, Simon P.; Fogh, Rasmus H.; Boucher, Wayne; Ragan, Timothy J.; Mureddu, Luca G.; Vuister, Geerten W.

2016-01-01

NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads http://www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.

CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis

Energy Technology Data Exchange (ETDEWEB)

Skinner, Simon P.; Fogh, Rasmus H. [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom); Boucher, Wayne [University of Cambridge, Department of Biochemistry (United Kingdom); Ragan, Timothy J.; Mureddu, Luca G.; Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom)

2016-10-15

NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads http://www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.

Fourier transform and its application to 1D and 2D NMR

International Nuclear Information System (INIS)

Canet, D.

1988-01-01

In this review article, the following points are developed: Pulsed NMR and Fourier transform; Fourier transform and two-dimensional spectroscopy; Mathematical properties of Fourier transform; Fourier transform of a sine function- one dimensional NMR; Fourier transform of a product of sine functions - two-dimensional NMR; Data manipulations in the time domain; Numerical Fourier transform [fr

Explorative data analysis of two-dimensional electrophoresis gels

DEFF Research Database (Denmark)

Schultz, J.; Gottlieb, D.M.; Petersen, Marianne Kjerstine

2004-01-01

of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine......Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening...... if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots...

Fundamentals of Protein NMR Spectroscopy

CERN Document Server

Rule, Gordon S

2006-01-01

NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data pr...

Linkage analysis by two-dimensional DNA typing

NARCIS (Netherlands)

te Meerman, G J; Mullaart, E; Meulen ,van der Martin; den Daas, J H; Morolli, B; Uitterlinden, A G; Vijg, J

1993-01-01

In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core

Cool-Climate Red Wines—Chemical Composition and Comparison of Two Protocols for 1H–NMR Analysis

Directory of Open Access Journals (Sweden)

Violetta Aru

2018-01-01

Full Text Available This study investigates the metabolome of 26 experimental cool-climate wines made from 22 grape varieties using two different protocols for wine analysis by proton nuclear magnetic resonance (1H–NMR spectroscopy. The wine samples were analyzed as-is (wet and as dried samples. The NMR datasets were preprocessed by alignment and mean centering. No normalization or scaling was performed. The “wet” method preserved the inherent properties of the samples and provided a fast and effective overview of the molecular composition of the wines. The “dried” method yielded a slightly better sensitivity towards a broader range of the compounds present in wines. A total of 27 metabolites including amino acids, organic acids, sugars, and alkaloids were identified in the 1H–NMR spectra of the wine samples. Principal component analysis was performed on both NMR datasets evidencing well-defined molecular fingerprints for ‘Baco Noir’, ‘Bolero’, ‘Cabernet Cantor’, ‘Cabernet Cortis’, ‘Don Muscat’, ‘Eszter’, ‘Golubok’, ‘New York Muscat’, ‘Regent’, ‘Rondo’, ‘Triomphe d’Alsace’, ‘Précose Noir’, and ‘Vinoslivy’ wines. Amongst the identified metabolites, lactic acid, succinic acid, acetic acid, gallic acid, glycerol, and methanol were found to drive sample groupings. The 1H–NMR data was compared to the absolute concentration values obtained from a reference Fourier transform infrared method, evidencing a high correlation.

Sequence-specific 1H NMR assignments and secondary structure of the Arc repressor of bacteriophage P22, as determined by two-dimensional 1H NMR spectroscopy

International Nuclear Information System (INIS)

Breg, J.N.; Boelens, R.; George, A.V.E.; Kaptein, R.

1989-01-01

The Arc repressor of bacteriophage P22 is a DNA binding protein that does not belong to any of the known classes of such proteins. The authors have undertaken a 1 H NMR study of the protein with the aim of elucidating its three-dimensional structure in solution and its mode of binding of operator DNA. Here the authors present the 1 H nuclear magnetic resonance (NMR) assignments of all backbone protons an most of the side-chain protons of Arc repressor. Elements of secondary structure have been identified on the basis of networks of characteristics sequential and medium-range nuclear Overhauser enhancements (NOEs). Two α-helical regions have been found in the peptide regions 16-29 and 35-45. The ends of the helices could not yet be firmly established and could extend to residue 31 for the first helix and to residue 49 for the second. Immediately before the first helix, between residues 8 and 14, a region is present with β-sheet characteristics dominated by a close proximity of the α-protons of residues 9 and 13. Because of the dimeric nature of the protein there are still two possible ways in which the NOEs in the β-sheet region can be interpreted. While the data presently do not allow an unambiguous choice between these two possibilities, some evidence is discussed that favors the latter (β-sheet between monomers). Since the N-terminal region of Arc is responsible for the sequence-specific recognition of its operator, the findings suggest the existence of a DNA binding motif in which a β-sheet region is present

Analysis of Two-Dimensional Electrophoresis Gel Images

DEFF Research Database (Denmark)

Pedersen, Lars

2002-01-01

This thesis describes and proposes solutions to some of the currently most important problems in pattern recognition and image analysis of two-dimensional gel electrophoresis (2DGE) images. 2DGE is the leading technique to separate individual proteins in biological samples with many biological...

Selective sensitivity enhancement in FT-NMR

International Nuclear Information System (INIS)

Farrar, T.C.

1987-01-01

In this article the basic two-spin nuclear magnetic resonance (NMR) experiment and the new sensitivity enhancement experiments are reviewed. In part two of this two-part series an overview of two-dimensional NMR experiments will be presented. Part two will appear in the June 1 issue of Analytical Chemistry

Two-dimensional errors

International Nuclear Information System (INIS)

Anon.

1991-01-01

This chapter addresses the extension of previous work in one-dimensional (linear) error theory to two-dimensional error analysis. The topics of the chapter include the definition of two-dimensional error, the probability ellipse, the probability circle, elliptical (circular) error evaluation, the application to position accuracy, and the use of control systems (points) in measurements

On the Analytical Superiority of 1D NMR for Fingerprinting the Higher Order Structure of Protein Therapeutics Compared to Multidimensional NMR Methods.

Science.gov (United States)

Poppe, Leszek; Jordan, John B; Rogers, Gary; Schnier, Paul D

2015-06-02

An important aspect in the analytical characterization of protein therapeutics is the comprehensive characterization of higher order structure (HOS). Nuclear magnetic resonance (NMR) is arguably the most sensitive method for fingerprinting HOS of a protein in solution. Traditionally, (1)H-(15)N or (1)H-(13)C correlation spectra are used as a "structural fingerprint" of HOS. Here, we demonstrate that protein fingerprint by line shape enhancement (PROFILE), a 1D (1)H NMR spectroscopy fingerprinting approach, is superior to traditional two-dimensional methods using monoclonal antibody samples and a heavily glycosylated protein therapeutic (Epoetin Alfa). PROFILE generates a high resolution structural fingerprint of a therapeutic protein in a fraction of the time required for a 2D NMR experiment. The cross-correlation analysis of PROFILE spectra allows one to distinguish contributions from HOS vs protein heterogeneity, which is difficult to accomplish by 2D NMR. We demonstrate that the major analytical limitation of two-dimensional methods is poor selectivity, which renders these approaches problematic for the purpose of fingerprinting large biological macromolecules.

Dosage Effects of Salt and pH Stresses on Saccharomyces cerevisiae as Monitored via Metabolites by Using Two Dimensional NMR Spectroscopy

International Nuclear Information System (INIS)

Chae, Young Kee; Kim, Seol Hyun; Ellinger, James E.; Markley, John L.

2013-01-01

Saccharomyces cerevisiae, which is a common species of yeast, is by far the most extensively studied model of a eukaryote because although it is one of the simplest eukaryotes, its basic cellular processes resemble those of higher organisms. In addition, yeast is a commercially valuable organism for ethanol production. Since the yeast data can be extrapolated to the important aspects of higher organisms, many researchers have studied yeast metabolism under various conditions. In this report, we analyzed and compared metabolites of Saccharomyces cerevisiae under salt and pH stresses of various strengths by using two-dimensional NMR spectroscopy. A total of 31 metabolites were identified for most of the samples. The levels of many identified metabolites showed gradual or drastic increases or decreases depending on the severity of the stresses involved. The statistical analysis produced a holistic outline: pH stresses were clustered together, but salt stresses were spread out depending on the severity. This work could provide a link between the metabolite profiles and mRNA or protein profiles under representative and well studied stress conditions

Two-dimensional NMR spectroscopy as a tool to link soil organic matter composition to ecosystem processes

Science.gov (United States)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Schleucher, Jürgen

2014-05-01

Environmental factors (e.g. temperature and moisture) and the size and composition of soil microbial populations are often considered the main drivers of soil organic matter (SOM) mineralization. Less consideration is given to the role of SOM as a substrate for microbial metabolism and the importance of the organo-chemical composition of SOM on decomposition. In addition, a fraction of the SOM is often considered as recalcitrant to mineralization leading to accumulation of SOM. However, recently the concept of intrinsic recalcitrance of SOM to mineralization has been questioned. The challenge in investigating the role of SOM composition on its mineralization to a large extent stems from the difficulties in obtaining high resolution characterization of a very complex matrix. 13C nuclear magnetic resonance (NMR) spectroscopy is a widely used tool to characterize SOM. However, SOM is a very complex mixture and in the resulting 13C NMR spectra, the identified functional groups may represent different molecular fragments that appear in the same spectral region leading to broad peaks. These overlaps defy attempts to identify molecular moieties, and this makes it impossible to derive information at a resolution needed for evaluating e.g. recalcitrance of SOM. Here we applied a method, developed in wood science for the pulp paper industry, to achieve a better characterization of SOM. We directly dissolved finely ground organic layers of boreal forest floors-litters, fibric and humic horizons of both coniferous and broadleaved stands-in dimethyl sulfoxide and analyzed the resulting solution with a two-dimensional (2D) 1H-13C NMR experiment. We will discuss methodological aspects related to the ability to identify and quantify individual molecular moieties in SOM. We will demonstrate how the spectra resolve signals of CH groups in a 2D plane determined by the 13C and 1H chemical shifts, thereby vastly increasing the resolving power and information content of NMR spectra. The

A global analysis of NMR distance constraints from the PDB

International Nuclear Information System (INIS)

Vranken, Wim

2007-01-01

Information obtained from Nuclear Magnetic Resonance (NMR) experiments is encoded as a set of constraint lists when calculating three-dimensional structures for a protein. With the amount of constraint data from the world wide Protein Data Bank (wwPDB) that is now available, it is possible to do a global, large-scale analysis using only information from the constraints, without taking the coordinate information into account. This article describes such an analysis of distance constraints from NOE data based on a set of 1834 NMR PDB entries containing 1909 protein chains. In order to best represent the quality and extent of the data that is currently deposited at the wwPDB, only the original data as deposited by the authors was used, and no attempt was made to 'clean up' and further interpret this information. Because the constraint lists provide a single set of data, and not an ensemble of structural solutions, they are easier to analyse and provide a reduced form of structural information that is relevant for NMR analysis only. The online resource resulting from this analysis makes it possible to check, for example, how often a particular contact occurs when assigning NOESY spectra, or to find out whether a particular sequence fragment is likely to be difficult to assign. In this respect it formalises information that scientists with experience in spectrum analysis are aware of but cannot necessarily quantify. The analysis described here illustrates the importance of depositing constraints (and all other possible NMR derived information) along with the structure coordinates, as this type of information can greatly assist the NMR community

Functional Groups Determine Biochar Properties (pH and EC as Studied by Two-Dimensional (13C NMR Correlation Spectroscopy.

Directory of Open Access Journals (Sweden)

Xiaoming Li

Full Text Available While the properties of biochar are closely related to its functional groups, it is unclear under what conditions biochar develops its properties. In this study, two-dimensional (2D (13C nuclear magnetic resonance (NMR correlation spectroscopy was for the first time applied to investigate the development of functional groups and establish their relationship with biochar properties. The results showed that the agricultural biomass carbonized to biochars was a dehydroxylation/dehydrogenation and aromatization process, mainly involving the cleavage of O-alkylated carbons and anomeric O-C-O carbons in addition to the production of fused-ring aromatic structures and aromatic C-O groups. With increasing charring temperature, the mass cleavage of O-alkylated groups and anomeric O-C-O carbons occurred prior to the production of fused-ring aromatic structures. The regression analysis between functional groups and biochar properties (pH and electrical conductivity further demonstrated that the pH and electrical conductivity of rice straw derived biochars were mainly determined by fused-ring aromatic structures and anomeric O-C-O carbons, but the pH of rice bran derived biochars was determined by both fused-ring aromatic structures and aliphatic O-alkylated (HCOH carbons. In summary, this work suggests a novel tool for characterising the development of functional groups in biochars.

A scaling analysis of electronic localization in two-dimensional random media

International Nuclear Information System (INIS)

Ye Zhen

2003-01-01

By an improved scaling analysis, we suggest that there may appear two possibilities concerning the electronic localization in two-dimensional random media. The first is that all electronic states are localized in two dimensions, as conjectured previously. The second possibility is that electronic behaviors in two- and three-dimensional random systems are similar, in agreement with a recent calculation based on a direct calculation of the conductance with the use of the Kubo formula. In this case, non-localized states are possible in two dimensions, and have some peculiar properties. A few predictions are proposed. Moreover, the present analysis accommodates results from the previous scaling analysis

Two-dimensional 1H NMR experiments show that the 23-residue magain in antibiotic peptide is an α-helix in dodecylphosphocholine micelles, sodium dodecylsulfate micelles, and trifluoroethanol/water solution

International Nuclear Information System (INIS)

Gesell, Jennifer; Zasloff, Michael; Opella, Stanley J.

1997-01-01

Magainin2 is a 23-residue antibiotic peptide that disrupts the ionic gradient across certain cell membranes. Two-dimensional 1H NMR spectroscopy was used to investigate the structure of the peptide in three of the membrane environments most commonly employed in biophysical studies. Sequence-specific resonance assignments were determined for the peptide in perdeuterated dodecylphosphocholine (DPC) and sodium dodecylsulfate micelles and confirmed for the peptide in 2,2,2-trifluoroethanol solution. The secondary structure is shown to be helical in all of the solvent systems. The NMR data were used as a set of restraints for a simulated annealing protocol that generated a family of three-dimensional structures of the peptide in DPC micelles, which superimposed best between residues 4 and 20. For these residues, the mean pairwise rms difference for the backbone atoms is 0.47 ± 0.10A from the average structure. The calculated peptide structures appear to be curved,with the bend centered at residues Phe12 and Gly13

On low-dimensional models at NMR line shape analysis in nanomaterial systems

Science.gov (United States)

Kucherov, M. M.; Falaleev, O. V.

2018-03-01

We present a model of localized spin dynamics at room temperature for the low-dimensional solid-state spin system, which contains small ensembles of magnetic nuclei (N ~ 40). The standard spin Hamiltonian (XXZ model) is the sum of the Zeeman term in a strong external magnetic field and the magnetic dipole interaction secular term. The 19F spins in a single crystal of fluorapatite [Ca5(PO4)3F] have often been used to approximate a one-dimensional spin system. If the constant external field is parallel to the c axis, the 3D 19F system may be treated as a collection of many identical spin chains. When considering the longitudinal part of the secular term, we suggest that transverse component of a spin in a certain site rotates in a constant local magnetic field. This field changes if the spin jumps to another site. On return, this spin continues to rotate in the former field. Then we expand the density matrix in a set of eigenoperators of the Zeeman Hamiltonian. A system of coupled differential equations for the expansion coefficients then solved by straightforward numerical methods, and the fluorine NMR line shapes of fluorapatite for different chain lengths are calculated.

Assignment strategies in homonuclear three-dimensional 1H NMR spectra of proteins

International Nuclear Information System (INIS)

Vuister, G.W.; Boelens, R.; Padilla, A.; Kleywegt, G.J.; Kaptein, R.

1990-01-01

The increase in dimensionality of three-dimensional (3D) NMR greatly enhances the spectral resolution in comparison to 2D NMR. It alleviates the problem of resonance overlap and may extend the range of molecules amenable to structure determination by high-resolution NMR spectroscopy. Here, the authors present strategies for the assignment of protein resonances from homonuclear nonselective 3D NOE-HOHAHA spectra. A notation for connectivities between protons, corresponding to cross peaks in 3D spectra, is introduced. They show how spin systems can be identified by tracing cross-peak patterns in cross sections perpendicular to the three frequency axes. The observable 3D sequential connectivities in proteins are tabulated, and estimates for the relative intensities of the corresponding cross peaks are given for α-helical and β-sheet conformations. Intensities of the cross peaks in the 3D spectrum of pike III paravalbumin follow the predictions. The sequential-assignment procedure is illustrated for loop regions, extended and α-helical conformations for the residues Ala 54-Leu 63 of paravalbumin. NOEs that were not previously identified in 2D spectra of paravalbumin due to overlap are found

Impact of comprehensive two-dimensional gas chromatography with mass spectrometry on food analysis.

Science.gov (United States)

Tranchida, Peter Q; Purcaro, Giorgia; Maimone, Mariarosa; Mondello, Luigi

2016-01-01

Comprehensive two-dimensional gas chromatography with mass spectrometry has been on the separation-science scene for about 15 years. This three-dimensional method has made a great positive impact on various fields of research, and among these that related to food analysis is certainly at the forefront. The present critical review is based on the use of comprehensive two-dimensional gas chromatography with mass spectrometry in the untargeted (general qualitative profiling and fingerprinting) and targeted analysis of food volatiles; attention is focused not only on its potential in such applications, but also on how recent advances in comprehensive two-dimensional gas chromatography with mass spectrometry will potentially be important for food analysis. Additionally, emphasis is devoted to the many instances in which straightforward gas chromatography with mass spectrometry is a sufficiently-powerful analytical tool. Finally, possible future scenarios in the comprehensive two-dimensional gas chromatography with mass spectrometry food analysis field are discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Filtering techniques for efficient inversion of two-dimensional Nuclear Magnetic Resonance data

Science.gov (United States)

Bortolotti, V.; Brizi, L.; Fantazzini, P.; Landi, G.; Zama, F.

2017-10-01

The inversion of two-dimensional Nuclear Magnetic Resonance (NMR) data requires the solution of a first kind Fredholm integral equation with a two-dimensional tensor product kernel and lower bound constraints. For the solution of this ill-posed inverse problem, the recently presented 2DUPEN algorithm [V. Bortolotti et al., Inverse Problems, 33(1), 2016] uses multiparameter Tikhonov regularization with automatic choice of the regularization parameters. In this work, I2DUPEN, an improved version of 2DUPEN that implements Mean Windowing and Singular Value Decomposition filters, is deeply tested. The reconstruction problem with filtered data is formulated as a compressed weighted least squares problem with multi-parameter Tikhonov regularization. Results on synthetic and real 2D NMR data are presented with the main purpose to deeper analyze the separate and combined effects of these filtering techniques on the reconstructed 2D distribution.

Complete resonance assignment for the polypeptide backbone of interleukin 1β using three-dimensional heteronuclear NMR spectroscopy

International Nuclear Information System (INIS)

Driscoll, P.C.; Clore, G.M.; Marion, D.; Gronenborn, A.M.; Wingfield, P.T.

1990-01-01

The complete sequence-specific assignment of the 15 N and 1 H backbone resonances of the NMR spectrum of recombinant human interleukin 1β has been obtained by using primarily 15 N- 1 H heteronuclear three-dimensional (3D) NMR techniques in combination with 15 N- 1 H heteronuclear and 1 H homonuclear two-dimensional NMR. The fingerprint region of the spectrum was analyzed by using a combination of 3D heteronuclear 1 H Hartmann-Hahn 15 N- 1 H multiple quantum coherence (3D HOHAHA-HMQC) and 3D heteronuclear 1 H nuclear Overhauser 15 N- 1 H multiple quantum coherence (3D NOESY-HMQC) spectroscopies. The authors show that the problems of amide NH and C α H chemical shift degeneracy that are prevalent for proteins of the size are readily overcome by using the 3D heteronuclear NMR technique. A doubling of some peaks in the spectrum was found to be due to N-terminal heterogeneity of the 15 N-labeled protein, corresponding to a mixture of wild-type and des-Ala-1-interleukin 1β. The complete list of 15 N and 1 H assignments is given for all the amide NH and C α H resonances of all non-proline residues, as well as the 1 H assignments for some of the amino acid side chains. This first example of the sequence-specific assignment of a protein using heteronuclear 3D NMR provides a basis for further conformational and dynamic studies of interleukin 1β

2D NMR studies of biomolecules

International Nuclear Information System (INIS)

Lamerichs, R.M.J.N.

1989-01-01

The work described in this thesis comprises two related subjects. The first part describes methods to derive high-resolution structures of proteins in solution using two-dimensional (2-D) NMR. The second part describes 2-D NMR studies on the interaction between proteins and DNA. (author). 261 refs.; 52 figs.; 23 tabs

Visualization of velocity field and phase distribution in gas-liquid two-phase flow by NMR imaging

International Nuclear Information System (INIS)

Matsui, G.; Monji, H.; Obata, J.

2004-01-01

NMR imaging has been applied in the field of fluid mechanics, mainly single phase flow, to visualize the instantaneous flow velocity field. In the present study, NMR imaging was used to visualize simultaneously both the instantaneous phase structure and velocity field of gas-liquid two-phase flow. Two methods of NMR imaging were applied. One is useful to visualize both the one component of liquid velocity and the phase distribution. This method was applied to horizontal two-phase flow and a bubble rising in stagnant oil. It was successful in obtaining some pictures of velocity field and phase distribution on the cross section of the pipe. The other is used to visualize a two-dimensional velocity field. This method was applied to a bubble rising in a stagnant water. The velocity field was visualized after and before the passage of a bubble at the measuring cross section. Furthermore, the distribution of liquid velocity was obtained. (author)

Two-dimensional gel electrophoresis analysis of different parts of ...

African Journals Online (AJOL)

Two-dimensional gel electrophoresis analysis of different parts of Panax quinquefolius L. root. ... From these results it was concluded that proteomic analysis method was an effective way to identify the different parts of quinquefolius L. root. These findings may contribute to further understanding of the physiological ...

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

International Nuclear Information System (INIS)

Zuiderweg, E.R.P.; Fesik, S.W.

1989-01-01

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of 1 H and 15 N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with 15 N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the 15 N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that 15 N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

Energy Technology Data Exchange (ETDEWEB)

Zuiderweg, E.R.P.; Fesik, S.W. (Abbott Laboratories, Abbott Park, IL (USA))

1989-03-21

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of {sup 1}H and {sup 15}N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with {sup 15}N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the {sup 15}N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that {sup 15}N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques.

Two-dimensional analysis of trapped-ion eigenmodes

International Nuclear Information System (INIS)

Marchand, R.; Tang, W.M.; Rewoldt, G.

1979-11-01

A fully two-dimensional eigenmode analysis of the trapped-ion instability in axisymmetric toroidal geometry is presented. The calculations also takes into account the basic dynamics associated with other low frequency modes such as the trapped-electron instability and the ion-temperature-gradient instability. The poloidal structure of the mode is taken into account by Fourier expanding the perturbed electrostatic potential, PHI, in theta

Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III

Energy Technology Data Exchange (ETDEWEB)

Krisnamoorthi, R.; Yuxi Gong; Chanlan Sun Lin (Kansas State Univ., Manhattan (United States)); VanderVelde, D. (Univ. of Kansas, Lawrence (United States))

1992-01-28

The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific {sup 1}H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns, a 3{sub 10}-helix, and a triple-stranded {beta}-sheet. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. These chemical shift changes were relatively small compared to changes that occurred upon hydrolysis of the reactive-site peptide bond between Arg 5 and Ile6 in CMTI-III.

Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis

Directory of Open Access Journals (Sweden)

Qu Lijia

2009-03-01

Full Text Available Abstract Background Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public. Results In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion, data reduction (PCA, LDA, ULDA, unsupervised clustering (K-Mean and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM. Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile. Conclusion Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases

Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.

Science.gov (United States)

Wang, Tao; Shao, Kang; Chu, Qinying; Ren, Yanfei; Mu, Yiming; Qu, Lijia; He, Jie; Jin, Changwen; Xia, Bin

2009-03-16

Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public. In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion), data reduction (PCA, LDA, ULDA), unsupervised clustering (K-Mean) and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM). Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile. Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases. Moreover, with its open source architecture, interested

Complete {sup 1}H and {sup 13}C NMR assignments and anti fungal activity of two 8-hydroxy flavonoids in mixture

Energy Technology Data Exchange (ETDEWEB)

Johann, Susana; Smania Junior, Artur [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Dept. de Microbiologia e Parasitologia. Lab. de Antibioticos; Pizzolatti, Moacir G. [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Dept. de Quimica; Schripsema, Jan; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacazes, RJ (Brazil). Setor de Quimica de Produtos Naturais. Lab. de Quimica e Funcao de Proteinas e Peptideos (LQFPP); Branco, Alexsandro [Universidade Estadual de Feira de Santana, BA (Brazil). Dept. de Saude. Lab. de Fitoquimica]. E-mail: branco@uefs.br

2007-06-15

A mixture of the two new flavonols 8-hydroxy-3, 4', 5, 6, 7-pentamethoxyflavone (1) and 8-hydroxy-3, 3', 4', 5, 6, 7-hexamethoxyflavone (2) was isolated from a commercial sample of Citrus aurantifolia. An array of one- ({sup 1}H NMR, {l_brace}{sup 1}H{r_brace} {sup -13}C NMR, and APT{sup -13}C NMR) and two-dimensional NMR techniques (COSY, NOESY, HMQC and HMBC) was used to achieve the structural elucidation and the complete {sup 1}H and {sup 13}C chemical shift assignments of these natural compounds. In addition, the antifungal activity of these compounds against phytopathogenic and human pathogenic fungi was investigated. (author)

Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and "hidden" dimensions.

Science.gov (United States)

Meng, Xi; Nguyen, Bao D; Ridge, Clark; Shaka, A J

2009-01-01

High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to "reduced-dimensionality" strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the filter diagonalization method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra-dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths.

Structure of the two-dimensional relaxation spectra seen within the eigenmode perturbation theory and the two-site exchange model.

Science.gov (United States)

Bytchenkoff, Dimitri; Rodts, Stéphane

2011-01-01

The form of the two-dimensional (2D) NMR-relaxation spectra--which allow to study interstitial fluid dynamics in diffusive systems by correlating spin-lattice (T(1)) and spin-spin (T(2)) relaxation times--has given rise to numerous conjectures. Herein we find analytically a number of fundamental structural properties of the spectra: within the eigen-modes formalism, we establish relationships between the signs and intensities of the diagonal and cross-peaks in spectra obtained by various 1 and 2D NMR-relaxation techniques, reveal symmetries of the spectra and uncover interdependence between them. We investigate more specifically a practically important case of porous system that has sets of T(1)- and T(2)-eigenmodes and eigentimes similar to each other by applying the perturbation theory. Furthermore we provide a comparative analysis of the application of the, mathematically more rigorous, eigen-modes formalism and the, rather more phenomenological, first-order two-site exchange model to diffusive systems. Finally we put the results that we could formulate analytically to the test by comparing them with computer-simulations for 2D porous model systems. The structural properties, in general, are to provide useful clues for assignment and analysis of relaxation spectra. The most striking of them--the presence of negative peaks--underlines an urgent need for improvement of the current 2D Inverse Laplace Transform (ILT) algorithm used for calculation of relaxation spectra from NMR raw data. Copyright © 2010 Elsevier Inc. All rights reserved.

Comparison of two three-dimensional cephalometric analysis computer software.

Science.gov (United States)

Sawchuk, Dena; Alhadlaq, Adel; Alkhadra, Thamer; Carlyle, Terry D; Kusnoto, Budi; El-Bialy, Tarek

2014-10-01

Three-dimensional cephalometric analyses are getting more attraction in orthodontics. The aim of this study was to compare two softwares to evaluate three-dimensional cephalometric analyses of orthodontic treatment outcomes. Twenty cone beam computed tomography images were obtained using i-CAT(®) imaging system from patient's records as part of their regular orthodontic records. The images were analyzed using InVivoDental5.0 (Anatomage Inc.) and 3DCeph™ (University of Illinois at Chicago, Chicago, IL, USA) software. Before and after orthodontic treatments data were analyzed using t-test. Reliability test using interclass correlation coefficient was stronger for InVivoDental5.0 (0.83-0.98) compared with 3DCeph™ (0.51-0.90). Paired t-test comparison of the two softwares shows no statistical significant difference in the measurements made in the two softwares. InVivoDental5.0 measurements are more reproducible and user friendly when compared to 3DCeph™. No statistical difference between the two softwares in linear or angular measurements. 3DCeph™ is more time-consuming in performing three-dimensional analysis compared with InVivoDental5.0.

Determination of structure of oriented samples using two-dimensional solid state NMR techniques

International Nuclear Information System (INIS)

Jin Hong; Harbison, G.S.

1990-01-01

One dimensional and two-dimensional MAS techniques can give detailed information about the structure and dynamics of oriented systems. We describe the application of such techniques to the liquid-crystalline polymer poly(p-phenyleneterphtalimide) (PPTA), and thence deduce the solid-state structure of the material. (author). 9 refs.; 6 figs

Comparative analysis of peak-detection techniques for comprehensive two-dimensional chromatography.

Science.gov (United States)

Latha, Indu; Reichenbach, Stephen E; Tao, Qingping

2011-09-23

Comprehensive two-dimensional gas chromatography (GC×GC) is a powerful technology for separating complex samples. The typical goal of GC×GC peak detection is to aggregate data points of analyte peaks based on their retention times and intensities. Two techniques commonly used for two-dimensional peak detection are the two-step algorithm and the watershed algorithm. A recent study [4] compared the performance of the two-step and watershed algorithms for GC×GC data with retention-time shifts in the second-column separations. In that analysis, the peak retention-time shifts were corrected while applying the two-step algorithm but the watershed algorithm was applied without shift correction. The results indicated that the watershed algorithm has a higher probability of erroneously splitting a single two-dimensional peak than the two-step approach. This paper reconsiders the analysis by comparing peak-detection performance for resolved peaks after correcting retention-time shifts for both the two-step and watershed algorithms. Simulations with wide-ranging conditions indicate that when shift correction is employed with both algorithms, the watershed algorithm detects resolved peaks with greater accuracy than the two-step method. Copyright © 2011 Elsevier B.V. All rights reserved.

Two-dimensional analysis of motion artifacts, including flow effects

International Nuclear Information System (INIS)

Litt, A.M.; Brody, A.S.; Spangler, R.A.; Scott, P.D.

1990-01-01

The effects of motion on magnetic resonance images have been theoretically analyzed for the case of a point-like object in simple harmonic motion and for other one-dimensional trajectories. The authors of this paper extend this analysis to a generalized two-dimensional magnetization with an arbitrary motion trajectory. The authors provide specific solutions for the clinically relevant cases of the cross-sections of cylindrical objects in the body, such as the aorta, which has a roughly one-dimensional, simple harmonic motion during respiration. By extending the solution to include inhomogeneous magnetizations, the authors present a model which allows the effects of motion artifacts and flow artifacts to be analyzed simultaneously

NMRKIN: Simulating line shapes from two-dimensional spectra of proteins upon ligand binding

International Nuclear Information System (INIS)

Guenther, Ulrich L.; Schaffhausen, Brian

2002-01-01

The analysis of the shape of signals in NMR spectra is a powerful tool to study exchange and reaction kinetics. Line shapes in two-dimensional spectra of proteins recorded for titrations with ligands provide information about binding rates observed at individual residues. Here we describe a fast method to simulate a series of line shapes derived from two-dimensional spectra of a protein during a ligand titration. This procedure, which takes the mutual effects of two dimensions into account, has been implemented in MATLAB as an add-on to NMRLab (Guenther et al., 2000). In addition, more complex kinetic models, including sequential and parallel reactions, were simulated to demonstrate common features of more complex line shapes which could be encountered in protein-ligand interactions. As an example of this method, we describe its application to line shapes obtained for a titration of the p85 N-SH2 domain of PI3-kinase with a peptide derived from polyomavirus middle T antigen (MT)

Search for a nematic phase in the quasi-two-dimensional antiferromagnet CuCrO2 by NMR in an electric field

Science.gov (United States)

Sakhratov, Yu. A.; Kweon, J. J.; Choi, E. S.; Zhou, H. D.; Svistov, L. E.; Reyes, A. P.

2018-03-01

The magnetic phase diagram of CuCrO2 was studied with an alternative method of simultaneous Cu NMR and electric polarization techniques with the primary goal of demonstrating that, regardless of cooling history of the sample, the magnetic phase with specific helmet-shaped NMR spectra associated with interplanar disorder possesses electric polarization. Our result unequivocally confirms the assumption of Sakhratov et al. [Phys. Rev. B 94, 094410 (2016), 10.1103/PhysRevB.94.094410] that the high-field low-temperature phase is in fact a three-dimensional (3D) polar phase characterized by a 3D magnetic order with tensor order parameter. In comparison with the results obtained in pulsed fields, a modified phase diagram is introduced defining the upper boundary of the first-order transition from the 3D spiral to the 3D polar phase.

Two-dimensional cross-section sensitivity and uncertainty analysis for fusion reactor blankets

International Nuclear Information System (INIS)

Embrechts, M.J.

1982-02-01

A two-dimensional sensitivity and uncertainty analysis for the heating of the TF coil for the FED (fusion engineering device) blanket was performed. The uncertainties calculated are of the same order of magnitude as those resulting from a one-dimensional analysis. The largest uncertainties were caused by the cross section uncertainties for chromium

On two flexible methods of 2-dimensional regression analysis

Czech Academy of Sciences Publication Activity Database

Volf, Petr

2012-01-01

Roč. 18, č. 4 (2012), s. 154-164 ISSN 1803-9782 Grant - others:GA ČR(CZ) GAP209/10/2045 Institutional support: RVO:67985556 Keywords : regression analysis * Gordon surface * prediction error * projection pursuit Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2013/SI/volf-on two flexible methods of 2-dimensional regression analysis.pdf

Structural consequences of the natural substitution, E9K, on reactive-site-hydrolyzed squash (Cucurbita maxima) trypsin inhibitor (CMTI), as studied by two-dimensional NMR.

Science.gov (United States)

Krishnamoorthi, R; Lin, C L; VanderVelde, D

1992-06-02

Sequence-specific hydrogen-1 NMR assignments were made to all of the 29 amino acid residues of reactive-site-hydrolyzed Cucurbita maxima trypsin inhibitor I (CMTI-I*) by the application of two-dimensional NMR (2D NMR) techniques, and its secondary structural elements (two tight turns, a 3(10)-helix, and a triple-stranded beta-sheet) were identified on the basis of short-range NOESY cross peaks and deuterium-exchange kinetics. These secondary structural elements are present in the intact inhibitor [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648] and are unaffected by the hydrolysis of the reactive-site peptide bond between Arg5 and Ile6, in accordance with the earlier conclusion reached for CMTI-III* [Krishnamoorthi, R., Gong, Y.-X., Lin, C. S., & VanderVelde, D. (1992) Biochemistry 31, 898-904]. Chemical shifts of backbone hydrogen atoms, peptide NH's, and C alpha H's, of CMTI-I* were compared with those of the intact inhibitor, CMTI-I, and of the reactive-site-hydrolyzed, natural, E9K variant, CMTI-III*. Cleavage of the Arg5-Ile6 peptide bond resulted in changes of chemical shifts of most of the backbone atoms of CMTI-I, in agreement with the earlier results obtained for CMTI-III. Comparison of chemical shifts of backbone hydrogen atoms of CMTI-I* and CMTI-III* revealed no changes, except for residues Glu9 and His25. However, the intact forms of the same two proteins, CMTI-I and CMTI-III, showed small but significant perturbations of chemical shifts of residues that made up the secondary structural elements of the inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)

Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

KAUST Repository

Cannistraci, Carlo Vittorio

2015-01-26

Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet\\'s performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.

Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

KAUST Repository

Cannistraci, Carlo Vittorio; Abbas, Ahmed; Gao, Xin

2015-01-01

Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet's performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.

Two-dimensional horizontal model seismic test and analysis for HTGR core

International Nuclear Information System (INIS)

Ikushima, Takeshi; Honma, Toshiaki.

1988-05-01

The resistance against earthquakes of high-temperature gas-cooled reactor (HTGR) core with block-type fuels is not fully ascertained yet. Seismic studies must be made if such a reactor plant is to be installed in areas with frequent earthquakes. The paper presented the test results of seismic behavior of a half scale two-dimensional horizontal slice core model and analysis. The following is a summary of the more important results. (1) When the core is subjected to the single axis excitation and simultaneous two-axis excitations to the core across-corners, it has elliptical motion. The core stays lumped motion at the low excitation frequencies. (2) When the load is placed on side fixed reflector blocks from outside to the core center, the core displacement and reflector impact reaction force decrease. (3) The maximum displacement occurs at simultaneous two-axis excitations. The maximum displacement occurs at the single axis excitation to the core across-flats. (4) The results of two-dimensional horizontal slice core model was compared with the results of two-dimensional vertical one. It is clarified that the seismic response of actual core can be predicted from the results of two-dimensional vertical slice core model. (5) The maximum reflector impact reaction force for seismic waves was below 60 percent of that for sinusoidal waves. (6) Vibration behavior and impact response are in good agreement between test and analysis. (author)

Two-Phase Extraction for Comprehensive Analysis of the Plant Metabolome by NMR.

Science.gov (United States)

Schripsema, Jan; Dagnino, Denise

2018-01-01

Metabolomics is the area of research, which strives to obtain complete metabolic fingerprints, to detect differences between them, and to provide hypothesis to explain those differences [1]. But obtaining complete metabolic fingerprints is not an easy task. Metabolite extraction is a key step during this process, and much research has been devoted to finding the best solvent mixture to extract as much metabolites as possible.Here a procedure is described for analysis of both polar and apolar metabolites using a two-phase extraction system. D 2 O and CDCl 3 are the solvents of choice, and their major advantage is that, for the identification of the compounds, standard databases can be used because D 2 O and CDCl 3 are the solvents most commonly used for pure compound NMR spectra. The procedure enables the absolute quantification of components via the addition of suitable internal standards. The extracts are also suitable for further analysis with other systems like LC-MS or GC-MS.

Complete 1H NMR assignments of pyrrolizidine alkaloids and a new eudesmanoid from Senecio polypodioides.

Science.gov (United States)

Villanueva-Cañongo, Claudia; Pérez-Hernández, Nury; Hernández-Carlos, Beatriz; Cedillo-Portugal, Ernestina; Joseph-Nathan, Pedro; Burgueño-Tapia, Eleuterio

2014-05-01

Chemical investigation of the aerial parts of Senecio polypodioides lead to the isolation of the new eudesmanoid 1β-angeloyloxyeudesm-7-ene-4β,9α-diol (1) and the known dirhamnosyl flavonoid lespidin (3), while from roots, the known 7β-angeloyloxy-1-methylene-8α-pyrrolizidine (5) and sarracine N-oxide (6), as well as the new neosarracine N-oxide (8), were obtained. The structure of 1 and 8 was elucidated by spectral means. Complete assignments of the (1)H NMR data for 5, 6, sarracine (7), and 8 were made using one-dimensional and two-dimensional NMR experiments and by application of the iterative full spin analysis of the PERCH NMR software. Copyright © 2014 John Wiley & Sons, Ltd.

Two- and three-dimensional CT analysis of ankle fractures

International Nuclear Information System (INIS)

Magid, D.; Fishman, E.K.; Ney, D.R.; Kuhlman, J.E.

1988-01-01

CT with coronal and sagittal reformatting (two-dimensional CT) and animated volumetric image rendering (three-dimensional CT) was used to assess ankle fractures. Partial volume limits transaxial CT in assessments of horizontally oriented structures. Two-dimensional CT, being orthogonal to the plafond, superior mortise, talar dome, and tibial epiphysis, often provides the most clinically useful images. Two-dimensional CT is most useful in characterizing potentially confusing fractures, such as Tillaux (anterior tubercle), triplane, osteochondral talar dome, or nondisplaced talar neck fractures, and it is the best study to confirm intraarticular fragments. Two-and three-dimensional CT best indicate the percentage of articular surface involvement and best demonstrate postoperative results or complications (hardware migration, residual step-off, delayed union, DJD, AVN, etc). Animated three-dimensional images are the preferred means of integrating the two-dimensional findings for surgical planning, as these images more closely simulate the clinical problem

Two-dimensional 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex and a quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex

International Nuclear Information System (INIS)

Powers, R.; Olsen, R.K.; Gorenstein, D.G.

1989-01-01

Assignment of the 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The 31P chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. While the 31P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine rules previously demonstrated. 31P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys3, MeCys7]TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small 31P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the 1H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a non-intercalative mode of association of the drug. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible

Applications of one-dimensional or two-dimensional nuclear magnetic resonance to the structural and conformational study of oligosaccharides. Design and adjustment of new techniques

International Nuclear Information System (INIS)

Berthault, Patrick

1988-01-01

Oligosaccharides are natural compounds of huge importance as they intervene in all metabolic processes of cell life. Before the determination of structure-activity relationships, a precise knowledge of their chemical nature is therefore required. Thus, this research thesis aims at describing various experiments of high resolution nuclear magnetic resonance (NMR), and at demonstrating their applications on four oligosaccharides. After a brief description of NMR principles by using a conventional description and also a formalism derived from quantum mechanics, the author outlines the weaknesses of old NMR techniques, and introduces new techniques by using scalar couplings, by processing magnetization transfers with one-dimensional hetero-nuclear experiments. General principles of two-dimensional experiments are then presented and developed in terms of simple correlations, multiple correlations, correlations via double quantum coherencies. Experiments with light water are then described, and different experiments are performed to determine the structure and conformation of each unit. Bipolar interactions are then addressed to highlight proximities between atoms [fr

Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis

Directory of Open Access Journals (Sweden)

Hsu Kimberly K

2005-06-01

Full Text Available Abstract Background The analysis of hydrophobic membrane proteins by two-dimensional gel electrophoresis has long been hampered by the concept of inherent difficulty due to solubility issues. We have optimized extraction protocols by varying the detergent composition of the solubilization buffer with a variety of commercially available non-ionic and zwitterionic detergents and detergent-like phospholipids. Results After initial analyses by one-dimensional SDS-PAGE, quantitative two-dimensional analyses of human erythrocyte membranes, mouse liver membranes, and mouse brain membranes, extracted with buffers that included the zwitterionic detergent MEGA 10 (decanoyl-N-methylglucamide and the zwitterionic lipid LPC (1-lauroyl lysophosphatidylcholine, showed selective improvement over extraction with the common 2-DE detergent CHAPS (3 [(3-cholamidopropyldimethylammonio]-1-propanesulfonate. Mixtures of the three detergents showed additive improvements in spot number, density, and resolution. Substantial improvements in the analysis of a brain membrane proteome were observed. Conclusion This study demonstrates that an optimized detergent mix, coupled with rigorous sample handling and electrophoretic protocols, enables simple and effective analysis of membrane proteomes using two-dimensional electrophoresis.

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

Science.gov (United States)

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. Copyright © 2014 John Wiley & Sons, Ltd.

Structure of the oligosaccharide of hen phosvitin as determined by two-dimensional 1H NMR of the intact glycoprotein

International Nuclear Information System (INIS)

Brockbank, R.L.; Vogel, H.J.

1990-01-01

The major form of the oligosaccharide of hen phosvitin was studied with two-dimensional 1 H NMR of the intact glycoprotein. Its structure was determined from an analysis of the chemical shifts of the structural reporter groups, and it was further confirmed by comparison to several related model oligosaccharides. The oligosaccharide is N-linked and is present in a 1:1 stoichiometry to the protein. It has a complex type 1 triantennary structure with two NeuAcα2,6Ga1β1,4G1cNAcβ1,2 arms linked to the Man-4 and Man-4' and a third Ga1β1,4G1cNAcβ1, 4 arm attached to the Man-4. the oligosaccharide contains the common core sequence which is present in all N-linked glycoproteins [Manα1,3(Manα1,6)Manβ1,4G1cNAcβ1,4G1cNAcβ1,N]. In the course of this study, we have found that unique spin systems for the G1cNAc and NeuAc are obtained for spectra recorded in 90% H 2 O. Their NH peaks were assigned at low pH, and these assignments proved useful for confirming the identify of cross-peaks in the anomeric region. In addition, the protons of G1cNAc-1 could be correlated to the NH of the asparagine link. The cross-peak patterns determined in phase-sensitive 2D experiments for the H1,H2 protons have a different appearance for each type of monosaccharide, and this information was also used for making first-order assignments. A comparison with model compounds suggests that the solution conformation of the oligosaccharide is not affected by its attachment to the protein

Analysis of the backbone dynamics of interleukin-1β using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy

International Nuclear Information System (INIS)

Clore, G.M.; Driscoll, P.C.; Wingfield, P.T.; Gronenborn, A.M.

1990-01-01

The backbone dynamics of uniformly 15 N-labeled interleukin-1β are investigated by using two-dimensional inverse detected heteronuclear 15 N- 1 H NMR spectroscopy. 15 N T 1 , T 2 , and NOE data at a spectrometer frequency of 600 MHz are obtained for 90% of the backbone amide groups. The data provide evidence for motions on three time scales. All the residues exhibit very fast motions on a time scale of approx-lt 20-50 ps that can be characterized by a single-order parameter with an average value of 0.82 ± 0.05. Thirty-two residues also display motions on a time scale of 0.5-4 ns, slightly less than the overall rotational correlation time of the protein (8.3 ns). While the simple formulation can account for the 15 N T 1 and T 2 data, it fails to account for the 15 N- 1 H NOE data and yields calculated values for the NOEs that are either too small or negative, whereas the observed NOEs are positive. Another 42 residues are characterized by some sort of motion on the 30-ns-10-ms time scale, which results in 15 N line broadening due to chemical exchange between different conformational substates with distinct 15 N chemical shifts. In general, the motions on both the 0.5-4-ns and 30-ns-10-ms time scales are localized in surface-accessible loops and turns connecting the β-strands, as well as at the beginning and end of strands. Finally, the kinetic and equilibrium properties of a slow conformational equilibrium between a major and a minor species, involving at least 19 residues and located on one contiguous face of the molecule, are characterized by using 1 H- 15 N correlation spectroscopy, 1 H- 15 N heteronuclear multiple quantum coherence-nuclear Overhauser enhancement spectroscopy, and 1 H- 1 H nuclear Overhauser enhancement spectroscopy

Three-dimensional structural analysis of the group B polysaccharide of Neisseria meningitidis 6275 by two-dimensional NMR: The polysaccharide is suggested to exist in helical conformations in solution

Energy Technology Data Exchange (ETDEWEB)

Yamasaki, Ryohei; Bacon, B. (Univ. of California, San Francisco (USA) Veterans Administration Medical Center, San Francisco, CA (USA))

1991-01-22

The solution conformations of the group B polysaccharide of Neisseria meningitidis were analyzed by DQF-COSY and pure absorption 2D NOE NMR with three mixing times. The pyranose ring of the sialic acid residue was found to be in the {sup 2}C{sub 5} conformation. The DQF-COSY analysis indicated that the orientations of H6 and H7 and of H7 and H8 are both gauche. In order to overcome the difficulties in analyzing the NOE data due to the two sets of proton overlaps, molecular modeling of {alpha}-2,8-linked sialic acid oligomers was carried out to investigate possible conformers, and theoretical NOE calculations were performed by using CORMA (complete relaxation matrix analysis). The analysis suggests that the polysaccharide adopts helical structures for which the {phi} (defined by O6-C2-O8-C8) and {psi} (C2-O8-C8-C7) angles are in the following ranges: {phi}-60 to 0{degree}, {psi} 115-175{degree} or {phi} 90-120{degree}, {psi}55-175{degree}. The weak affinity of anti-B antibodies for smaller {alpha}-2,8-linked oligosaccharides may be due to the fact that such oligomers are more flexible and may not form an ordered structure as the poly(sialic acid) does.

Two-dimensional imaging of Debye-Scherrer ring for tri-axial stress analysis of industrial materials

International Nuclear Information System (INIS)

Sasaki, T; Maruyama, Y; Ohba, H; Ejiri, S

2014-01-01

In this study, an application of the two-dimensional imaging technology to the X ray tri-axial stress analysis was studied. An image plate (IP) was used to obtain a Debye-Scherre ring and the image data was analized for determining stress. A new principle for stress analysis which is suitable to two-dimensional imaging data was used. For the verification of this two-dimensional imaging type X-ray stress measurement method, an experiment was conducted using a ferritic steel sample which was processed with a surface grinder. Tri-axial stress analysis was conducted to evaluate the sample. The conventional method for X-ray tri-axial stress analysis proposed by Dölle and Hauk was used to evaluate residual stress in order to compare with the present method. As a result, it was confirmed that a sufficiently highly precise and high-speed stress measurement was enabled with the two-dimensional imaging technology compared with the conventional method

Analysis of two dimensional signals via curvelet transform

Science.gov (United States)

Lech, W.; Wójcik, W.; Kotyra, A.; Popiel, P.; Duk, M.

2007-04-01

This paper describes an application of curvelet transform analysis problem of interferometric images. Comparing to two-dimensional wavelet transform, curvelet transform has higher time-frequency resolution. This article includes numerical experiments, which were executed on random interferometric image. In the result of nonlinear approximations, curvelet transform obtains matrix with smaller number of coefficients than is guaranteed by wavelet transform. Additionally, denoising simulations show that curvelet could be a very good tool to remove noise from images.

Comprehensive two-dimensional liquid chromatographic analysis of poloxamers.

Science.gov (United States)

Malik, Muhammad Imran; Lee, Sanghoon; Chang, Taihyun

2016-04-15

Poloxamers are low molar mass triblock copolymers of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), having number of applications as non-ionic surfactants. Comprehensive one and two-dimensional liquid chromatographic (LC) analysis of these materials is proposed in this study. The separation of oligomers of both types (PEO and PPO) is demonstrated for several commercial poloxamers. This is accomplished at the critical conditions for one of the block while interaction for the other block. Reversed phase LC at CAP of PEO allowed for oligomeric separation of triblock copolymers with regard to PPO block whereas normal phase LC at CAP of PPO renders oligomeric separation with respect to PEO block. The oligomeric separation with regard to PEO and PPO are coupled online (comprehensive 2D-LC) to reveal two-dimensional contour plots by unconventional 2D IC×IC (interaction chromatography) coupling. The study provides chemical composition mapping of both PEO and PPO, equivalent to combined molar mass and chemical composition mapping for several commercial poloxamers. Copyright © 2016 Elsevier B.V. All rights reserved.

Ratiometric analysis in hyperpolarized NMR (I): test of the two-site exchange model and the quantification of reaction rate constants.

Science.gov (United States)

Li, Lin Z; Kadlececk, Stephen; Xu, He N; Daye, Dania; Pullinger, Benjamin; Profka, Harrilla; Chodosh, Lewis; Rizi, Rahim

2013-10-01

Conventional methods for the analysis of in vivo hyperpolarized (13) C NMR data from the lactate dehydrogenase (LDH) reaction usually make assumptions on the stability of rate constants and/or the validity of the two-site exchange model. In this study, we developed a framework to test the validity of the assumption of stable reaction rate constants and the two-site exchange model in vivo via ratiometric fitting of the time courses of the signal ratio L(t)/P(t). Our analysis provided evidence that the LDH enzymatic kinetics observed by hyperpolarized NMR are in near-equilibrium and satisfy the two-site exchange model for only a specific time window. In addition, we quantified both the forward and reverse exchange rate constants of the LDH reaction for the transgenic and mouse xenograft models of breast cancer using the ratio fitting method developed, which includes only two modeling parameters and is less sensitive to the influence of instrument settings/protocols, such as flip angles, degree of polarization and tracer dosage. We further compared the ratio fitting method with a conventional two-site exchange modeling method, i.e. the differential equation fitting method, using both the experimental and simulated hyperpolarized NMR data. The ratio fitting method appeared to fit better than the differential equation fitting method for the reverse rate constant on the mouse tumor data, with less relative errors on average, whereas the differential equation fitting method also resulted in a negative reverse rate constant for one tumor. The simulation results indicated that the accuracy of both methods depends on the width of the transport function, noise level and rate constant ratio; one method may be more accurate than the other based on the experimental/biological conditions aforementioned. We were able to categorize our tumor models into specific conditions of the computer simulation and to estimate the errors of rate quantification. We also discussed possible

Two dimensional kinetic analysis of electrostatic harmonic plasma waves

Energy Technology Data Exchange (ETDEWEB)

Fonseca-Pongutá, E. C.; Ziebell, L. F.; Gaelzer, R. [Instituto de Física, UFRGS, 91501-970 Porto Alegre, RS (Brazil); Yoon, P. H. [IPST, University of Maryland, College Park, Maryland 20742 (United States); SSR, Kyung Hee University, Yongin, Gyeonggi 446-701 (Korea, Republic of)

2016-06-15

Electrostatic harmonic Langmuir waves are virtual modes excited in weakly turbulent plasmas, first observed in early laboratory beam-plasma experiments as well as in rocket-borne active experiments in space. However, their unequivocal presence was confirmed through computer simulated experiments and subsequently theoretically explained. The peculiarity of harmonic Langmuir waves is that while their existence requires nonlinear response, their excitation mechanism and subsequent early time evolution are governed by essentially linear process. One of the unresolved theoretical issues regards the role of nonlinear wave-particle interaction process over longer evolution time period. Another outstanding issue is that existing theories for these modes are limited to one-dimensional space. The present paper carries out two dimensional theoretical analysis of fundamental and (first) harmonic Langmuir waves for the first time. The result shows that harmonic Langmuir wave is essentially governed by (quasi)linear process and that nonlinear wave-particle interaction plays no significant role in the time evolution of the wave spectrum. The numerical solutions of the two-dimensional wave spectra for fundamental and harmonic Langmuir waves are also found to be consistent with those obtained by direct particle-in-cell simulation method reported in the literature.

Fourier two-level analysis for higher dimensional discontinuous Galerkin discretisation

NARCIS (Netherlands)

P.W. Hemker (Piet); M.H. van Raalte (Marc)

2002-01-01

textabstractIn this paper we study the convergence of a multigrid method for the solution of a two-dimensional linear second order elliptic equation, discretized by discontinuous Galerkin (DG) methods. For the Baumann-Oden and for the symmetric DG method, we give a detailed analysis of the

Comparison of two intraoral scanners based on three-dimensional surface analysis

Directory of Open Access Journals (Sweden)

Kyung-Min Lee

2018-02-01

Full Text Available Abstract Background This in vivo study evaluated the difference of two well-known intraoral scanners used in dentistry, namely iTero (Align Technology and TRIOS (3Shape. Methods Thirty-two participants underwent intraoral scans with TRIOS and iTero scanners, as well as conventional alginate impressions. The scans obtained with the two intraoral scanners were compared with each other and were also compared with the corresponding model scans by means of three-dimensional surface analysis. The average differences between the two intraoral scans on the surfaces were evaluated by color-mapping. The average differences in the three-dimensional direction between each intraoral scans and its corresponding model scan were calculated at all points on the surfaces. Results The average differences between the two intraoral scanners were 0.057 mm at the maxilla and 0.069 mm at the mandible. Color histograms showed that local deviations between the two scanners occurred in the posterior area. As for difference in the three-dimensional direction, there was no statistically significant difference between two scanners. Conclusions Although there were some deviations in visible inspection, there was no statistical significance between the two intraoral scanners.

Two-dimensional x-ray diffraction

CERN Document Server

He, Bob B

2009-01-01

Written by one of the pioneers of 2D X-Ray Diffraction, this useful guide covers the fundamentals, experimental methods and applications of two-dimensional x-ray diffraction, including geometry convention, x-ray source and optics, two-dimensional detectors, diffraction data interpretation, and configurations for various applications, such as phase identification, texture, stress, microstructure analysis, crystallinity, thin film analysis and combinatorial screening. Experimental examples in materials research, pharmaceuticals, and forensics are also given. This presents a key resource to resea

Comprehensive two-dimensional gas chromatography applied to illicit drug analysis.

Science.gov (United States)

Mitrevski, Blagoj; Wynne, Paul; Marriott, Philip J

2011-11-01

Multidimensional gas chromatography (MDGC), and especially its latest incarnation--comprehensive two-dimensional gas chromatography (GC × GC)--have proved advantageous over and above classic one-dimensional gas chromatography (1D GC) in many areas of analysis by offering improved peak capacity, often enhanced sensitivity and, especially in the case of GC × GC, the unique feature of 'structured' chromatograms. This article reviews recent advances in MDGC and GC × GC in drug analysis with special focus on ecstasy, heroin and cocaine profiling. Although 1D GC is still the method of choice for drug profiling in most laboratories because of its simplicity and instrument availability, GC × GC is a tempting proposition for this purpose because of its ability to generate a higher net information content. Effluent refocusing due to the modulation (compression) process, combined with the separation on two 'orthogonal' columns, results in more components being well resolved and therefore being analytically and statistically useful to the profile. The spread of the components in the two-dimensional plots is strongly dependent on the extent of retention 'orthogonality' (i.e. the extent to which the two phases possess different or independent retention mechanisms towards sample constituents) between the two columns. The benefits of 'information-driven' drug profiling, where more points of reference are usually required for sample differentiation, are discussed. In addition, several limitations in application of MDGC in drug profiling, including data acquisition rate, column temperature limit, column phase orthogonality and chiral separation, are considered and discussed. Although the review focuses on the articles published in the last decade, a brief chronological preview of the profiling methods used throughout the last three decades is given.

Analysis of Polycyclic Aromatic Hydrocarbon (PAH Mixtures Using Diffusion-Ordered NMR Spectroscopy and Adsorption by Powdered Activated Carbon and Biochar

Directory of Open Access Journals (Sweden)

Dong An

2018-03-01

Full Text Available Analysis of polycyclic aromatic hydrocarbons (PAHs in air and water sources is a key part of environmental chemistry research, since most PAHs are well known to be associated with negative health impacts on humans. This study explores an approach for analyzing PAH mixtures with advanced nuclear magnetic resonance (NMR spectroscopic techniques including high-resolution one-dimensional (1D NMR spectroscopy and diffusion-ordered NMR spectroscopy (DOSY NMR. With this method, different kinds of PAHs can be detected and differentiated from a mixture with high resolution. The adsorption process of PAH mixtures by PAC and biochar was studied to understand the mechanism and assess the method.

Structural studies of the activation of the two component receiver domain NTRC by multidimensional heteronuclear NMR

Energy Technology Data Exchange (ETDEWEB)

Nohaile, Michael James [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

1996-05-01

Multidimensional heteronuclear NMR spectroscopy was used to investigate the N-terminal domain of the transcriptional enhancer NTRC (NiTrogen Regulatory protein C). This domain belongs to the family of receiver domains of two-component regulatory systems involved in signal transduction. Phosphorylation of NTRC at D54 leads to an activated form of the molecule which stimulates transcription of genes involved in nitrogen regulation. Three and four dimensional NMR techniques were used to determine an intermediate resolution structure of the unphosphorylated, inactive form of the N-terminal domain of NTRC. The structure is comprised of five α-helices and a five-stranded β-sheet in a (β/α)₅ topology. Analysis of the backbone dynamics of NTRC indicate that helix 4 and strand 5 are significantly more flexible than the rest of the secondary structure of the protein and that the loops making up the active site are flexible. The short lifetime of phospho-NTRC hampers the study of this form. However, conditions for determining the resonance assignments and, possibly, the three dimensional structure of phosphorylated NTRC have been obtained. Tentative assignments of the phosphorylated form indicate that the majority of the changes that NTRC experiences upon phosphorylation occur in helix 3, strand 4, helix 4, strand 5, and the loop between strand 5 and helix 5 (the 3445 face of NTRC) as well as near the site of phosphorylation. In order to examine a stable, activated form of the protein, constitutively active mutants of NTRC were investigated.

Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

Science.gov (United States)

Krishnamoorthi, R; Gong, Y X; Lin, C L; VanderVelde, D

1992-01-28

The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific 1H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns (residues 8-12 and 24-27), a 3(10)-helix (residues 13-16), and a triple-stranded beta-sheet (residues 8-10, 29-27, and 21-25). This secondary structure is similar to that of CMTI-I [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648], which has a Glu instead of a Lys at position 9. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30 degrees C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. Many of these residues are functionally important in that they make contact with atoms of the enzyme in the trypsin-inhibitor complex, as revealed by X-ray crystallography [Bode, W., Greyling, H. J., Huber, R., Otlewski, J., & Wilusz, T. (1989) FEBS Lett. 242, 285-292].(ABSTRACT TRUNCATED AT 250 WORDS)

Moderator feedback effects in two-dimensional nodal methods for pressurized water reactor analysis

International Nuclear Information System (INIS)

Downar, T.J.

1987-01-01

A method was developed for incorporating moderator feedback effects in two-dimensional nodal codes used for pressurized water reactor (PWR) neutronic analysis. Equations for the assembly average quality and density are developed in terms of the assembly power calculated in two dimensions. The method is validated with a Westinghouse PWR using the Electric Power Research Institute code SIMULATE-E. Results show a several percent improvement is achieved in the two-dimensional power distribution prediction compared to methods without moderator feedback

Accelerating two-dimensional nuclear magnetic resonance correlation spectroscopy via selective coherence transfer

Science.gov (United States)

Ye, Qimiao; Chen, Lin; Qiu, Wenqi; Lin, Liangjie; Sun, Huijun; Cai, Shuhui; Wei, Zhiliang; Chen, Zhong

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy serves as an important tool for both qualitative and quantitative analyses of various systems in chemistry, biology, and medicine. However, applications of one-dimensional 1H NMR are often restrained by the presence of severe overlap among different resonances. The advent of two-dimensional (2D) 1H NMR constitutes a promising alternative by extending the crowded resonances into a plane and thereby alleviating the spectral congestions. However, the enhanced ability in discriminating resonances is achieved at the cost of extended experimental duration due to necessity of various scans with progressive delays to construct the indirect dimension. Therefore, in this study, we propose a selective coherence transfer (SECOT) method to accelerate acquisitions of 2D correlation spectroscopy by converting chemical shifts into spatial positions within the effective sample length and then performing an echo planar spectroscopic imaging module to record the spatial and spectral information, which generates 2D correlation spectrum after 2D Fourier transformation. The feasibility and effectiveness of SECOT have been verified by a set of experiments under both homogeneous and inhomogeneous magnetic fields. Moreover, evaluations of SECOT for quantitative analyses are carried out on samples with a series of different concentrations. Based on these experimental results, the SECOT may open important perspectives for fast, accurate, and stable investigations of various chemical systems both qualitatively and quantitatively.

Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and “hidden” dimensions

Science.gov (United States)

Meng, Xi; Nguyen, Bao D.; Ridge, Clark; Shaka, A. J.

2009-01-01

High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to “reduced-dimensionality” strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the Filter Diagonalization Method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths. PMID:18926747

Analysis of human muscle extracts by proton NMR

International Nuclear Information System (INIS)

Venkatasubramanian, P.N.; Barany, M.; Arus, C.

1986-01-01

Perchloric acid extracts were prepared from pooled human muscle biopsies from patients diagnosed with scoliosis (SCOL) and cerebral palsy (CP). After neutralization with KOH and removal of perchlorate, the extracts were concentrated by freeze drying and dissolved in 2 H 2 O to contain 120 O.D. units at 280 nm per 0.5 ml. 1 H NMR spectroscopy was performed with the 5 mm probe of a Varian XL300 instrument. Creatine, lactate, carnosine, and choline were the major resonances in the one-dimensional spectra of both extracts. With creatine as reference, 2.5-fold more lactate was found in SCOL than in CP, and a much smaller difference was also found in their carnosine content. Two-dimensional COSY comparison revealed several differences between the two extracts. Taurine, N-acetyl glutamate, glycerophosphoryl choline (or phosphoryl choline) and an unidentified spot were present only in the extract from SCOL but not in that from CP. On the other hand, aspartate, hydroxy-proline, carnitine and glycerophosphoryl ethanolamine were only present in CP but absent in SCOL. Alanine, cysteine, lysine and arginine appeared in both extracts without an apparent intensity difference

Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex

International Nuclear Information System (INIS)

Nikonowicz, E.; Roongta, V.; Jones, C.R.; Gorenstein, D.G.

1989-01-01

Assignment of the 1H and 31P NMR spectra of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d(CGCAGAATTCGCG)2, has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The downfield 31P resonance previously noted by Patel et al. (1982) has been assigned by both 17O labeling of the phosphate as well as a pure absorption phase constant-time heteronuclear 31P-1H correlated spectrum and has been associated with the phosphate on the 3' side of the extrahelical adenosine. JH3'-P coupling constants for each of the phosphates of the tridecamer were obtained from the 1H-31P J-resolved selective proton-flip 2D spectrum. By use of a modified Karplus relationship the C4-C3'-O3-P torsional angles (epsilon) were obtained. There exists a good linear correlation between 31P chemical shifts and the epsilon torsional angle. The 31P chemical shifts and epsilon torsional angles follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. Because the extrahelical adenosine significantly distorts the deoxyribose phosphate backbone conformation even several bases distant from the extrahelical adenosine, 31P chemical shifts show complex site- and sequence-specific variations. Modeling and NOESY distance-restrained energy minimization and restrained molecular dynamics suggest that the extrahelical adenosine stacks into the duplex. However, a minor conformation is also observed in the 1H NMR, which could be associated with a structure in which the extrahelical adenosine loops out into solution

NMR studies of isotopically labeled RNA

Energy Technology Data Exchange (ETDEWEB)

Pardi, A. [Univ. of Colorado, Boulder, CO (United States)

1994-12-01

In summary, the ability to generate NMR quantities of {sup 15}N and {sup 13}C-labeled RNAs has led to the development of heteronuclear multi-dimensional NMR techniques for simplifying the resonance assignment and structure determination of RNAs. These methods for synthesizing isotopically labeled RNAs are only several years old, and thus there are still relatively few applications of heteronuclear multi-dimensional NMR techniques to RNA. However, given the critical role that RNAs play in cellular function, one can expect to see an increasing number of NMR structural studies of biologically active RNAs.

One- and two-dimensional chemical exchange nuclear magnetic resonance studies of the creatine kinase catalyzed reaction

International Nuclear Information System (INIS)

Gober, J.R.

1988-01-01

The equilibrium chemical exchange dynamics of the creatine kinase enzyme system were studied by one- and two-dimensional 31 P NMR techniques. Pseudo-first-order reaction rate constants were measured by the saturation transfer method under an array of experimental conditions of pH and temperature. Quantitative one-dimensional spectra were collected under the same conditions in order to calculate the forward and reverse reaction rates, the K eq , the hydrogen ion stoichiometry, and the standard thermodynamic functions. The pure absorption mode in four quadrant two-dimensional chemical exchange experiment was employed so that the complete kinetic matrix showing all of the chemical exchange process could be realized

Investigation of zeolites by solid state quadrapole NMR

International Nuclear Information System (INIS)

Janssen, R.

1990-01-01

The subject of this thesis is the NMR investigation of zeolites. The nature and properties of zeolites are discussed. Some of the basic priniples of NMR techniques on quadrupole nuclei are presented. A special technique, namely a two-dimensional nutation experiment is discussed in detail. The theory of the nutation experiment for quadrupole spin species with spin quantum number 3/2 as well as 5/2 is presented. For both spin spcies the theoretical spectra are compared with experimental results. It is also shown that the nutation expeirment can be performed with several pulse schemes. It is shown how phase-sensitive pure-absorption nutation spectra can be obtained and an NMR-probe is presented that is capable of performing NMR experiments at high (up to 500 degree C) temperatures. The two-dimensional nutation NMR technique has been applied to sodium cations in zeolite NaA. For this purpose a numbre of zeolite samples were prepared that contained different amounts of water. With the aid of nutation NMR the hydration of the zeolite can be studied and conclusions can be drawn about the symmetry of the surrounding of the sodium cations. With the aid of an extension of the nutation NMR experiment: Rotary Echo Nutation NMR, it is shown that in zeolite NaA, in various stages of hydration, the sodium cations or water molecules are mobile. Proof is given by means of high-temperature 23 Na-NMR that dehydrates zeolite NaA undergoes a phase transition at ca. 120 degree C. In a high-temperature NMR investigation of zeolite ZSM-5 it is shown that the sodium ions start to execute motions when the temperature is increased. (author). 198 refs.; 72 figs.; 6 tabs

NMR imaging: A 'chemical' microscope for coal analysis

International Nuclear Information System (INIS)

French, D.C.; Dieckman, S.L.; Gopalsami, N.; Botto, R.E.

1991-01-01

This paper presents a new three-dimensional (3-D) nuclear magnetic resonance (NMR) imaging technique for spatially mapping proton distributions in whole coals and solvent-swollen coal samples. The technique is based on a 3-D back-projection protocol for data acquisition, and a reconstruction technique based on 3-D Radon transform inversion. In principle, the 3-D methodology provides higher spatial resolution of solid materials than is possible with conventional slice-selection protocols. The applicability of 3-D NMR imaging has been demonstrated by mapping the maceral phases in Utah Blind Canyon (APCS number-sign 6) coal and the distribution of mobile phases in Utah coal swollen with deuterated and protic pyridine. 7 refs., 5 figs

Theory and design of compact hybrid microphone arrays on two-dimensional planes for three-dimensional soundfield analysis.

Science.gov (United States)

Chen, Hanchi; Abhayapala, Thushara D; Zhang, Wen

2015-11-01

Soundfield analysis based on spherical harmonic decomposition has been widely used in various applications; however, a drawback is the three-dimensional geometry of the microphone arrays. In this paper, a method to design two-dimensional planar microphone arrays that are capable of capturing three-dimensional (3D) spatial soundfields is proposed. Through the utilization of both omni-directional and first order microphones, the proposed microphone array is capable of measuring soundfield components that are undetectable to conventional planar omni-directional microphone arrays, thus providing the same functionality as 3D arrays designed for the same purpose. Simulations show that the accuracy of the planar microphone array is comparable to traditional spherical microphone arrays. Due to its compact shape, the proposed microphone array greatly increases the feasibility of 3D soundfield analysis techniques in real-world applications.

Functional Parallel Factor Analysis for Functions of One- and Two-dimensional Arguments.

Science.gov (United States)

Choi, Ji Yeh; Hwang, Heungsun; Timmerman, Marieke E

2018-03-01

Parallel factor analysis (PARAFAC) is a useful multivariate method for decomposing three-way data that consist of three different types of entities simultaneously. This method estimates trilinear components, each of which is a low-dimensional representation of a set of entities, often called a mode, to explain the maximum variance of the data. Functional PARAFAC permits the entities in different modes to be smooth functions or curves, varying over a continuum, rather than a collection of unconnected responses. The existing functional PARAFAC methods handle functions of a one-dimensional argument (e.g., time) only. In this paper, we propose a new extension of functional PARAFAC for handling three-way data whose responses are sequenced along both a two-dimensional domain (e.g., a plane with x- and y-axis coordinates) and a one-dimensional argument. Technically, the proposed method combines PARAFAC with basis function expansion approximations, using a set of piecewise quadratic finite element basis functions for estimating two-dimensional smooth functions and a set of one-dimensional basis functions for estimating one-dimensional smooth functions. In a simulation study, the proposed method appeared to outperform the conventional PARAFAC. We apply the method to EEG data to demonstrate its empirical usefulness.

The analysis of carbohydrates in milk powder by a new "heart-cutting" two-dimensional liquid chromatography method.

Science.gov (United States)

Ma, Jing; Hou, Xiaofang; Zhang, Bing; Wang, Yunan; He, Langchong

2014-03-01

In this study, a new"heart-cutting" two-dimensional liquid chromatography method for the simultaneous determination of carbohydrate contents in milk powder was presented. In this two dimensional liquid chromatography system, a Venusil XBP-C4 analysis column was used in the first dimension ((1)D) as a pre-separation column, a ZORBAX carbohydrates analysis column was used in the second dimension ((2)D) as a final-analysis column. The whole process was completed in less than 35min without a particular sample preparation procedure. The capability of the new two dimensional HPLC method was demonstrated in the determination of carbohydrates in various brands of milk powder samples. A conventional one dimensional chromatography method was also proposed. The two proposed methods were both validated in terms of linearity, limits of detection, accuracy and precision. The comparison between the results obtained with the two methods showed that the new and completely automated two dimensional liquid chromatography method is more suitable for milk powder sample because of its online cleanup effect involved. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

Quantitative analysis of protein-ligand interactions by NMR.

Science.gov (United States)

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

Assessment of 1H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

Science.gov (United States)

Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

2017-01-01

Proton nuclear magnetic resonance ( 1 H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R 2 =0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R 2 =0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

Two-dimensional disruption thermal analysis code DREAM

International Nuclear Information System (INIS)

Yamazaki, Seiichiro; Kobayashi, Takeshi; Seki, Masahiro.

1988-08-01

When a plasma disruption takes place in a tokamak type fusion reactor, plasma facing components such as first wall and divertor/limiter are subjected to an intense heat load with very high heat flux and short duration. At the surface of the wall, temperature rapidly rises, and melting and evaporation occurs, it causes reduction of wall thickness and crack initiation/propagation. As lifetime of the components is significantly affected by them, the transient analysis in consideration of phase changes (melting/evaporation) and radiation heat loss is required in the design of these components. This paper describes the computer code DREAM developed to perform the two-dimensional transient thermal analysis that takes phase changes and radiation into account. The input and output of the code and a sample analysis on a disruption simulation experiment are also reported. The user's input manual is added as an appendix. The profiles and time variations of temperature, and melting and evaporated thicknesses of the material subjected to intense heat load can be obtained, using this computer code. This code also gives the temperature data for elastoplastic analysis with FEM structural analysis codes (ADINA, MARC, etc.) to evaluate the thermal stress and crack propagation behavior within the wall materials. (author)

DNA hairpin structures in solution: 500-MHz two-dimensional 1H NMR studies on d(CGCCGCAGC) and d(CGCCGTAGC)

International Nuclear Information System (INIS)

Gupta, G.; Sarma, M.H.; Sarma, R.H.

1987-01-01

A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz 1 H NMR studies in H 2 O and D 2 O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2'', it was concluded that in D(CGCCGCAGC) and d(CGCCCTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins

Quantitative analysis of target components by comprehensive two-dimensional gas chromatography

NARCIS (Netherlands)

Mispelaar, V.G. van; Tas, A.C.; Smilde, A.K.; Schoenmakers, P.J.; Asten, A.C. van

2003-01-01

Quantitative analysis using comprehensive two-dimensional (2D) gas chromatography (GC) is still rarely reported. This is largely due to a lack of suitable software. The objective of the present study is to generate quantitative results from a large GC x GC data set, consisting of 32 chromatograms.

Using 2D NMR to determine the degree of branching of complicated hyperbranched polymers

Institute of Scientific and Technical Information of China (English)

2008-01-01

Degree of branching (DB) is a crucial structure parameter of hyperbranched polymers, which can be determined by 1H NMR, quantitative 13C NMR, degradative method, etc. However, for complicated hy-perbranched polymers, intricate structure and severe overlap of spectral signals hinder the determina-tion of DB using traditional methods. In this work, the architecture of complicated hyperbranched polymers has been elucidated with the help of 2D NMR techniques. Using such a method, overlapped NMR signals can be well separated into a two-dimensional space, and additional structural information is also available. Correspondingly, quantitative analysis for complicated systems can be realized. De-termination of DBs for three types of complicated hyperbranched polymers synthesized from step-polymerization, self-condensation vinyl polymerization and self-condensation ring-opening po-lymerization is shown as examples.

Non-uniform sampling of NMR relaxation data

DEFF Research Database (Denmark)

Schwarz-Linnet, Troels; Teilum, Kaare

2016-01-01

The use of non-uniform sampling of NMR spectra may give significant reductions in the data acquisition time. For quantitative experiments such as the measurement of spin relaxation rates, non-uniform sampling is however not widely used as inaccuracies in peak intensities may lead to errors...... in the extracted dynamic parameters. By systematic reducing the coverage of the Nyquist grid of (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion datasets for four different proteins and performing a full data analysis of the resulting non-uniform sampled datasets, we have compared the performance...... of the multi-dimensional decomposition and iterative re-weighted least-squares algorithms in reconstructing spectra with accurate peak intensities. As long as a single fully sampled spectrum is included in a series of otherwise non-uniform sampled two-dimensional spectra, multi-dimensional decomposition...

NMR relaxation rate in quasi one-dimensional antiferromagnets

Science.gov (United States)

Capponi, Sylvain; Dupont, Maxime; Laflorencie, Nicolas; Sengupta, Pinaki; Shao, Hui; Sandvik, Anders W.

We compare results of different numerical approaches to compute the NMR relaxation rate 1 /T1 in quasi one-dimensional (1d) antiferromagnets. In the purely 1d regime, recent numerical simulations using DMRG have provided the full crossover behavior from classical regime at high temperature to universal Tomonaga-Luttinger liquid at low-energy (in the gapless case) or activated behavior (in the gapped case). For quasi 1d models, we can use mean-field approaches to reduce the problem to a 1d one that can be studied using DMRG. But in some cases, we can also simulate the full microscopic model using quantum Monte-Carlo techniques. This allows to compute dynamical correlations in imaginary time and we will discuss recent advances to perform stochastic analytic continuation to get real frequency spectra. Finally, we connect our results to experiments on various quasi 1d materials.

TG/DTG, FT-ICR Mass Spectrometry, and NMR Spectroscopy Study of Heavy Fuel Oil

KAUST Repository

Elbaz, Ayman M.; Abdul Jameel, Abdul Gani; Hourani, Nadim; Emwas, Abdul-Hamid M.; Sarathy, Mani; Roberts, William L.

2015-01-01

infusion atmospheric pressure chemical ionization Fourier transform ion cyclotron resonance mass spectrometry (APCI-FTICR MS), high resolution 1H nuclear magnetic resonance (NMR), 13C NMR, and two-dimensional heteronuclear multiple bond correlation (HMBC

Tunable states of interlayer cations in two-dimensional materials

International Nuclear Information System (INIS)

Sato, K.; Numata, K.; Dai, W.; Hunger, M.

2014-01-01

The local state of cations inside the Ångstrom-scale interlayer spaces is one of the controlling factors for designing sophisticated two-dimensional (2D) materials consisting of 2D nanosheets. In the present work, the molecular mechanism on how the interlayer cation states are induced by the local structures of the 2D nanosheets is highlighted. For this purpose, the local states of Na cations in inorganic 2D materials, in which the compositional fluctuations of a few percent are introduced in the tetrahedral and octahedral units of the 2D nanosheets, were systematically studied by means of 23 Na magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) and 23 Na multiple-quantum MAS (MQMAS) NMR spectroscopy. In contrast with an uniform distribution of Na cations expected so far, various well-defined cation states sensitive to the local structures of the 2D nanosheets were identified. The tunability of the interlayer cation states along with the local structure of the 2D nanosheets, as the smallest structural unit of the 2D material, is discussed

Tunable states of interlayer cations in two-dimensional materials

Energy Technology Data Exchange (ETDEWEB)

Sato, K.; Numata, K. [Department of Environmental Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501 (Japan); Dai, W. [Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, Tianjin 300071 (China); Hunger, M. [Institute of Chemical Technology, University of Stuttgart, 70550 Stuttgart (Germany)

2014-03-31

The local state of cations inside the Ångstrom-scale interlayer spaces is one of the controlling factors for designing sophisticated two-dimensional (2D) materials consisting of 2D nanosheets. In the present work, the molecular mechanism on how the interlayer cation states are induced by the local structures of the 2D nanosheets is highlighted. For this purpose, the local states of Na cations in inorganic 2D materials, in which the compositional fluctuations of a few percent are introduced in the tetrahedral and octahedral units of the 2D nanosheets, were systematically studied by means of {sup 23}Na magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) and {sup 23}Na multiple-quantum MAS (MQMAS) NMR spectroscopy. In contrast with an uniform distribution of Na cations expected so far, various well-defined cation states sensitive to the local structures of the 2D nanosheets were identified. The tunability of the interlayer cation states along with the local structure of the 2D nanosheets, as the smallest structural unit of the 2D material, is discussed.

Optimizing separations in online comprehensive two-dimensional liquid chromatography.

Science.gov (United States)

Pirok, Bob W J; Gargano, Andrea F G; Schoenmakers, Peter J

2018-01-01

Online comprehensive two-dimensional liquid chromatography has become an attractive option for the analysis of complex nonvolatile samples found in various fields (e.g. environmental studies, food, life, and polymer sciences). Two-dimensional liquid chromatography complements the highly popular hyphenated systems that combine liquid chromatography with mass spectrometry. Two-dimensional liquid chromatography is also applied to the analysis of samples that are not compatible with mass spectrometry (e.g. high-molecular-weight polymers), providing important information on the distribution of the sample components along chemical dimensions (molecular weight, charge, lipophilicity, stereochemistry, etc.). Also, in comparison with conventional one-dimensional liquid chromatography, two-dimensional liquid chromatography provides a greater separation power (peak capacity). Because of the additional selectivity and higher peak capacity, the combination of two-dimensional liquid chromatography with mass spectrometry allows for simpler mixtures of compounds to be introduced in the ion source at any given time, improving quantitative analysis by reducing matrix effects. In this review, we summarize the rationale and principles of two-dimensional liquid chromatography experiments, describe advantages and disadvantages of combining different selectivities and discuss strategies to improve the quality of two-dimensional liquid chromatography separations. © 2017 The Authors. Journal of Separation Science published by WILEY-VCH Verlag GmbH & Co. KGaA.

Crystallographically-based analysis of the NMR spectra of maghemite

International Nuclear Information System (INIS)

Spiers, K.M.; Cashion, J.D.

2012-01-01

All possible iron environments with respect to nearest neighbour vacancies in vacancy-ordered and vacancy-disordered maghemite have been evaluated and used as the foundation for a crystallographically-based analysis of the published NMR spectra of maghemite. The spectral components have been assigned to particular configurations and excellent agreement obtained in comparing predicted spectra with published spectra taken in applied magnetic fields. The broadness of the published NMR lines has been explained by calculations of the magnetic dipole fields at the various iron sites and consideration of the supertransferred hyperfine fields. - Highlights: ► Analysis of 57 Fe NMR of maghemite based on vacancy ordering and nearest neighbour vacancies. ► Assignment of NMR spectral components based on crystallographic analysis of unique iron sites. ► Strong agreement between predicted spectra and published spectra taken in applied magnetic fields. ► Maghemite NMR spectral broadening due to various iron sites and supertransferred hyperfine field.

One-dimensional scanning of moisture in heated porous building materials with NMR.

Science.gov (United States)

van der Heijden, G H A; Huinink, H P; Pel, L; Kopinga, K

2011-02-01

In this paper we present a new dedicated NMR setup which is capable of measuring one-dimensional moisture profiles in heated porous materials. The setup, which is placed in the bore of a 1.5 T whole-body scanner, is capable of reaching temperatures up to 500 °C. Moisture and temperature profiles can be measured quasi simultaneously with a typical time resolution of 2-5 min. A methodology is introduced for correcting temperature effects on NMR measurements at these elevated temperatures. The corrections are based on the Curie law for paramagnetism and the observed temperature dependence of the relaxation mechanisms occurring in porous materials. Both these corrections are used to obtain a moisture content profile from the raw NMR signal profile. To illustrate the methodology, a one-sided heating experiment of concrete with a moisture content in equilibrium with 97% RH is presented. This kind of heating experiment is of particular interest in the research on fire spalling of concrete, since it directly reveals the moisture and heat transport occurring inside the concrete. The obtained moisture profiles reveal a moisture peak building up behind the boiling front, resulting in a saturated layer. To our knowledge the direct proof of the formation of a moisture peak and subsequent moisture clogging has not been reported before. Copyright © 2010 Elsevier Inc. All rights reserved.

Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR Methodology

Directory of Open Access Journals (Sweden)

Run-Cang Sun

2013-01-01

Full Text Available The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA, nitrobenzene oxidation (NBO, and derivatization followed by reductive cleavage (DFRC. Recent advances in nuclear magnetic resonance (NMR technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ, as well as their applications are reviewed.

Computer compensation for NMR quantitative analysis of trace components

International Nuclear Information System (INIS)

Nakayama, T.; Fujiwara, Y.

1981-01-01

A computer program has been written that determines trace components and separates overlapping components in multicomponent NMR spectra. This program uses the Lorentzian curve as a theoretical curve of NMR spectra. The coefficients of the Lorentzian are determined by the method of least squares. Systematic errors such as baseline/phase distortion are compensated and random errors are smoothed by taking moving averages, so that there processes contribute substantially to decreasing the accumulation time of spectral data. The accuracy of quantitative analysis of trace components has been improved by two significant figures. This program was applied to determining the abundance of 13C and the saponification degree of PVA

Comprehensive two-dimensional gas chromatography for the analysis of organohalogenated micro-contaminants

NARCIS (Netherlands)

Korytar, P.; Haglund, P.; Boer, de J.; Brinkman, U.A.Th.

2006-01-01

We explain the principles of comprehensive two-dimensional gas chromatography (GC × GC), and discuss key instrumental aspects - with emphasis on column combinations and mass spectrometric detection. As the main item of interest, we review the potential of GC × GC for the analysis of

Two-dimensional cross-section sensitivity and uncertainty analysis of the LBM [Lithium Blanket Module] experiments at LOTUS

International Nuclear Information System (INIS)

Davidson, J.W.; Dudziak, D.J.; Pelloni, S.; Stepanek, J.

1988-01-01

In a recent common Los Alamos/PSI effort, a sensitivity and nuclear data uncertainty path for the modular code system AARE (Advanced Analysis for Reactor Engineering) was developed. This path includes the cross-section code TRAMIX, the one-dimensional finite difference S/sub N/-transport code ONEDANT, the two-dimensional finite element S/sub N/-transport code TRISM, and the one- and two-dimensional sensitivity and nuclear data uncertainty code SENSIBL. Within the framework of the present work a complete set of forward and adjoint two-dimensional TRISM calculations were performed both for the bare, as well as for the Pb- and Be-preceeded, LBM using MATXS8 libraries. Then a two-dimensional sensitivity and uncertainty analysis for all cases was performed. The goal of this analysis was the determination of the uncertainties of a calculated tritium production per source neutron from lithium along the central Li 2 O rod in the LBM. Considered were the contributions from 1 H, 6 Li, 7 Li, 9 Be, /sup nat/C, 14 N, 16 O, 23 Na, 27 Al, /sup nat/Si, /sup nat/Cr, /sup nat/Fe, /sup nat/Ni, and /sup nat/Pb. 22 refs., 1 fig., 3 tabs

A two-dimensional vibration analysis of piezoelectrically actuated microbeam with nonideal boundary conditions

Science.gov (United States)

Rezaei, M. P.; Zamanian, M.

2017-01-01

In this paper, the influences of nonideal boundary conditions (due to flexibility) on the primary resonant behavior of a piezoelectrically actuated microbeam have been studied, for the first time. The structure has been assumed to treat as an Euler-Bernoulli beam, considering the effects of geometric nonlinearity. In this work, the general nonideal supports have been modeled as a the combination of horizontal, vertical and rotational springs, simultaneously. Allocating particular values to the stiffness of these springs provides the mathematical models for the majority of boundary conditions. This consideration leads to use a two-dimensional analysis of the multiple scales method instead of previous works' method (one-dimensional analysis). If one neglects the nonideal effects, then this paper would be an effort to solve the two-dimensional equations of motion without a need of a combination of these equations using the shortening or stretching effect. Letting the nonideal effects equal to zero and comparing their results with the results of previous approaches have been demonstrated the accuracy of the two-dimensional solutions. The results have been identified the unique effects of constraining and stiffening of boundaries in horizontal, vertical and rotational directions. This means that it is inaccurate to suppose the nonideality of supports only in one or two of these directions like as previous works. The findings are of vital importance as a better prediction of the frequency response for the nonideal supports. Furthermore, the main findings of this effort can help to choose appropriate boundary conditions for desired systems.

Pixel-based analysis of comprehensive two-dimensional gas chromatograms (color plots) of petroleum

DEFF Research Database (Denmark)

Furbo, Søren; Hansen, Asger B.; Skov, Thomas

2014-01-01

We demonstrate how to process comprehensive two-dimensional gas chromatograms (GC × GC chromatograms) to remove nonsample information (artifacts), including background and retention time shifts. We also demonstrate how this, combined with further reduction of the influence of irrelevant informati......, allows for data analysis without integration or peak deconvolution (pixelbased analysis)....

PR-CALC: A Program for the Reconstruction of NMR Spectra from Projections

International Nuclear Information System (INIS)

Coggins, Brian E.; Zhou Pei

2006-01-01

Projection-reconstruction NMR (PR-NMR) has attracted growing attention as a method for collecting multidimensional NMR data rapidly. The PR-NMR procedure involves measuring lower-dimensional projections of a higher-dimensional spectrum, which are then used for the mathematical reconstruction of the full spectrum. We describe here the program PR-CALC, for the reconstruction of NMR spectra from projection data. This program implements a number of reconstruction algorithms, highly optimized to achieve maximal performance, and manages the reconstruction process automatically, producing either full spectra or subsets, such as regions or slices, as requested. The ability to obtain subsets allows large spectra to be analyzed by reconstructing and examining only those subsets containing peaks, offering considerable savings in processing time and storage space. PR-CALC is straightforward to use, and integrates directly into the conventional pipeline for data processing and analysis. It was written in standard C+ + and should run on any platform. The organization is flexible, and permits easy extension of capabilities, as well as reuse in new software. PR-CALC should facilitate the widespread utilization of PR-NMR in biomedical research

Sensitivity analysis explains quasi-one-dimensional current transport in two-dimensional materials

DEFF Research Database (Denmark)

Boll, Mads; Lotz, Mikkel Rønne; Hansen, Ole

2014-01-01

We demonstrate that the quasi-one-dimensional (1D) current transport, experimentally observed in graphene as measured by a collinear four-point probe in two electrode configurations A and B, can be interpreted using the sensitivity functions of the two electrode configurations (configurations...... A and B represents different pairs of electrodes chosen for current sources and potential measurements). The measured sheet resistance in a four-point probe measurement is averaged over an area determined by the sensitivity function. For a two-dimensional conductor, the sensitivity functions for electrode...... configurations A and B are different. But when the current is forced to flow through a percolation network, e.g., graphene with high density of extended defects, the two sensitivity functions become identical. This is equivalent to a four-point measurement on a line resistor, hence quasi-1D transport...

Detailed 1H and 13C NMR spectral data assignment for two dihydrobenzofuran neolignans

International Nuclear Information System (INIS)

Medeiros, Talita C.T.; Dias, Herbert J.; Crotti, Antônio E.M.

2016-01-01

In this work we present a complete proton ( 1 H) and carbon 13 ( 13 C) nuclear magnetic resonance (NMR) spectral analysis of two synthetic dihydrofuran neolignans (±)-trans-dehydrodicoumarate dimethyl ester and (±)-trans-dehydrodiferulate dimethyl ester. Unequivocal assignments were achieved by 1 H NMR, proton decoupled 13 C ( 13 C{ 1 H}) NMR spectra, gradient-selected correlation spectroscopy (gCOSY), J-resolved, gradient-selected heteronuclear multiple quantum coherence (gHMQC), gradient-selected heteronuclear multiple bond coherence (gHMBC) and nuclear Overhauser effect spectroscopy (NOESY) experiments. All hydrogen coupling constants were measured, clarifying all the hydrogen signals multiplicities. Computational methods were also used to simulate the 1 H and 13 C chemical shifts and showed good agreement with the trans configuration of the substituents at C 7 and C 8 . (author)

Analysis of the OPERA-15 two-dimensional voiding experiment using the SAS4A code

International Nuclear Information System (INIS)

Briggs, L.L.

1984-01-01

Overall, SAS4A appears to do a good job for simulating the OPERA-15 experiment. For most of the experiment parameters, the code calculations compare quite well with the experimental data. The lack of a multi-dimensional voiding model has the effect of extending the flow coastdown time until voiding starts; otherwise, the code simulates the accident progression satisfactorily. These results indicate a need for further work in this area in the form of a tandem analysis by a two-dimensional flow code and a one-dimensional version of that code to confirm the observations derived from the SAS4A analysis

Two-dimensional over-all neutronics analysis of the ITER device

Science.gov (United States)

Zimin, S.; Takatsu, Hideyuki; Mori, Seiji; Seki, Yasushi; Satoh, Satoshi; Tada, Eisuke; Maki, Koichi

1993-07-01

The present work attempts to carry out a comprehensive neutronics analysis of the International Thermonuclear Experimental Reactor (ITER) developed during the Conceptual Design Activities (CDA). The two-dimensional cylindrical over-all calculational models of ITER CDA device including the first wall, blanket, shield, vacuum vessel, magnets, cryostat and support structures were developed for this purpose with a help of the DOGII code. Two dimensional DOT 3.5 code with the FUSION-40 nuclear data library was employed for transport calculations of neutron and gamma ray fluxes, tritium breeding ratio (TBR), and nuclear heating in reactor components. The induced activity calculational code CINAC was employed for the calculations of exposure dose rate after reactor shutdown around the ITER CDA device. The two-dimensional over-all calculational model includes the design specifics such as the pebble bed Li2O/Be layered blanket, the thin double wall vacuum vessel, the concrete cryostat integrated with the over-all ITER design, the top maintenance shield plug, the additional ring biological shield placed under the top cryostat lid around the above-mentioned top maintenance shield plug etc. All the above-mentioned design specifics were included in the employed calculational models. Some alternative design options, such as the water-rich shielding blanket instead of lithium-bearing one, the additional biological shield plug at the top zone between the poloidal field (PF) coil No. 5, and the maintenance shield plug, were calculated as well. Much efforts have been focused on analyses of obtained results. These analyses aimed to obtain necessary recommendations on improving the ITER CDA design.

Two-dimensional over-all neutronics analysis of the ITER device

International Nuclear Information System (INIS)

Zimin, S.; Takatsu, Hideyuki; Mori, Seiji; Seki, Yasushi; Satoh, Satoshi; Tada, Eisuke; Maki, Koichi.

1993-07-01

The present work attempts to carry out a comprehensive neutronics analysis of the International Thermonuclear Experimental Reactor (ITER) developed during the Conceptual Design Activities (CDA). The two-dimensional cylindrical over-all calculational models of ITER CDA device including the first wall, blanket, shield, vacuum vessel, magnets, cryostat and support structures were developed for this purpose with a help of the DOGII code. Two dimensional DOT 3.5 code with the FUSION-40 nuclear data library was employed for transport calculations of neutron and gamma ray fluxes, tritium breeding ratio (TBR) and nuclear heating in reactor components. The induced activity calculational code CINAC was employed for the calculations of exposure dose rate after reactor shutdown around the ITER CDA device. The two-dimensional over-all calculational model includes the design specifics such as the pebble bed Li 2 O/Be layered blanket, the thin double wall vacuum vessel, the concrete cryostat integrated with the over-all ITER design, the top maintenance shield plug, the additional ring biological shield placed under the top cryostat lid around the above-mentioned top maintenance shield plug etc. All the above-mentioned design specifics were included in the employed calculational models. Some alternative design options, such as the water-rich shielding blanket instead of lithium-bearing one, the additional biological shield plug at the top zone between the poloidal field (PF) coil No.5 and the maintenance shield plug, were calculated as well. Much efforts have been focused on analyses of obtained results. These analyses aimed to obtain necessary recommendations on improving the ITER CDA design. (author)

Applying Clustering to Statistical Analysis of Student Reasoning about Two-Dimensional Kinematics

Science.gov (United States)

Springuel, R. Padraic; Wittman, Michael C.; Thompson, John R.

2007-01-01

We use clustering, an analysis method not presently common to the physics education research community, to group and characterize student responses to written questions about two-dimensional kinematics. Previously, clustering has been used to analyze multiple-choice data; we analyze free-response data that includes both sketches of vectors and…

ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

Science.gov (United States)

Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

International Nuclear Information System (INIS)

Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten

2015-01-01

UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications

Molecular dynamics computer simulations based on NMR data

International Nuclear Information System (INIS)

Vlieg, J. de.

1989-01-01

In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs

Study on the Effects of Oligo chitosan and Bioliquifert on Two Rice Mutants, NMR 151 and NMR 152

International Nuclear Information System (INIS)

Shakinah Salleh; Faiz Ahmad; Sobri Hussein

2016-01-01

Nuclear Malaysia has successfully developed two new rice mutants namely NMR 151 and NMR 152. In addition, Nuclear Malaysia has also successfully developed Oligo chitosan and liquid bio fertilizer (Bioliquifert). Oligo chitosan acts as elicitor that has been proven to be very effective in controlling disease infections and improving yield productivity. Bioliquifert on the other hand is a mixture of microbes containing major nutrient-providing microorganisms. The objective of this study is to observe the effects of Oligo chitosan and Bioliquifert on rice mutants, NMR 151 and NMR 152. The treatment was applied on 14 day old seedlings of MR 219, NMR 151 and NMR 152 sowed in 20 cm pots containing silty clay from the paddy soil of Tanjung Karang, Selangor. The seedlings were then placed in the greenhouse at Nuclear Malaysia until it reaches 110 days old. Study was conducted in a Complete Randomized Design (CRD) with 3 replications was used and each replication consisted of three plants. All treatments received compound and single dressing fertilizer as recommended by National Rice Production Package except for Treatment 2 and 3, in which Treatment 2 received Oligo chitosan and Bioliquifert while Treatment 3 only received Bioliquifert. Results on plant height, number of tiller and plant fresh weight are not significantly different for all cultivar except for seed dry weight of NMR 152 and MR 219. (author)

ONE-DIMENSIONAL AND TWO-DIMENSIONAL LEADERSHIP STYLES

Directory of Open Access Journals (Sweden)

Nikola Stefanović

2007-06-01

Full Text Available In order to motivate their group members to perform certain tasks, leaders use different leadership styles. These styles are based on leaders' backgrounds, knowledge, values, experiences, and expectations. The one-dimensional styles, used by many world leaders, are autocratic and democratic styles. These styles lie on the two opposite sides of the leadership spectrum. In order to precisely define the leadership styles on the spectrum between the autocratic leadership style and the democratic leadership style, leadership theory researchers use two dimensional matrices. The two-dimensional matrices define leadership styles on the basis of different parameters. By using these parameters, one can identify two-dimensional styles.

Quali- and quantitative analysis of commercial coffee by NMR

International Nuclear Information System (INIS)

Tavares, Leila Aley; Ferreira, Antonio Gilberto

2006-01-01

Coffee is one of the beverages most widely consumed in the world and the 'cafezinho' is normally prepared from a blend of roasted powder of two species, Coffea arabica and Coffea canephora. Each one exhibits differences in their taste and in the chemical composition, especially in the caffeine percentage. There are several procedures proposed in the literature for caffeine determination in different samples like soft drinks, coffee, medicines, etc but most of them need a sample workup which involves at least one step of purification. This work describes the quantitative analysis of caffeine using 1 H NMR and the identification of the major components in commercial coffee samples using 1D and 2D NMR techniques without any sample pre-treatment. (author)

Fluid-Rock Characterization and Interactions in NMR Well Logging

Energy Technology Data Exchange (ETDEWEB)

George J. Hirasaki; Kishore K. Mohanty

2005-09-05

The objective of this report is to characterize the fluid properties and fluid-rock interactions that are needed for formation evaluation by NMR well logging. The advances made in the understanding of NMR fluid properties are summarized in a chapter written for an AAPG book on NMR well logging. This includes live oils, viscous oils, natural gas mixtures, and the relation between relaxation time and diffusivity. Oil based drilling fluids can have an adverse effect on NMR well logging if it alters the wettability of the formation. The effect of various surfactants on wettability and surface relaxivity are evaluated for silica sand. The relation between the relaxation time and diffusivity distinguishes the response of brine, oil, and gas in a NMR well log. A new NMR pulse sequence in the presence of a field gradient and a new inversion technique enables the T{sub 2} and diffusivity distributions to be displayed as a two-dimensional map. The objectives of pore morphology and rock characterization are to identify vug connectivity by using X-ray CT scan, and to improve NMR permeability correlation. Improved estimation of permeability from NMR response is possible by using estimated tortuosity as a parameter to interpolate between two existing permeability models.

Two and dimensional heat analysis inside a high pressure electrical discharge tube

International Nuclear Information System (INIS)

Aghanajafi, C.; Dehghani, A. R.; Fallah Abbasi, M.

2005-01-01

This article represents the heat transfer analysis for a horizontal high pressure mercury steam tube. To get a more realistic numerical simulation, heat radiation at different wavelength width bands, has been used besides convection and conduction heat transfer. The analysis for different gases with different pressure in two and three dimensional cases has been investigated and the results compared with empirical and semi empirical values. The effect of the environmental temperature on the arc tube temperature is also studied

Characterization of Two Distinct Amorphous Forms of Valsartan by Solid-State NMR.

Science.gov (United States)

Skotnicki, Marcin; Apperley, David C; Aguilar, Juan A; Milanowski, Bartłomiej; Pyda, Marek; Hodgkinson, Paul

2016-01-04

Valsartan (VAL) is an antihypertensive drug marketed in an amorphous form. Amorphous materials can have different physicochemical properties depending on preparation method, thermal history, etc., but the nature of such materials is difficult to study by diffraction techniques. This study characterizes two different amorphous forms of valsartan (AR and AM) using solid-state NMR (SSNMR) as a primary investigation tool, supported by solution-state NMR, FT-IR, TMDSC, and dissolution tests. The two forms are found to be clearly distinct, with a significantly higher level of structural arrangement in the AR form, as observed in (13)C, (15)N, and (1)H SSNMR. (13)C and (15)N NMR indicates that the fully amorphous material (AM) contains an approximately equal ratio of cis-trans conformers about the amide bond, whereas the AR form exists mainly as one conformer, with minor conformational "defects". (1)H ultrafast MAS NMR shows significant differences in the hydrogen bonding involving the tetrazole and acid hydrogens between the two materials, while (15)N NMR shows that both forms exist as a 1,2,3,4-tetrazole tautomer. NMR relaxation times show subtle differences in local and bulk molecular mobility, which can be connected with the glass transition, the stability of the glassy material, and its response to aging. Counterintuitively the fully amorphous material is found to have a significantly lower dissolution rate than the apparently more ordered AR material.

Two-dimensional cross-section sensitivity and uncertainty analysis of the LBM experience at LOTUS

International Nuclear Information System (INIS)

Davidson, J.W.; Dudziak, D.J.; Pelloni, S.; Stepanek, J.

1989-01-01

In recent years, the LOTUS fusion blanket facility at IGA-EPF in Lausanne provided a series of irradiation experiments with the Lithium Blanket Module (LBM). The LBM has both realistic fusion blanket and materials and configuration. It is approximately an 80-cm cube, and the breeding material is Li 2 . Using as the D-T neutron source the Haefely Neutron Generator (HNG) with an intensity of about 5·10 12 n/s, a series of experiments with the bare LBM as well as with the LBM preceded by Pb, Be and ThO 2 multipliers were carried out. In a recent common Los Alamos/PSI effort, a sensitivity and nuclear data uncertainty path for the modular code system AARE (Advanced Analysis for Reactor Engineering) was developed. This path includes the cross-section code TRAMIX, the one-dimensional finite difference S n -transport code ONEDANT, the two-dimensional finite element S n -transport code TRISM, and the one- and two-dimensional sensitivity and nuclear data uncertainty code SENSIBL. For the nucleonic transport calculations, three 187-neutron-group libraries are presently available: MATXS8A and MATXS8F based on ENDF/B-V evaluations and MAT187 based on JEF/EFF evaluations. COVFILS-2, a 74-group library of neutron cross-sections, scattering matrices and covariances, is the data source for SENSIBL; the 74-group structure of COVFILS-2 is a subset of the Los Alamos 187-group structure. Within the framework of the present work a complete set of forward and adjoint two-dimensional TRISM calculations were performed both for the bare, as well as for the Pb- and Be-preceded, LBM using MATXS8 libraries. Then a two-dimensional sensitivity and uncertainty analysis for all cases was performed

Preliminary Study on J-Resolved NMR Method Usability for Toxic Kidney's Injury Assessment.

Science.gov (United States)

Doskocz, Marek; Marchewka, Zofia; Jeż, Magdalena; Passowicz-Muszyńska, Ewa; Długosz, Anna

2015-01-01

Nowadays, the Nuclear Magnetic Resonance (NMR) techniques are tested for metabolomic urine profile in order to detect early damage of kidney. The purpose of this investigation was the initial assessment of two-dimensional J-resolved NMR urine spectra analysis usability for early kidney injuries detection. The amino acids (AA) and acids profile change after the exposure to nephrotoxic agent (the cisplatin infusion) was examined. The material was the urine of patients with non-small-cell lung cancer, treated with cisplatin in Pulmonology and Lung Cancers Clinic in Wrocław. The urine of healthy volunteers was also examined. The identification of metabolites in urine was based on two-dimensional JRES signals in spectra, described in Human Metabolites Database (HMD). The molar concentration of metabolites was calculated from the volume under the signals. The analysis was focused on amino acids and organic acids (lactid acid and pyruvic acid) profiles. Any specific amino acids were identified after cisplatin infusion in comparison to the state before infusion. However, the differences in concentration were observed over 2-fold increase in valine, isoleucine and leucine, over 3-fold in alanine. Also, the concentration of pyruvic and lactic acids increased significantly (p≤0.05, p≤0.01). There were no specific amino acids identified in response to the infusion of cisplatin; however, some changes in the concentrations of amino acids and other small molecules were found. The analysis of two-dimensional JRES spectra showed an increase of alanine, leucine, isoleucine and valine concentration after the application of cisplatin. It seems that it is worth developing the JRES method based on special computer program.

Synergistic effect of the simultaneous chemometric analysis of {sup 1}H NMR spectroscopic and stable isotope (SNIF-NMR, {sup 18}O, {sup 13}C) data: Application to wine analysis

Energy Technology Data Exchange (ETDEWEB)

Monakhova, Yulia B., E-mail: yul-monakhova@mail.ru [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, Karlsruhe 76187 (Germany); Bruker Biospin GmbH, Silberstreifen, Rheinstetten 76287 (Germany); Department of Chemistry, Saratov State University, Astrakhanskaya Street 83, Saratov 410012 (Russian Federation); Godelmann, Rolf [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, Karlsruhe 76187 (Germany); Hermann, Armin [Landesuntersuchungsamt -Institut für Lebensmittelchemie und Arzneimittelprüfung, Emy-Roeder-Straße 1, Mainz 55129 (Germany); Kuballa, Thomas [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, Karlsruhe 76187 (Germany); Cannet, Claire; Schäfer, Hartmut; Spraul, Manfred [Bruker Biospin GmbH, Silberstreifen, Rheinstetten 76287 (Germany); Rutledge, Douglas N. [AgroParisTech, UMR 1145, Ingénierie Procédés Aliments, 16 rue Claude Bernard, Paris F-75005 (France)

2014-06-23

Highlights: • {sup 1}H NMR profilings of 718 wines were fused with stable isotope analysis data (SNIF-NMR, {sup 18}O, {sup 13}C). • The best improvement was obtained for prediction of the geographical origin of wine. • Certain enhancement was also obtained for the year of vintage (from 88 to 97% for {sup 1}H NMR to 99% for the fused data). • Independent component analysis was used as an alternative chemometric tool for classification. - Abstract: It is known that {sup 1}H NMR spectroscopy represents a good tool for predicting the grape variety, the geographical origin, and the year of vintage of wine. In the present study we have shown that classification models can be improved when {sup 1}H NMR profiles are fused with stable isotope (SNIF-NMR, {sup 18}O, {sup 13}C) data. Variable selection based on clustering of latent variables was performed on {sup 1}H NMR data. Afterwards, the combined data of 718 wine samples from Germany were analyzed using linear discriminant analysis (LDA), partial least squares-discriminant analysis (PLS-DA), factorial discriminant analysis (FDA) and independent components analysis (ICA). Moreover, several specialized multiblock methods (common components and specific weights analysis (ComDim), consensus PCA and consensus PLS-DA) were applied to the data. The best improvement in comparison with {sup 1}H NMR data was obtained for prediction of the geographical origin (up to 100% for the fused data, whereas stable isotope data resulted only in 60–70% correct prediction and {sup 1}H NMR data alone in 82–89% respectively). Certain enhancement was obtained also for the year of vintage (from 88 to 97% for {sup 1}H NMR to 99% for the fused data), whereas in case of grape varieties improved models were not obtained. The combination of {sup 1}H NMR data with stable isotope data improves efficiency of classification models for geographical origin and vintage of wine and can be potentially used for other food products as well.

Novel sst2-selective somatostatin agonists. Three-dimensional consensus structure by NMR

Science.gov (United States)

Grace, Christy Rani R.; Erchegyi, Judit; Koerber, Steven C.; Reubi, Jean Claude; Rivier, Jean; Riek, Roland

2008-01-01

The three-dimensional NMR structures of six octapeptide agonist analogues of somatostatin (SRIF) in the free form are described. These analogues, with the basic sequence H-DPhe/Phe2-c[Cys3-Xxx7-DTrp8-Lys9-Thr10-Cys14]-Thr-NH2 (the numbering refers to the position in native SRIF), with Xxx7 being Ala/Aph, exhibit potent and highly selective binding to human SRIF type 2 (sst2) receptors. The backbone of these sst2-selective analogues have the usual type-II’ β-turn reported in the literature for sst2/3/5-subtype-selective analogues. Correlating biological results and NMR studies led to the identification of the side chains of DPhe2, DTrp8 and Lys9 as the necessary components of the sst2 pharmacophore. This is the first study to show that the aromatic ring at position 7 (Phe7) is not critical for sst2 binding and that it plays an important role in sst3 and sst5 binding. This pharmacophore is therefore different from that proposed by others for sst2/3/5 analogues. PMID:16854054

Use of 15N reverse gradient two-dimensional nuclear magnetic resonance spectroscopy to follow metabolic activity in Nicotiana plumbaginifolia cell-suspension cultures.

Science.gov (United States)

Mesnard, F; Azaroual, N; Marty, D; Fliniaux, M A; Robins, R J; Vermeersch, G; Monti, J P

2000-02-01

Nitrogen metabolism was monitored in suspension cultured cells of Nicotiana plumbaginifolia Viv. using nuclear magnetic resonance (NMR) spectroscopy following the feeding of (15NH4)2SO4 and K15NO3. By using two-dimensional 15N-1H NMR with heteronuclear single-quantum-coherence spectroscopy and heteronuclear multiple-bond-coherence spectroscopy sequences, an enhanced resolution of the incorporation of 15N label into a range of compounds could be detected. Thus, in addition to the amino acids normally observed in one-dimensional 15N NMR (glutamine, aspartate, alanine), several other amino acids could be resolved, notably serine, glycine and proline. Furthermore, it was found that the peak normally assigned to the non-protein amino-acid gamma-aminobutyric acid in the one-dimensional 15N NMR spectrum was resolved into a several components. A peak of N-acetylated compounds was resolved, probably composed of the intermediates in arginine biosynthesis, N-acetylglutamate and N-acetylornithine and, possibly, the intermediate of putrescine degradation into gamma-aminobutyric acid, N-acetylputrescine. The occurrence of 15N-label in agmatine and the low detection of labelled putrescine indicate that crucial intermediates of the pathway from glutamate to polyamines and/or the tobacco alkaloids could be monitored. For the first time, labelling of the peptide glutathione and of the nucleotide uridine could be seen.

Combined chemometric analysis of (1)H NMR, (13)C NMR and stable isotope data to differentiate organic and conventional milk.

Science.gov (United States)

Erich, Sarah; Schill, Sandra; Annweiler, Eva; Waiblinger, Hans-Ulrich; Kuballa, Thomas; Lachenmeier, Dirk W; Monakhova, Yulia B

2015-12-01

The increased sales of organically produced food create a strong need for analytical methods, which could authenticate organic and conventional products. Combined chemometric analysis of (1)H NMR-, (13)C NMR-spectroscopy data, stable-isotope data (IRMS) and α-linolenic acid content (gas chromatography) was used to differentiate organic and conventional milk. In total 85 raw, pasteurized and ultra-heat treated (UHT) milk samples (52 organic and 33 conventional) were collected between August 2013 and May 2014. The carbon isotope ratios of milk protein and milk fat as well as the α-linolenic acid content of these samples were determined. Additionally, the milk fat was analyzed by (1)H and (13)C NMR spectroscopy. The chemometric analysis of combined data (IRMS, GC, NMR) resulted in more precise authentication of German raw and retail milk with a considerably increased classification rate of 95% compared to 81% for NMR and 90% for IRMS using linear discriminate analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Observation of exchange of micropore water in cement pastes by two-dimensional T(2)-T(2) nuclear magnetic resonance relaxometry.

Science.gov (United States)

Monteilhet, L; Korb, J-P; Mitchell, J; McDonald, P J

2006-12-01

The first detailed analysis of the two-dimensional (2D) NMR T(2)-T(2) exchange experiment with a period of magnetization storage between the two T(2) relaxation encoding periods (T(2)-store-T(2)) is presented. It is shown that this experiment has certain advantages over the T(1)-T(2) variant for the quantization of chemical exchange. New T(2)-store-T(2) 2D 1H NMR spectra of the pore water within white cement paste are presented. Based on these spectra, the exchange rate of water between the two smallest porosity reservoirs is estimated for the first time. It is found to be of the order of 5 ms{-1}. Further, a careful estimate of the pore sizes of these reservoirs is made. They are found to be of the order of 1.4 nm and 10-30 nm , respectively. A discussion of the results is developed in terms of possible calcium silicate hydrate products. A water diffusion coefficient inferred from the exchange rate and the cement particle size is found to compare favorably with the results of molecular-dynamics simulations to be found in the literature.

Emission Properties, Solubility, Thermodynamic Analysis and NMR Studies of Rare-Earth Complexes with Two Different Phosphine Oxides

Directory of Open Access Journals (Sweden)

Hiroki Iwanaga

2010-07-01

Full Text Available The paper proposes novel molecular designs for rare-earth complexes involving the introduction of two different phosphine oxide structures into one rare-earth ion. These designs are effective for improving solubility and emission intensity. Additionally, the complexes are indispensable for realizing high performances in LEDs and security media. The thermodynamic properties of Eu(III complexes are correlated with the solubility. Correlations between coordination structures and emission intensity were explained by NMR analysis. The luminous flux of red LED devices with Eu(III complexes is very high (20 mA, 870 m lumen. A new white LED has its largest spectra intensity in the red region and a human look much more vividly under this light.

Two-dimensional polyacrylamide gel analysis of Plodia interpunctella granulosis virus

International Nuclear Information System (INIS)

Russell, D.L.; Consigli, R.A.

1986-01-01

The structural polypeptides of purified Plodia interpunctella granulosis virus were analyzed by three different two-dimensional gel systems. Isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of 53 acidic polypeptides in the enveloped nucleocapsid of the virus ranging in molecular weight from 97,300 to 8000. Nine of these polypeptides were shown to be glycoproteins by the technique of radiolabeled lectin blotting. Separation of the granulin in this system allowed resolution of five species, all of which have identical tryptic peptide maps. This matrix protein was demonstrated to be a phosphoglycoprotein by radiolabeled lectin blotting and acid phosphatase dephosphorylation. Nonequilibrium pH gel electrophoresis followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of the major basic protein of the virus, VP12, from a more acidic protein of the same molecular weight. Tryptic peptide analysis demonstrated that these two proteins were indeed different and acid urea gels followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed localization of the acidic protein to the envelope and the basic protein to the nucleocapsid of the virus. Finally, probing of the separated envelope nucleocapsid proteins in both the isoelectric focusing and nonequilibrium pH gel electrophoresis two-dimensional systems after transfer to nitrocellulose with iodinated, purified viral proteins allowed further insight into reactions which may be important in the maintenance of the virion structure

The theory of critical phenomena in two-dimensional systems

International Nuclear Information System (INIS)

Olvera de la C, M.

1981-01-01

An exposition of the theory of critical phenomena in two-dimensional physical systems is presented. The first six chapters deal with the mean field theory of critical phenomena, scale invariance of the thermodynamic functions, Kadanoff's spin block construction, Wilson's renormalization group treatment of critical phenomena in configuration space, and the two-dimensional Ising model on a triangular lattice. The second part of this work is made of four chapters devoted to the application of the ideas expounded in the first part to the discussion of critical phenomena in superfluid films, two-dimensional crystals and the two-dimensional XY model of magnetic systems. Chapters seven to ten are devoted to the following subjects: analysis of long range order in one, two, and three-dimensional physical systems. Topological defects in the XY model, in superfluid films and in two-dimensional crystals. The Thouless-Kosterlitz iterated mean field theory of the dipole gas. The renormalization group treatment of the XY model, superfluid films and two-dimensional crystal. (author)

Two-dimensional DFA scaling analysis applied to encrypted images

Science.gov (United States)

Vargas-Olmos, C.; Murguía, J. S.; Ramírez-Torres, M. T.; Mejía Carlos, M.; Rosu, H. C.; González-Aguilar, H.

2015-01-01

The technique of detrended fluctuation analysis (DFA) has been widely used to unveil scaling properties of many different signals. In this paper, we determine scaling properties in the encrypted images by means of a two-dimensional DFA approach. To carry out the image encryption, we use an enhanced cryptosystem based on a rule-90 cellular automaton and we compare the results obtained with its unmodified version and the encryption system AES. The numerical results show that the encrypted images present a persistent behavior which is close to that of the 1/f-noise. These results point to the possibility that the DFA scaling exponent can be used to measure the quality of the encrypted image content.

The fluorescence properties and NMR analysis of protopine and allocryptopine

International Nuclear Information System (INIS)

Kubala, Martin; Vacek, Jan; Popa, Igor; Janovska, Marika; Kosina, Pavel; Ulrichova, Jitka; Travnicek, Zdenek; Simanek, Vilim

2011-01-01

The fluorescence properties of protopine and allocryptopine in aqueous and organic environments are described for the first time. The fluorescence of alkaloids and their pH-dependent interconversion to cationic forms (transannular interaction) were studied using steady-state and time-resolved fluorescence techniques. For the analysis of tricyclic base and cis/trans tetracyclic cations of the alkaloids, NMR and X-ray crystallography were used. - Highlights: → We describe fundamental fluorescence characteristics of alkaloids protopine and allocryptopine. → We analyzed the pH-dependent transitions and cis/trans isomerization. → These two alkaloids can be better distinguished by their fluorescence decay characteristics. → The fluorescence parameters are related to the NMR and crystallographic structural data.

Two-dimensional simulation of sintering process

International Nuclear Information System (INIS)

Vasconcelos, Vanderley de; Pinto, Lucio Carlos Martins; Vasconcelos, Wander L.

1996-01-01

The results of two-dimensional simulations are directly applied to systems in which one of the dimensions is much smaller than the others, and to sections of three dimensional models. Moreover, these simulations are the first step of the analysis of more complex three-dimensional systems. In this work, two basic features of the sintering process are studied: the types of particle size distributions related to the powder production processes and the evolution of geometric parameters of the resultant microstructures during the solid-state sintering. Random packing of equal spheres is considered in the sintering simulation. The packing algorithm does not take into account the interactive forces between the particles. The used sintering algorithm causes the densification of the particle set. (author)

Computer-assisted structure elucidation from 13C-NMR-Spectra. I. The development of a three-dimensional structure code. II. The development of an isomer generating program

International Nuclear Information System (INIS)

Schuetz, V.

1999-05-01

The presented thesis consists of two separate programs which both aid the automated structure elucidation in the CSEARCH database system. A successful utilization of a large collection of NMR reference spectra for the prediction of chemical shift values is dependent on a strong correlation between the spectral data and the structural information via unique coding. By now, this was done using the two-dimensional HOSE code, which turned out to be insufficient whenever stereochemical effects other than cis/trans-isomerism contribute to the chemical shift values. Therefore, this new algorithm has been developed to derive the demanded three-dimensional descriptors. The calculation is performed by matching the query structures against pattern molecules taken from a carefully selected library of ring skeletons. No three-dimensional coordinates are necessary, since the algorithm elucidates the descriptors on base of two-dimensional structures having their stereocenters specified using 'up/down' bonds. The descriptors are defined as number of interactions over 3 to 5 bonds, number of cis-substituents over 1 to 2 ringbonds and markers for axial substituents. This approach of deriving descriptors for steric interactions has successfully extended the HOSE coding scheme and has been implemented into a neural network; both methods allow for high-quality prediction of 13 C-NMR chemical shift values. The second algorithm is an isomer generating program named GENERAL, which efficiently supports the structure elucidation process by calculating all mathematically possible structures to a given molecular formula. The resulting list of structures is exhaustive and free of redundancy. Besides the basic input information - like the molecular formula and the specification of structural fragments, constraints can be defined to restrict the number of resulting structures. The most valuable information is provided by state-of-the-art 2D-NMR experiments and can be easily incorporated into

Sensitivity analysis using two-dimensional models of the Whiteshell geosphere

Energy Technology Data Exchange (ETDEWEB)

Scheier, N. W.; Chan, T.; Stanchell, F. W.

1992-12-01

As part of the assessment of the environmental impact of disposing of immobilized nuclear fuel waste in a vault deep within plutonic rock, detailed modelling of groundwater flow, heat transport and containment transport through the geosphere is being performed using the MOTIF finite-element computer code. The first geosphere model is being developed using data from the Whiteshell Research Area, with a hypothetical disposal vault at a depth of 500 m. This report briefly describes the conceptual model and then describes in detail the two-dimensional simulations used to help initially define an adequate three-dimensional representation, select a suitable form for the simplified model to be used in the overall systems assessment with the SYVAC computer code, and perform some sensitivity analysis. The sensitivity analysis considers variations in the rock layer properties, variations in fracture zone configurations, the impact of grouting a vault/fracture zone intersection, and variations in boundary conditions. This study shows that the configuration of major fracture zones can have a major influence on groundwater flow patterns. The flows in the major fracture zones can have high velocities and large volumes. The proximity of the radionuclide source to a major fracture zone may strongly influence the time it takes for a radionuclide to be transported to the surface. (auth)

Chemical characterization of a chelator-treated soil humate by solution-state multinuclear two-dimensional NMR and FTIR and pyrolysis-GCMS

Energy Technology Data Exchange (ETDEWEB)

Fan, T.W.M.; Higashi, R.M.; Lane, A.N.

2000-05-01

A California forest soil used for contaminant bioavailability studies was extracted for humic substances (HS) and then treated with 4,5-dihydroxy-1,3-benzene disulfonate (Tiron) to remove exchangeable metal ions. This yielded HS that was readily water-soluble at neutral pH without residual Tiron contamination, and the gel electrophoretic pattern was very similar to an international reference HS. The improved solubility facilitated analysis of HS by solution-state 1-D and 2-D {sup 1}H, {sup 13}C, {sup 31}P, and {sup 13}C-{sup 1}H NMR. The amino acids Gly, Ala, Leu, lle, Val, Asp, Ser, Thr, Glu, and Pro were identified in intact HS as peptidic from scalar coupling in TOCSY and dipolar interactions in NOESY and then confirmed by acid digestion of HS with 2-D {sup 1}H NMR and GCMS analysis. The presence of peptides was also corroborated by FT-IR and pyrolysis-GCMS results. Carbohydrates containing {alpha}- and {beta}-pyranoses, methoxy-phenylpropanyl structures, phosphate mono/diesters, polyphosphates, plus phosphatidic acid esters were also evident. Furthermore, the {sup 1}H NOESY, TOCSY, and HSQC together indicated that the peptidic side chains were mobile, whereas aromatic groups were relatively rigid. Thus the peptidic moieties may be more readily accessible to aqueous contaminants than aromatic groups.

Teaching NMR spectra analysis with nmr.cheminfo.org.

Science.gov (United States)

Patiny, Luc; Bolaños, Alejandro; Castillo, Andrés M; Bernal, Andrés; Wist, Julien

2018-06-01

Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of exercises and tools to help solving them. Only a small number of exercises are currently available, but contributors are invited to submit new ones and suggest new types of problems. Copyright © 2018 John Wiley & Sons, Ltd.

COBRA/TRAC analysis of two-dimensional thermal-hydraulic behavior in SCTF reflood tests

International Nuclear Information System (INIS)

Iwamura, Takamichi; Ohnuki, Akira; Sobajima, Makoto; Adachi, Hiromichi

1987-01-01

The effects of radial power distribution and non-uniform upper plenum water accumulation on thermal-hydraulic behavior in the core were observed in the reflood tests with Slab Core Test Facility (SCTF). In order to examine the predictability of these two effects by a multi-dimensional analysis code, the COBRA/TRAC calculations were made. The calculated results indicated that the heat transfer enhancement in high power bundles above quench front was caused by high vapor flow rate in those bundles due to the radial power distribution. On the other hand, the heat transfer degradation in the peripheral bundles under the condition of non-uniform upper plenum water accumulation was caused by the lower flow rates of vapor and entrained liquid above the quench front in those bundles by the reason that vapor concentrated in the center bundles due to the cross flow induced by the horizontal pressure gradient in the core. The above-mentioned two-dimensional heat transfer behaviors calculated with the COBRA/TRAC code is similar to those observed in SCTF tests and therefore those calculations are useful to investigate the mechanism of the two-dimensional effects in SCTF reflood tests. (author)

Numerical analysis of biological clogging in two-dimensional sand box experiments

DEFF Research Database (Denmark)

Kildsgaard, J.; Engesgaard, Peter Knudegaard

2001-01-01

Two-dimensional models for biological clogging and sorptive tracer transport were used to study the progress of clogging in a sand box experiment. The sand box had been inoculated with a strip of bacteria and exposed to a continuous injection of nitrate and acetate. Brilliant Blue was regularly...... injected during the clogging experiment and digital images of the tracer movement had been converted to concentration maps using an image analysis. The calibration of the models to the Brilliant Blue observations shows that Brilliant Blue has a solid biomass dependent sorption that is not compliant...... with the assumed linear constant Kd behaviour. It is demonstrated that the dimensionality of sand box experiments in comparison to column experiments results in a much lower reduction in hydraulic conductivity Žfactor of 100. and that the bulk hydraulic conductivity of the sand box decreased only slightly. However...

Two-dimensional Simulations of Correlation Reflectometry in Fusion Plasmas

International Nuclear Information System (INIS)

Valeo, E.J.; Kramer, G.J.; Nazikian, R.

2001-01-01

A two-dimensional wave propagation code, developed specifically to simulate correlation reflectometry in large-scale fusion plasmas is described. The code makes use of separate computational methods in the vacuum, underdense and reflection regions of the plasma in order to obtain the high computational efficiency necessary for correlation analysis. Simulations of Tokamak Fusion Test Reactor (TFTR) plasma with internal transport barriers are presented and compared with one-dimensional full-wave simulations. It is shown that the two-dimensional simulations are remarkably similar to the results of the one-dimensional full-wave analysis for a wide range of turbulent correlation lengths. Implications for the interpretation of correlation reflectometer measurements in fusion plasma are discussed

Evaluating two-dimensional skeletal structure parameters using radiological bone morphometric analysis

International Nuclear Information System (INIS)

Asa, Kensuke; Sakurai, Takashi; Kashima, Isamu; Kumasaka, Satsuki

2005-01-01

The objectives of this study was to investigate the reliability of two-dimensional (2D) skeletal structure parameters obtained using radiological bone morphometric analysis. The 2D skeletal parameters in the regions of interest (ROIs) were measured on computed radiography (CR) images of first phalanges from racehorses, using radiological bone morphometric analysis. Cancellous bone blocks were made from the phalanges in the same position as the ROI determined on CR images. Three-dimensional (3D) trabecular parameters were measured using micro-computed tomography (μCT). The correlations between the 2D skeletal parameters and 3D trabecular parameters were evaluated in relation to the measured bone strength. The following 2D skeletal structure parameters were correlated with bone strength (r=0.61-0.69): skeletal perimeter (Sk.Pm), skeletal number (Sk.N), skeletal separation (Sk.Sp), skeletal spacing (Sk.Spac), fractal dimension (FD), and skeletal pattern factor (SkPf). The 3D trabecular structure parameters were closely correlated with bone strength (r=0.74-0.86). The 2D skeletal parameters Sk.N, Sk.Pm, FD, SkPf, and Sk.Spac were correlated with the 3D trabecular parameters (r=0.61-0.70). The 2D skeletal parameters obtained using radiological bone morphometric analysis may be useful indicators of trabecular strength. (author)

NMR spectroscopy and drug development

International Nuclear Information System (INIS)

Craik, D.; Munro, S.

1990-01-01

The use of nuclear magnetic resonance (NMR) spectroscopy for structural and conformational studies on drug molecules, the three-dimensional investigation of proteins structure and their interactions with ligands are discussed. In-vivo NMR studies of the effects of drugs on metabolism in perfused organs and whole animals are also briefly presented. 5 refs., ills

Structural studies of bacterial transcriptional regulatory proteins by multidimensional heteronuclear NMR

Energy Technology Data Exchange (ETDEWEB)

Volkman, Brian Finley [Univ. of California, Berkeley, CA (United States)

1995-02-01

Nuclear magnetic resonance spectroscopy was used to elucidate detailed structural information for peptide and protein molecules. A small peptide was designed and synthesized, and its three-dimensional structure was calculated using distance information derived from two-dimensional NMR measurements. The peptide was used to induce antibodies in mice, and the cross-reactivity of the antibodies with a related protein was analyzed with enzyme-linked immunosorbent assays. Two proteins which are involved in regulation of transcription in bacteria were also studied. The ferric uptake regulation (Fur) protein is a metal-dependent repressor which controls iron uptake in bacteria. Two- and three-dimensional NMR techniques, coupled with uniform and selective isotope labeling allowed the nearly complete assignment of the resonances of the metal-binding domain of the Fur protein. NTRC is a transcriptional enhancer binding protein whose N-terminal domain is a "receiver domain" in the family of "two-component" regulatory systems. Phosphorylation of the N-terminal domain of NTRC activates the initiation of transcription of aeries encoding proteins involved in nitrogen regulation. Three- and four-dimensional NMR spectroscopy methods have been used to complete the resonance assignments and determine the solution structure of the N-terminal receiver domain of the NTRC protein. Comparison of the solution structure of the NTRC receiver domain with the crystal structures of the homologous protein CheY reveals a very similar fold, with the only significant difference being the position of helix 4 relative to the rest of the protein. The determination of the structure of the NTRC receiver domain is the first step toward understanding a mechanism of signal transduction which is common to many bacterial regulatory systems.

Biomolecular solid state NMR with magic-angle spinning at 25K.

Science.gov (United States)

Thurber, Kent R; Tycko, Robert

2008-12-01

A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.

Comparison of two three-dimensional cephalometric analysis computer software

OpenAIRE

Sawchuk, Dena; Alhadlaq, Adel; Alkhadra, Thamer; Carlyle, Terry D; Kusnoto, Budi; El-Bialy, Tarek

2014-01-01

Background: Three-dimensional cephalometric analyses are getting more attraction in orthodontics. The aim of this study was to compare two softwares to evaluate three-dimensional cephalometric analyses of orthodontic treatment outcomes. Materials and Methods: Twenty cone beam computed tomography images were obtained using i-CAT® imaging system from patient's records as part of their regular orthodontic records. The images were analyzed using InVivoDental5.0 (Anatomage Inc.) and 3DCeph™ (Unive...

Two-Dimensional Liquid Chromatography Analysis of Polystyrene/Polybutadiene Block Copolymers.

Science.gov (United States)

Lee, Sanghoon; Choi, Heejae; Chang, Taihyun; Staal, Bastiaan

2018-05-15

A detailed characterization of a commercial polystyrene/polybutadiene block copolymer material (Styrolux) was carried out using two-dimensional liquid chromatography (2D-LC). The Styrolux is prepared by statistical linking reaction of two different polystyrene- block-polybutadienyl anion precursors with a multivalent linking agent. Therefore, it is a mixture of a number of branched block copolymers different in molecular weight, composition, and chain architecture. While individual LC analysis, including size exclusion chromatography, interaction chromatography, or liquid chromatography at critical condition, is not good enough to resolve all the polymer species, 2D-LC separations coupling two chromatography methods were able to resolve all polymer species present in the sample; at least 13 block copolymer species and a homopolystyrene blended. Four different 2D-LC analyses combining a different pair of two LC methods provide their characteristic separation results. The separation characteristics of the 2D-LC separations are compared to elucidate the elution characteristics of the block copolymer species.

Sequence-specific 1H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

International Nuclear Information System (INIS)

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-01-01

On the basis of an analysis of two-dimensional 1 H NMR spectra, the complete sequence-specific 1 H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four β-strands that form a single antiparallel β-sheet and two well-defined α-helices. There are two stretches of extended backbone structure, one of which contains the active site His 15 . The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies

Structural elucidation and NMR assignments of a new pyrrolizidine alkaloid from Crotalaria vitellina Ker Gawl.

Science.gov (United States)

Casimiro Bezerra, Denise Aline; Fechine Tavares, Josean; dos Santos, Paula Ferreira; Castello Branco, Marianna Vieira Sobral; de Fátima Agra, Maria; Subrinho, Fernanda Lima; Braz-Filho, Raimundo; da Silva, Marcelo Sobral

2013-08-01

A new pyrrolizidine alkaloid, named crotavitelin, was isolated from fruits of Crotalaria vitellina, Fabaceae (Papilionoideae). The structure was established by spectroscopic techniques such as one-dimensional and two-dimensional NMR, IR, and MS. Copyright © 2013 John Wiley & Sons, Ltd.

Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server

Energy Technology Data Exchange (ETDEWEB)

Bingol, Kerem [Environmental; Li, Da-Wei; Zhang, Bo; Brüschweiler, Rafael

2016-12-06

Identification of metabolites in complex mixtures represents a key step in metabolomics. A new strategy is introduced, which is implemented in a new public web server, COLMARm, that permits the co-analysis of up to three 2D NMR spectra, namely 13C-1H HSQC, 1H-1H TOCSY, and 13C-1H HSQC-TOCSY for the comprehensive, accurate, and efficient performance of this task. The highly versatile and interactive nature of COLMARm permits its application to a wide range of metabolomics samples independent of the magnetic field. Database query is performed using the HSQC spectrum and the top metabolite hits are then validated against the TOCSY-type experiment(s) by superimposing the expected cross-peaks on the mixture spectrum. In this way the user can directly accept or reject candidate metabolites by taking advantage of the complementary spectral information offered by these experiments and their different sensitivities. The power of COLMARm is demonstrated for a human serum sample uncovering the existence of 14 metabolites that hitherto were not identified by NMR.

NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

Science.gov (United States)

Bingol, Kerem; Brüschweiler, Rafael

2015-06-05

A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence, and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture, and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously, further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only a few seconds on a computer workstation. NMR/MS Translator synergistically uses the power of NMR and MS, enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases.

Construction of two-dimensional quantum chromodynamics

Energy Technology Data Exchange (ETDEWEB)

Klimek, S.; Kondracki, W.

1987-12-01

We present a sketch of the construction of the functional measure for the SU(2) quantum chromodynamics with one generation of fermions in two-dimensional space-time. The method is based on a detailed analysis of Wilson loops.

Detailed {sup 1}H and {sup 13}C NMR spectral data assignment for two dihydrobenzofuran neolignans

Energy Technology Data Exchange (ETDEWEB)

Medeiros, Talita C.T.; Dias, Herbert J.; Crotti, Antônio E.M., E-mail: millercrotti@ffclrp.usp.br [Universidade de São Paulo (USP), Ribeirão Preto, SP (Brazil). Faculdade de Filosofia, Ciências e Letras. Departamento de Química

2016-07-01

In this work we present a complete proton ({sup 1}H) and carbon 13 ({sup 13}C) nuclear magnetic resonance (NMR) spectral analysis of two synthetic dihydrofuran neolignans (±)-trans-dehydrodicoumarate dimethyl ester and (±)-trans-dehydrodiferulate dimethyl ester. Unequivocal assignments were achieved by 1 H NMR, proton decoupled {sup 13}C ({sup 13}C{"1H}) NMR spectra, gradient-selected correlation spectroscopy (gCOSY), J-resolved, gradient-selected heteronuclear multiple quantum coherence (gHMQC), gradient-selected heteronuclear multiple bond coherence (gHMBC) and nuclear Overhauser effect spectroscopy (NOESY) experiments. All hydrogen coupling constants were measured, clarifying all the hydrogen signals multiplicities. Computational methods were also used to simulate the {sup 1}H and {sup 13}C chemical shifts and showed good agreement with the trans configuration of the substituents at C{sub 7} and C{sub 8}. (author)

Application of 1D- and 2D-NMR techniques for the structural studies of glycoprotein-derived carbohydrates

International Nuclear Information System (INIS)

Breg, J.N.

1989-01-01

The first part of this thesis (Chapters 1 to 4) describe the determination of the primary structure for a large number of oligosaccharide-alditols obtained from bronchial sputum of cystic fibrosis patients suffering from chronic bronchitis. The second part (Chapters 5 to 8) is devoted to the application of two-dimensional NMR methods for the structural analysis of oligosaccharides. (H.W.). 163 refs.; 50 figs.; 25 tabs

Applying clustering to statistical analysis of student reasoning about two-dimensional kinematics

Directory of Open Access Journals (Sweden)

R. Padraic Springuel

2007-12-01

Full Text Available We use clustering, an analysis method not presently common to the physics education research community, to group and characterize student responses to written questions about two-dimensional kinematics. Previously, clustering has been used to analyze multiple-choice data; we analyze free-response data that includes both sketches of vectors and written elements. The primary goal of this paper is to describe the methodology itself; we include a brief overview of relevant results.

Two-Dimensional Raman Correlation Analysis of Diseased Esophagus in a Rat

Science.gov (United States)

Takanezawa, Sota; Morita, Shin-ichi; Maruyama, Atsushi; Murakami, Takurou N.; Kawashima, Norimichi; Endo, Hiroyuki; Iijima, Katsunori; Asakura, Tohru; Shimosegawa, Tooru; Sato, Hidetoshi

2010-07-01

Generalized two-dimensional (2D) Raman correlation analysis effectively distinguished a benign tumor from normal tissue. Line profiling Raman spectra of a rat esophagus, including a benign tumor, were measured and the generalized 2D synchronous and asynchronous spectra were calculated. In the autocorrelation area of the amide I band of proteins in the asynchronous map, a cross-like pattern was observed. A simulation study indicated that the pattern was caused by a sharp band component in the amide I band region. We considered that the benign tumor corresponded to the sharp component.

Non-Linear Non Stationary Analysis of Two-Dimensional Time-Series Applied to GRACE Data, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — The proposed innovative two-dimensional (2D) empirical mode decomposition (EMD) analysis was applied to NASA's Gravity Recovery and Climate Experiment (GRACE)...

Comprehensive two-dimensional gas chromatography for biogas and biomethane analysis.

Science.gov (United States)

Hilaire, F; Basset, E; Bayard, R; Gallardo, M; Thiebaut, D; Vial, J

2017-11-17

The gas industry is going to be revolutionized by being able to generate bioenergy from biomass. The production of biomethane - a green substitute of natural gas - is growing in Europe and the United-States of America. Biomethane can be injected into the gas grid or used as fuel for vehicles after compression. Due to various biomass inputs (e.g. agricultural wastes, sludges from sewage treatment plants, etc.), production processes (e.g. anaerobic digestion, municipal solid waste (MSW) landfills), seasonal effects and purification processes (e.g. gas scrubbers, pressure swing adsorption, membranes for biogas upgrading), the composition and quality of biogas and biomethane produced is difficult to assess. All previous publications dealing with biogas analysis reported that hundreds of chemicals from ten chemical families do exist in trace amounts in biogas. However, to the best of our knowledge, no study reported a detailed analysis or the implementation of comprehensive two-dimensional gas chromatography (GC×GC) for biogas matrices. This is the reason why the benefit of implementing two-dimensional gas chromatography for the characterization of biogas and biomethane samples was evaluated. In a first step, a standard mixture of 89 compounds belonging to 10 chemical families, representative of those likely to be found, was used to optimize the analytical method. A set consisting of a non-polar and a polar columns, respectively in the first and the second dimension, was used with a modulation period of six seconds. Applied to ten samples of raw biogas, treated biogas and biomethane collected on 4 industrial sites (two MSW landfills, one anaerobic digester on a wastewater treatment plant and one agricultural biogas plant), this analytical method provided a "fingerprint" of the gases composition at the molecular level in all biogas and biomethane samples. Estimated limits of detection (far below the μgNm -3 ) coupled with the resolution of GC×GC allowed the comparison

Two-dimensional versus three-dimensional CT angiography in analysis of anatomical suitability for stentgraft repair of abdominal aortic aneurysms

International Nuclear Information System (INIS)

Pitoulias, Georgios A.; Aslanidou, Eleni A.; Papadimitriou, Dimitrios K.; Donas, Konstantinos P.; Schulte, Stefan

2011-01-01

Background The morphological analysis prior to endovascular abdominal aneurysm repair (EVAR) plays an important role in long-term outcomes. Post-imaging analysis of computed tomographic angiography (CTA) by three-dimensional reconstruction with central lumen line detection (CLL 3D-CTA) enables measurements to be made in orthogonal slices. This might be more precise than equal post-imaging analysis in axial slices by two-dimensional computed tomographic angiography (2D-CTA). Purpose To evaluate the intra- and interobserver variability of CLL 3D-CTA and 2D-CTA post-imaging analysis methods and the agreement between them in pre-EVAR suitability analysis of patients with abdominal aortic aneurysm (AAA). Material and Methods Anonymized CTA data-sets from 70 patients with AAA were analyzed retrospectively. Length measurements included proximal and distal aortic neck lengths and total distance from the lower renal artery to the higher iliac bifurcation. Width measurements included proximal and distal neck diameters, maximum AAA diameter and common iliac diameters just above the iliac bifurcations. The measurements were performed in random order by two vascular surgeons, twice per method with 1-month interval between readings. In the CLL 3D-CTA method we used semi-automated CLL detection by software and manual measurements on CTA slices perpendicular to CLL. The equal measurements in 2D-CTA were performed manually on axial CTA slices using a DICOM viewer workstation. The intra- and interobserver variability, as well as the agreement between the two methods were assessed by Bland-Altman test and bivariate correlation analysis. Results The intraobserver variability was significantly higher in 2D-CTA measurements for both readers. The interobserver variability was significant in 2D-CTA measurements of proximal neck dimensions while the agreement in CLL 3D-CTA analysis between the two readers was excellent in all studied parameters. The agreement between the two suitability

LC-NMR coupling technology: recent advancements and applications in natural products analysis

NARCIS (Netherlands)

Exarchou, V.; Krucker, M.; Beek, van T.A.; Vervoort, J.J.M.; Gerothanassis, I.P.; Albert, K.

2005-01-01

An overview of recent advances in nuclear magnetic resonance (NMR) coupled with separation technologies and their application in natural product analysis is given and discussed. The different modes of LC-NMR operation are described, as well as how technical improvements assist in establishing LC-NMR

Two-dimensional effects in nonlinear Kronig-Penney models

DEFF Research Database (Denmark)

Gaididei, Yuri Borisovich; Christiansen, Peter Leth; Rasmussen, Kim

1997-01-01

An analysis of two-dimensional (2D) effects in the nonlinear Kronig-Penney model is presented. We establish an effective one-dimensional description of the 2D effects, resulting in a set of pseudodifferential equations. The stationary states of the 2D system and their stability is studied...

1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

Directory of Open Access Journals (Sweden)

Myrna J. Simpson

2013-08-01

Full Text Available 1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS, betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA of contaminants is not clearly defined.

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

International Nuclear Information System (INIS)

Kobayashi, Naohiro; Iwahara, Junji; Koshiba, Seizo; Tomizawa, Tadashi; Tochio, Naoya; Guentert, Peter; Kigawa, Takanori; Yokoyama, Shigeyuki

2007-01-01

The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets. In combination with CYANA, the program for automated NOE assignment and structure determination, we have established a robust and highly optimized strategy for comprehensive protein structure analysis. An application of KUJIRA in accordance with our new strategy was carried out by a non-expert in NMR structure analysis, demonstrating that the accurate assignment of the chemical shifts and a high-quality structure of a small protein can be completed in a few weeks. The high completeness of the chemical shift assignment and the NOE assignment achieved by the systematic analysis using KUJIRA and CYANA led, in practice, to increased reliability of the determined structure

Field analysis of two-dimensional focusing grating

OpenAIRE

Borsboom, P.P.; Frankena, H.J.

1995-01-01

The method that we have developed [P-P. Borsboom, Ph.D. dissertation (Delft University of Technology, Delft, The Netherlands); P-P. Borsboom and H. J. Frankena, J. Opt. Soc. Am. A 12, 1134–1141 (1995)] is successfully applied to a two-dimensional focusing grating coupler. The field in the focal region has been determined for symmetrical chirped gratings consisting of as many as 124 corrugations. The intensity distribution in the focal region agrees well with the approximate predictions of geo...

Analysis of the two dimensional Datta-Das Spin Field Effect Transistor

OpenAIRE

Bandyopadhyay, S.

2010-01-01

An analytical expression is derived for the conductance modulation of a ballistic two dimensional Datta-Das Spin Field Effect Transistor (SPINFET) as a function of gate voltage. Using this expression, we show that the recently observed conductance modulation in a two-dimensional SPINFET structure does not match the theoretically expected result very well. This calls into question the claimed demonstration of the SPINFET and underscores the need for further careful investigation.

Analysis of the two-dimensional Datta-Das spin field effect transistor

Science.gov (United States)

Agnihotri, P.; Bandyopadhyay, S.

2010-03-01

An analytical expression is derived for the conductance modulation of a ballistic two-dimensional Datta-das spin field effect transistor (SPINFET) as a function of gate voltage. Using this expression, we show that the recently observed conductance modulation in a two-dimensional SPINFET structure does not match the theoretically expected result very well. This calls into question the claimed demonstration of the SPINFET and underscores the need for further careful investigation.

Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba.

Science.gov (United States)

Napolitano, José G; Lankin, David C; Chen, Shao-Nong; Pauli, Guido F

2012-08-01

The complete and unambiguous (1)H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive (1)H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d(6) were obtained through the examination of 1D (1)H NMR and 2D (1)H,(1)H-COSY data, in combination with (1)H iterative full spin analysis (HiFSA). The computational analysis of discrete spin systems allowed a detailed characterization of all the (1)H NMR signals in terms of chemical shifts (δ(H)) and spin-spin coupling constants (J(HH)), regardless of signal overlap and higher order coupling effects. The capability of the HiFSA-generated (1)H fingerprints to reproduce experimental (1)H NMR spectra at different field strengths was also evaluated. As a result of this analysis, a revised set of (1)H NMR parameters for all ten phytoconstituents was assembled. Furthermore, precise (1)H NMR assignments of the sugar moieties of isoquercetin and rutin are reported for the first time. Copyright © 2012 John Wiley & Sons, Ltd.

Optimizing nanodiscs and bicelles for solution NMR studies of two β-barrel membrane proteins

International Nuclear Information System (INIS)

Kucharska, Iga; Edrington, Thomas C.; Liang, Binyong; Tamm, Lukas K.

2015-01-01

Solution NMR spectroscopy has become a robust method to determine structures and explore the dynamics of integral membrane proteins. The vast majority of previous studies on membrane proteins by solution NMR have been conducted in lipid micelles. Contrary to the lipids that form a lipid bilayer in biological membranes, micellar lipids typically contain only a single hydrocarbon chain or two chains that are too short to form a bilayer. Therefore, there is a need to explore alternative more bilayer-like media to mimic the natural environment of membrane proteins. Lipid bicelles and lipid nanodiscs have emerged as two alternative membrane mimetics that are compatible with solution NMR spectroscopy. Here, we have conducted a comprehensive comparison of the physical and spectroscopic behavior of two outer membrane proteins from Pseudomonas aeruginosa, OprG and OprH, in lipid micelles, bicelles, and nanodiscs of five different sizes. Bicelles stabilized with a fraction of negatively charged lipids yielded spectra of almost comparable quality as in the best micellar solutions and the secondary structures were found to be almost indistinguishable in the two environments. Of the five nanodiscs tested, nanodiscs assembled from MSP1D1ΔH5 performed the best with both proteins in terms of sample stability and spectral resolution. Even in these optimal nanodiscs some broad signals from the membrane embedded barrel were severely overlapped with sharp signals from the flexible loops making their assignments difficult. A mutant OprH that had two of the flexible loops truncated yielded very promising spectra for further structural and dynamical analysis in MSP1D1ΔH5 nanodiscs

Fourier analysis of cell-wise Block-Jacobi splitting in two-dimensional geometry

International Nuclear Information System (INIS)

Rosa, M.; Warsa, J. S.; Kelley, T. M.

2009-01-01

A Fourier analysis is conducted in two-dimensional (2D) geometry for the discrete ordinates (S N ) approximation of the neutron transport problem solved with Richardson iteration (Source Iteration) using the cell-wise Block-Jacobi (BJ) algorithm. The results of the Fourier analysis show that convergence of cell-wise BJ can degrade, leading to a spectral radius equal to 1, in problems containing optically thin cells. For problems containing cells that are optically thick, instead, the spectral radius tends to 0. Hence, in the optically thick-cell regime, cell-wise BJ is rapidly convergent even for problems that are scattering dominated, with a scattering ratio c close to 1. (authors)

Sequence-specific assignments in the 1H NMR spectrum of the human inflammatory protein C5a

International Nuclear Information System (INIS)

Zuiderweg, E.R.P.; Mollison, K.W.; Henkin, J.; Carter, G.W.

1988-01-01

Full sequence-specific assignments for the 1 H NMR lines of the backbone protons of the human complement factor C5a are described and documented. The results were obtained by largely following the methodology developed by Wuethrich et al. Assignments for the majority of the amino acid side chain protons were obtained by using a comparison of double- and triple-quantum-filtered two-dimensional correlated experiments together with the analysis of relayed coherence transfer spectra. The assignments provide the basis for the determination of the thus far unknown three-dimensional structure of C5a from nuclear Overhauser enhancement distance constraints

Two-dimensional cross-section and SED uncertainty analysis for the Fusion Engineering Device (FED)

International Nuclear Information System (INIS)

Embrechts, M.J.; Urban, W.T.; Dudziak, D.J.

1982-01-01

The theory of two-dimensional cross-section and secondary-energy-distribution (SED) sensitivity was implemented by developing a two-dimensional sensitivity and uncertainty analysis code, SENSIT-2D. Analyses of the Fusion Engineering Design (FED) conceptual inboard shield indicate that, although the calculated uncertainties in the 2-D model are of the same order of magnitude as those resulting from the 1-D model, there might be severe differences. The more complex the geometry, the more compulsory a 2-D analysis becomes. Specific results show that the uncertainty for the integral heating of the toroidal field (TF) coil for the FED is 114.6%. The main contributors to the cross-section uncertainty are chromium and iron. Contributions to the total uncertainty were smaller for nickel, copper, hydrogen and carbon. All analyses were performed with the Los Alamos 42-group cross-section library generated from ENDF/B-V data, and the COVFILS covariance matrix library. The large uncertainties due to chromium result mainly from large convariances for the chromium total and elastic scattering cross sections

Characterization of natural bentonite by NMR

International Nuclear Information System (INIS)

Leite, Sidnei Q.M.; Dieguez, Lidia C.; Menezes, Sonia M.C.; San Gil, Rosane A.S.

1993-01-01

Solid state NMR as well as several other instrumental chemical analysis techniques were used in order to characterize two natural occurring bentonite. The methodology is described. The NMR spectra, together with the other used techniques suggest that the observed differences are due to iron inclusions in tetrahedral and octahedral sites

Painleve analysis and transformations for a generalized two-dimensional variable-coefficient Burgers model from fluid mechanics, acoustics and cosmic-ray astrophysics

International Nuclear Information System (INIS)

Wei, Guang-Mei

2006-01-01

Generalized two-dimensional variable-coefficient Burgers model is of current value in fluid mechanics, acoustics and cosmic-ray astrophysics. In this paper, Painleve analysis leads to the constraints on the variable coefficients for such a model to pass the Painleve test and to an auto-Baecklund transformation. Moreover, four transformations from this model are constructed, to the standard two-dimensional and one-dimensional Burgers models with the relevant constraints on the variable coefficients via symbolic computation. By virtue of the given transformations the properties and solutions of this model can be obtained from those of the standard two-dimensional and one-dimensional ones

Stability analysis of nonlinear Roesser-type two-dimensional systems via a homogenous polynomial technique

Science.gov (United States)

Zhang, Tie-Yan; Zhao, Yan; Xie, Xiang-Peng

2012-12-01

This paper is concerned with the problem of stability analysis of nonlinear Roesser-type two-dimensional (2D) systems. Firstly, the fuzzy modeling method for the usual one-dimensional (1D) systems is extended to the 2D case so that the underlying nonlinear 2D system can be represented by the 2D Takagi—Sugeno (TS) fuzzy model, which is convenient for implementing the stability analysis. Secondly, a new kind of fuzzy Lyapunov function, which is a homogeneous polynomially parameter dependent on fuzzy membership functions, is developed to conceive less conservative stability conditions for the TS Roesser-type 2D system. In the process of stability analysis, the obtained stability conditions approach exactness in the sense of convergence by applying some novel relaxed techniques. Moreover, the obtained result is formulated in the form of linear matrix inequalities, which can be easily solved via standard numerical software. Finally, a numerical example is also given to demonstrate the effectiveness of the proposed approach.

Stability analysis of nonlinear Roesser-type two-dimensional systems via a homogenous polynomial technique

International Nuclear Information System (INIS)

Zhang Tie-Yan; Zhao Yan; Xie Xiang-Peng

2012-01-01

This paper is concerned with the problem of stability analysis of nonlinear Roesser-type two-dimensional (2D) systems. Firstly, the fuzzy modeling method for the usual one-dimensional (1D) systems is extended to the 2D case so that the underlying nonlinear 2D system can be represented by the 2D Takagi—Sugeno (TS) fuzzy model, which is convenient for implementing the stability analysis. Secondly, a new kind of fuzzy Lyapunov function, which is a homogeneous polynomially parameter dependent on fuzzy membership functions, is developed to conceive less conservative stability conditions for the TS Roesser-type 2D system. In the process of stability analysis, the obtained stability conditions approach exactness in the sense of convergence by applying some novel relaxed techniques. Moreover, the obtained result is formulated in the form of linear matrix inequalities, which can be easily solved via standard numerical software. Finally, a numerical example is also given to demonstrate the effectiveness of the proposed approach. (general)

Quantitative two-dimensional gel electrophoresis analysis of human fibroblasts transformed by ras oncogenes.

Science.gov (United States)

Miller, M J; Maher, V M; McCormick, J J

1992-11-01

Quantitative two-dimensional gel electrophoresis was used to compare the cellular protein patterns of a normal foreskin-derived human fibroblasts cell line (LG1) and three immortal derivatives of LG1. One derivative, designated MSU-1.1 VO, was selected for its ability to grow in the absence of serum and is non-tumorigenic in athymic mice. The other two strains were selected for focus-formation following transfection with either Ha-ras or N-ras oncogenes and form high grade malignant tumors. Correspondence and cluster analysis provided a nonbiased estimate of the relative similarity of the different two-dimensional patterns. These techniques separated the gel patterns into three distinct classes: LG1, MSU-1.1 VO, and the ras transformed cell strains. The MSU-1.1 VO cells were more closely related to the parental LG1 than to the ras-transformed cells. The differences between the three classes were primarily quantitative in nature: 16% of the spots demonstrated statistically significant changes (P 2) in the rate of incorporation of radioactive amino acids. The patterns from the two ras-transformed cell strains were similar, and variations in the expression of proteins that occurred between the separate experiments obscured consistent differences between the Ha-ras and N-ras transformed cells. However, while only 9 out of 758 spots were classified as different (1%), correspondence analysis could consistently separate the two ras transformants. One of these spots was five times more intense in the Ha-ras transformed cells than the N-ras.(ABSTRACT TRUNCATED AT 250 WORDS)

NMR studies of granular media and two-phase flow in porous media

Science.gov (United States)

Yang, Xiaoyu

This dissertation describes two experimental studies of a vibrofluidized granular medium and a preliminary study of two-phase fluid flow in a porous medium using Nuclear Magnetic Resonance (NMR). The first study of granular medium is to test a scaling law of the rise in center of mass in a three-dimensional vibrofluidized granular system. Our granular system consisted of mustard seeds vibrated vertically at 40 Hz from 0g to 14g. We used Magnetic Resonance Imaging (MRI) to measure density profile in vibrated direction. We observed that the rise in center of mass scaled as nu 0alpha/Nlbeta with alpha = 1.0 +/- 0.2 and beta = 0.5 +/- 0.1, where nu 0 is the vibration velocity and Nl is the number of layers of grains in the container. A simple theory was proposed to explain the scaling exponents. In the second study we measured both density and velocity information in the same setup of the first study. Pulsed Field Gradient (PFG)-NMR combined with MRI was used to do this measurement. The granular system was fully fluidized at 14.85g 50 Hz with Nl ≤ 4. The velocity distributions at horizontal and vertical direction at different height were measured. The distributions were nearly-Gaussian far from sample bottom and non-Gaussian near sample bottom. Granular temperature profiles were calculated from the velocity distributions. The density and temperature profile were fit to a hydrodynamic theory. The theory agreed with experiments very well. A temperature inversion near top was also observed and explained by additional transport coefficient from granular hydrodynamics. The third study was the preliminary density measurement of invading phase profile in a two-phase flow in porous media. The purpose of this study was to test an invasion percolation with gradient (IPG) theory in two-phase flow of porous media. Two phases are dodecane and water doped with CuSO4. The porous medium was packed glass beads. The front tail width sigma and front width of invading phase were

A solid-phase extraction procedure coupled to 1H NMR, with chemometric analysis, to seek reliable markers of the botanical origin of honey

International Nuclear Information System (INIS)

Beretta, Giangiacomo; Caneva, Enrico; Regazzoni, Luca; Bakhtyari, Nazanin Golbamaki; Maffei Facino, Roberto

2008-01-01

The aim of this work was to establish an analytical method for identifying the botanical origin of honey, as an alternative to conventional melissopalynological, organoleptic and instrumental methods (gas-chromatography coupled to mass spectrometry (GC-MS), high-performance liquid chromatography HPLC). The procedure is based on the 1 H nuclear magnetic resonance (NMR) profile coupled, when necessary, with electrospray ionisation-mass spectrometry (ESI-MS) and two-dimensional NMR analyses of solid-phase extraction (SPE)-purified honey samples, followed by chemometric analyses. Extracts of 44 commercial Italian honeys from 20 different botanical sources were analyzed. Honeydew, chestnut and linden honeys showed constant, specific, well-resolved resonances, suitable for use as markers of origin. Honeydew honey contained the typical resonances of an aliphatic component, very likely deriving from the plant phloem sap or excreted into it by sap-sucking aphids. Chestnut honey contained the typical signals of kynurenic acid and some structurally related metabolite. In linden honey the 1 H NMR profile gave strong signals attributable to the mono-terpene derivative cyclohexa-1,3-diene-1-carboxylic acid (CDCA) and to its 1-O-β-gentiobiosyl ester (CDCA-GBE). These markers were not detectable in the other honeys, except for the less common nectar honey from rosa mosqueta. We compared and analyzed the data by multivariate techniques. Principal component analysis found different clusters of honeys based on the presence of these specific markers. The results, although obviously only preliminary, suggest that the 1 H NMR profile (with HPLC-MS analysis when necessary) can be used as a reference framework for identifying the botanical origin of honey

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR

International Nuclear Information System (INIS)

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M.; Montelione, Gaetano T.

2013-01-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR

Energy Technology Data Exchange (ETDEWEB)

Tejero, Roberto [Rutgers, The State University of New Jersey, Center for Advanced Biotechnology and Medicine (United States); Snyder, David [William Paterson University, Department of Chemistry (United States); Mao, Binchen; Aramini, James M.; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.edu [Rutgers, The State University of New Jersey, Center for Advanced Biotechnology and Medicine (United States)

2013-08-15

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

Drifting plasmons in open two-dimensional channels: modal analysis

International Nuclear Information System (INIS)

Sydoruk, O

2013-01-01

Understanding the properties of plasmons in two-dimensional channels is important for developing methods of terahertz generation. This paper presents a modal analysis of plasmonic reflection in open channels supporting dc currents. As it shows, the plasmons can be amplified upon reflection if a dc current flows away from a conducting boundary; de-amplification occurs for the opposite current direction. The problem is solved analytically, based on a perturbation calculation, and numerically, and agreement between the methods is demonstrated. The power radiated by a channel is found to be negligible, and plasmon reflection in open channels is shown to be similar to that in closed channels. Based on this similarity, the oscillator designs developed earlier for closed channels could be applicable also for open ones. The results develop the modal-decomposition technique further as an instrument for the design of terahertz plasmonic sources. (paper)

Two-dimensional coherence analysis of magnetic and gravity data from the Cascer Quadrangle, Wyoming. Final report

International Nuclear Information System (INIS)

QEB, Inc. has completed a two-dimensional coherence analysis of gravity and magnetic data from the Casper, Wyoming NTMS quadrangle. Magnetic data from an airborne survey were reduced to produce a Residual Magnetic map, and gravity data obtained from several sources were reduced to produce a Complete Bouguer Gravity map. Both sets of data were upward continued to a plane one kilometer above the surface; and then, to make the magnetic and gravity data comparable, the magnetic data were transformed to pseudo-gravity data by the application of Poisson's relationship for rocks that are both dense and magnetic relative to the surrounding rocks. A pseudo-gravity map was then produced and an analysis made of the two-dimensional coherence between the upward continued Bouguer gravity and the pseudo-gravity data. Based on the results of the coherence analysis, digital filters were designed to either pass or reject wavelength bands with high coherence

The quantum spectral analysis of the two-dimensional annular billiard system

International Nuclear Information System (INIS)

Yan-Hui, Zhang; Ji-Quan, Zhang; Xue-You, Xu; Sheng-Lu, Lin

2009-01-01

Based on the extended closed-orbit theory together with spectral analysis, this paper studies the correspondence between quantum mechanics and the classical counterpart in a two-dimensional annular billiard. The results demonstrate that the Fourier-transformed quantum spectra are in very good accordance with the lengths of the classical ballistic trajectories, whereas spectral strength is intimately associated with the shapes of possible open orbits connecting arbitrary two points in the annular cavity. This approach facilitates an intuitive understanding of basic quantum features such as quantum interference, locations of the wavefunctions, and allows quantitative calculations in the range of high energies, where full quantum calculations may become impractical in general. This treatment provides a thread to explore the properties of microjunction transport and even quantum chaos under the much more general system. (general)

Local magnetic susceptibility, spin dynamics, and charge order in the quasi-one-dimensional conductor β -Li0.33V2O5 investigated by site-selective 51V NMR

Science.gov (United States)

Yamauchi, Ichihiro; Itoh, Masayuki; Yamauchi, Touru; Yamaura, Jun-Ichi; Ueda, Yutaka

2017-11-01

51V NMR measurements have been conducted on a single crystal of the quasi-one-dimensional conductor β -Li0.33V2O5 which undergoes a metal-insulator (MI) transition at TMI˜170 K. In the metallic phase, we obtain 51V Knight shift and electric field gradient tensors. From the analysis of the 51V Knight shifts, we find that the charge disproportionation appears even in the metallic state and the electronic structure is represented within a model of weakly coupled ladders containing two types of ladders with distinct carrier densities. Based on the 51V nuclear spin-lattice relaxation rate, we discuss the spin dynamics within the one-dimensional electron gas model. From the analysis of several nonmagnetic V5 + spectra observed in the insulating phase, we propose a possible charge-order pattern which has a superlattice modulation larger than those in other family members of β -A0.33V2O5 (A =Na and Ag). Finally, we discuss the A -ion dependence of the electronic structure, the charge disproportionation, and the charge order in β -A0.33V2O5 .

Functional Analysis of the Nitrogen Metabolite Repression Regulator Gene nmrA in Aspergillus flavus

Directory of Open Access Journals (Sweden)

Xiaoyun Han

2016-11-01

Full Text Available In Aspergillus nidulans, the nitrogen metabolite repression regulator NmrA plays a major role in regulating the activity of the GATA transcription factor AreA during nitrogen metabolism. However, the function of nmrA in Aspergillus flavus has notbeen previously studied. Here, we report the identification and functional analysis of nmrA in A. flavus. Our work showed that the amino acid sequences of NmrA are highly conserved among Aspergillus species and that A. flavus NmrA protein contains a canonical Rossmann fold motif. Deletion of nmrA slowed the growth of A. flavus but significantly increased conidiation and sclerotia production. Moreover, seed infection experiments indicated that nmrA is required for the invasive virulence of A. flavus. In addition, the ΔnmrA mutant showed increased sensitivity to rapamycin and methyl methanesulfonate, suggesting that nmrA could be responsive to target of rapamycin signaling and DNA damage. Furthermore, quantitative real-time reverse transcription polymerase chain reaction analysis suggested that nmrA might interact with other nitrogen regulatory and catabolic genes. Our study provides a better understanding of nitrogen metabolite repression and the nitrogen metabolism network in fungi.

Procedures for two-dimensional electrophoresis of proteins

Energy Technology Data Exchange (ETDEWEB)

Tollaksen, S.L.; Giometti, C.S.

1996-10-01

High-resolution two-dimensional gel electrophoresis (2DE) of proteins, using isoelectric focusing in the first dimension and sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) in the second, was first described in 1975. In the 20 years since those publications, numerous modifications of the original method have evolved. The ISO-DALT system of 2DE is a high-throughput approach that has stood the test of time. The problem of casting many isoelectric focusing gels and SDS-PAGE slab gels (up to 20) in a reproducible manner has been solved by the use of the techniques and equipment described in this manual. The ISO-DALT system of two-dimensional gel electrophoresis originated in the late 1970s and has been modified many times to improve its high-resolution, high-throughput capabilities. This report provides the detailed procedures used with the current ISO-DALT system to prepare, run, stain, and photograph two-dimensional gels for protein analysis.

Fast screening of turkish olive oil by NMR spectroscopy for geographical determination and discrimination purposes

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Ok, S.

2014-06-01

Full Text Available The main goal of this study is to rapidly screen olive oil contents by acquiring one dimensional (1D 1H NMR spectra of 38 samples from Turkey, The Middle East, and Libya. The quantitative analysis of the 1H NMR helped in distinguishing the geographical origin of the olive oil samples. The intensity of 1H NMR variables was submitted to the statistical method, analysis of variance (ANOVA. As a result of combining the NMR data and ANOVA, olive oils were discriminated based on regional origin rather than province. This less time consuming discriminative screening by 1H NMR does not require any further analysis of the olive oil, including oxidative stability measurements or gas chromatography. The possibility of determining authenticity, even in an olive growing area of a small village was also shown. The two-dimensional (2D non-invasive 1H DOSY NMR experiment, known as “NMR chromatography”, was used to determine the olive oil sub-fraction.El objetivo es conocer de manera rápida el contenido de aceite de oliva mediante la adquisición de espectros de 1H RMN de una dimensión (1D. El estudio se ha realizado con 38 muestras procedentes de Turquía, Oriente Medio y Libia. El análisis cuantitativo de 1H RMN ayudó a distinguir el origen geográfico de las muestras de aceites de oliva. La intensidad de las señales de 1H RMN se sometió a estudio estadístico mediante análisis de varianza (ANOVA. Como resultado de la combinación de los datos de RMN y ANOVA, los aceites de oliva fueron discriminados por origen regional antes que por provincia. Esta técnica de discriminación rápida por 1H RMN no requiere ningún análisis adicional de los aceites de oliva mediante estudios de estabilidad a la oxidación o cromatografía de gases. También se demostró la posibilidad de determinar la autenticidad, incluso en el área de cultivo del olivo de una pequeña aldea. Los experimentos de RMN bi-dimensionales (2D no invasiva 1H DOSY, conocido como �

Mechanical exfoliation of two-dimensional materials

Science.gov (United States)

Gao, Enlai; Lin, Shao-Zhen; Qin, Zhao; Buehler, Markus J.; Feng, Xi-Qiao; Xu, Zhiping

2018-06-01

Two-dimensional materials such as graphene and transition metal dichalcogenides have been identified and drawn much attention over the last few years for their unique structural and electronic properties. However, their rise begins only after these materials are successfully isolated from their layered assemblies or adhesive substrates into individual monolayers. Mechanical exfoliation and transfer are the most successful techniques to obtain high-quality single- or few-layer nanocrystals from their native multi-layer structures or their substrate for growth, which involves interfacial peeling and intralayer tearing processes that are controlled by material properties, geometry and the kinetics of exfoliation. This procedure is rationalized in this work through theoretical analysis and atomistic simulations. We propose a criterion to assess the feasibility for the exfoliation of two-dimensional sheets from an adhesive substrate without fracturing itself, and explore the effects of material and interface properties, as well as the geometrical, kinetic factors on the peeling behaviors and the torn morphology. This multi-scale approach elucidates the microscopic mechanism of the mechanical processes, offering predictive models and tools for the design of experimental procedures to obtain single- or few-layer two-dimensional materials and structures.

On-line comprehensive two-dimensional normal-phase liquid chromatography × reversed-phase liquid chromatography for preparative isolation of Peucedanum praeruptorum.

Science.gov (United States)

Wang, Xin-Yuan; Li, Jia-Fu; Jian, Ya-Mei; Wu, Zhen; Fang, Mei-Juan; Qiu, Ying-Kun

2015-03-27

A new on-line comprehensive preparative two-dimensional normal-phase liquid chromatography × reversed-phase liquid chromatography (2D NPLC × RPLC) system was developed for the separation of complicated natural products. It was based on the use of a silica gel packed medium-pressure column as the first dimension and an ODS preparative HPLC column as the second dimension. The two dimensions were connected with normal-phase (NP) and reversed-phase (RP) enrichment units, involving a newly developed airflow assisted adsorption (AAA) technique. The instrument operation and the performance of this NPLC × RPLC separation method were illustrated by gram-scale isolation of ethanol extract from the roots of Peucedanum praeruptorum. In total, 19 compounds with high purity were obtained via automated multi-step preparative separation in a short period of time using this system, and their structures were comprehensively characterized by ESI-MS, (1)H NMR, and (13)C NMR. Including two new compounds, five isomers in two groups with identical HPLC and TLC retention values were also obtained and identified by 1D NMR and 2D NMR. This is the first report of an NPLC × RPLC system successfully applied in an on-line preparative process. This system not only solved the interfacing problem of mobile-phase immiscibility caused by NP and RP separation, it also exhibited apparent advantages in separation efficiency and sample treatment capacity compared with conventional methods. Copyright © 2015 Elsevier B.V. All rights reserved.

1H NMR analysis of the heteroassociation of antitumor antibiotics novotrone and actinomycin D in aqueous solution

International Nuclear Information System (INIS)

Evstigneev, M.P.; Rozvadovskaya, A.O.; Kisurkin, D.V.; Dehvis, D.B.; Veselkov, A.N.

2004-01-01

The heteroassociation of antitumor antibiotics novotrone (NOV) and actinomycin D (AMD) in aqueous solution has been studied by one- and two-dimensional 1 H-NMR spectroscopy (500 MHz) in order to elucidate the molecular mechanism of the action of antibiotics in combination. It has been shown that heterocomplexes become predominant in the mixed solution at r > 12. It is concluded that aromatic antibiotics (e. g. novotrone and actinomycin D) may form energetically stable heteroassociation complexes in aqueous solution and hence affect their medical-biological activity

Two dimensional analysis of MHD generator by means of equivalent circuit

International Nuclear Information System (INIS)

Yoshida, Masaharu; Umoto, Juro

1975-01-01

The authors report on the method analyzing generally the MHD generator by means of the equivalent circuit including the negative resistance. At first, they divide the duct space into many space elements, and for each space element they derive the fundamental equivalent four-terminal circuit which satisfies the two-dimensional Ohm's law. Next, they make an attempt to apply the equivalent circuits to the typical MHD generators such as diagonal, Faraday and Hall generators considering the boundary layer in the duct and the wall leakage current. Using their analysis, the current density, Joul's heat, generated and output electrical powers, electrical efficiency etc. in the generator can be fairly easily calculated. (auth.)

Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure

Science.gov (United States)

Shawkey, Matthew D.; Saranathan, Vinodkumar; Pálsdóttir, Hildur; Crum, John; Ellisman, Mark H.; Auer, Manfred; Prum, Richard O.

2009-01-01

Organismal colour can be created by selective absorption of light by pigments or light scattering by photonic nanostructures. Photonic nanostructures may vary in refractive index over one, two or three dimensions and may be periodic over large spatial scales or amorphous with short-range order. Theoretical optical analysis of three-dimensional amorphous nanostructures has been challenging because these structures are difficult to describe accurately from conventional two-dimensional electron microscopy alone. Intermediate voltage electron microscopy (IVEM) with tomographic reconstruction adds three-dimensional data by using a high-power electron beam to penetrate and image sections of material sufficiently thick to contain a significant portion of the structure. Here, we use IVEM tomography to characterize a non-iridescent, three-dimensional biophotonic nanostructure: the spongy medullary layer from eastern bluebird Sialia sialis feather barbs. Tomography and three-dimensional Fourier analysis reveal that it is an amorphous, interconnected bicontinuous matrix that is appropriately ordered at local spatial scales in all three dimensions to coherently scatter light. The predicted reflectance spectra from the three-dimensional Fourier analysis are more precise than those predicted by previous two-dimensional Fourier analysis of transmission electron microscopy sections. These results highlight the usefulness, and obstacles, of tomography in the description and analysis of three-dimensional photonic structures. PMID:19158016

NMR-Assisted Structure Elucidation of an Anticancer Steroid-β-Enaminone Derivative

Directory of Open Access Journals (Sweden)

Donald Poirier

2017-11-01

Full Text Available The fortuitous modification of a quinoline-proline-piperazine side chain linked to a steroid in the presence of lithium (trimethylsilyl acetylide has generated an unknown product that is more active than its precursor. After having characterized two β-enaminones (two-carbon homologation compounds that were generated from a simplified model side chain, we have identified the unknown product as being the β-enaminone steroid derivative 1. NMR analysis, especially two-dimensional (2D experiments (correlation spectroscopy (COSY, NOE spectroscopy (NOESY, heteronuclear single-quantum correlation (HSQC and heteronuclear multiple-bond correlation (HMBC provided crucial information that was found essential in the characterization of enaminone 1. We also proposed a mechanism to rationalize the formation of this biologically active compound.

Conformational studies of human [15-2-aminohexanoic acid]little gastrin in sodium dodecyl sulfate micelles by 1H NMR

International Nuclear Information System (INIS)

Mammi, S.; Peggion, E.

1990-01-01

Human little gastrin is a 17 amino acid peptide that adopts a random conformation in water and an ordered structure in sodium dodecyl sulfate (SDS) micelles as well as in trifluoroethanol (TFE). The circular dichroism spectra in these two media have the same shape, indicative of a similar preferred conformation. The authors describe here the assignment of the proton NMR resonances and the conformational analysis of [Ahx 15 ] little gastrin in SDS micelles. Two-dimensional correlation techniques form the basis for the assignment. The conformational analysis utilizes NOE's, NH to C α H coupling constants, and the temperature coefficients of the amide chemical shifts. The NMR data indicate a helical structure in the N-terminal portion of the peptide. These results are compared with the conformation that the authors recently proposed for a minigastrin analogue (fragment 5-17 of [Ahx 15 ] little gastrin) in TFE

Equivalence of two-dimensional gravities

International Nuclear Information System (INIS)

Mohammedi, N.

1990-01-01

The authors find the relationship between the Jackiw-Teitelboim model of two-dimensional gravity and the SL(2,R) induced gravity. These are shown to be related to a two-dimensional gauge theory obtained by dimensionally reducing the Chern-Simons action of the 2 + 1 dimensional gravity. The authors present an explicit solution to the equations of motion of the auxiliary field of the Jackiw-Teitelboim model in the light-cone gauge. A renormalization of the cosmological constant is also given

Symmetrical analysis of the defect level splitting in two-dimensional photonic crystals

International Nuclear Information System (INIS)

Malkova, N; Kim, S; Gopalan, V

2003-01-01

In this paper doubly degenerate defect states in the band gap of the two-dimensional photonic crystal are studied. These states can be split by a convenient distortion of the lattice. Through analogy with the Jahn-Teller effect in solids, we present a group theoretical analysis of the lifting of the degeneracy of doubly degenerate states in a square lattice by different vibronic modes. The effect is supported by the supercell plane-wave model and by the finite difference time domain technique. We suggest ways for using the effect in photonic switching devices and waveguides

Comparative 1H NMR-based metabonomic analysis of HIV-1 sera

International Nuclear Information System (INIS)

Philippeos, C.; Steffens, F. E.; Meyer, D.

2009-01-01

1 H NMR spectroscopy of sera from HIV-1 infected and uninfected individuals was performed on 300 and 600 MHz instruments. The resultant spectra were automatically data reduced to 90 and 180 integral segments of equal length. Analysis of variance identified significant differences between the sample groups, especially for the samples analyzed on 600 MHz and reduced to fewer segments. Linear discriminant analysis correctly classified 100% of the samples analyzed on the 300 MHz NMR (reduced to 180 segments); an increase in instrument sensitivity resulted in lower percentages of correctly classified samples. Multinomial logistic regression (MLR) resulted in 100% correct classification of all samples from both instruments. Thus 1 H-NMR metabonomics on either instrument distinguishes HIV-positive individuals using or not using anti retroviral therapy, but the sensitivity of the instrument impacts on data reduction. Furthermore, MLR is a novel multivariate statistical technique for improved classification of biological data analyzed in NMR

Two-dimensional metamaterial optics

International Nuclear Information System (INIS)

Smolyaninov, I I

2010-01-01

While three-dimensional photonic metamaterials are difficult to fabricate, many new concepts and ideas in the metamaterial optics can be realized in two spatial dimensions using planar optics of surface plasmon polaritons. In this paper we review recent progress in this direction. Two-dimensional photonic crystals, hyperbolic metamaterials, and plasmonic focusing devices are demonstrated and used in novel microscopy and waveguiding schemes

Piperamides from Piper ottonoides by NMR and GC-MS based mixture analysis

International Nuclear Information System (INIS)

Wolff, Thiago; Valente, Ligia M.M.; Magalhães, Alvicler; Guimarães, Elsie F.

2015-01-01

The species Piper ottonoides Yuncker (Piperaceae), known as 'joão-brandim', is a shrub that occurs in the Brazilian Amazon rainforest. Its roots and leaves are used in traditional medicine as local anesthetic to treat toothache and sore throat. In this study, the structural characterization in mixture of isobutyl amides present in semi-purified fractions from fruits, leaves, stems and roots of P. ottonoides was achieved by employing gas chromatography-mass spectrometry (GC-MS) and a combination of nuclear magnetic resonance (NMR) techniques ( 1 H, 1 H- 1 H COSY, 1 H- 13 CHSQC, 1 H- 13 CHMBC, TOCSY and 1 H- 1 H J-RES). The MS fragmentation patterns and the NMR chemical shifts, multiplicities, coupling constants and the signal correlations in the two-dimensional spectra were carefully analyzed also taking into account some key elements of differentiation among the compounds. The data set allowed identifying unequivocally the new amide N-isobutyl-7-(4'- methoxyphenyl)-2E,4E-heptadienamide, which we named ottonoidenamide as well as piperovatine and chingchengenamide A in all parts of the plant, the additional presence of pipercallosine and pipercallosidine in roots and of dihydropiperlonguminine in fruits and leaves. The presence of piperovatine and pipercallosine in P. ottonoides should be associated to its traditional use. (author)

A solid-phase extraction procedure coupled to {sup 1}H NMR, with chemometric analysis, to seek reliable markers of the botanical origin of honey

Energy Technology Data Exchange (ETDEWEB)

Beretta, Giangiacomo [Istituto di Chimica Farmaceutica e Tossicologica ' Pietro Pratesi' , Faculty of Pharmacy, University of Milan, via Mangiagalli 25, 20133 Milan (Italy)], E-mail: giangiacomo.beretta@unimi.it; Caneva, Enrico [Ciga - Centro Interdipartimentale Grandi Apparecchiature, University of Milan, via Golgi 19, 20133 Milan (Italy); Regazzoni, Luca; Bakhtyari, Nazanin Golbamaki; Maffei Facino, Roberto [Istituto di Chimica Farmaceutica e Tossicologica ' Pietro Pratesi' , Faculty of Pharmacy, University of Milan, via Mangiagalli 25, 20133 Milan (Italy)

2008-07-14

The aim of this work was to establish an analytical method for identifying the botanical origin of honey, as an alternative to conventional melissopalynological, organoleptic and instrumental methods (gas-chromatography coupled to mass spectrometry (GC-MS), high-performance liquid chromatography HPLC). The procedure is based on the {sup 1}H nuclear magnetic resonance (NMR) profile coupled, when necessary, with electrospray ionisation-mass spectrometry (ESI-MS) and two-dimensional NMR analyses of solid-phase extraction (SPE)-purified honey samples, followed by chemometric analyses. Extracts of 44 commercial Italian honeys from 20 different botanical sources were analyzed. Honeydew, chestnut and linden honeys showed constant, specific, well-resolved resonances, suitable for use as markers of origin. Honeydew honey contained the typical resonances of an aliphatic component, very likely deriving from the plant phloem sap or excreted into it by sap-sucking aphids. Chestnut honey contained the typical signals of kynurenic acid and some structurally related metabolite. In linden honey the {sup 1}H NMR profile gave strong signals attributable to the mono-terpene derivative cyclohexa-1,3-diene-1-carboxylic acid (CDCA) and to its 1-O-{beta}-gentiobiosyl ester (CDCA-GBE). These markers were not detectable in the other honeys, except for the less common nectar honey from rosa mosqueta. We compared and analyzed the data by multivariate techniques. Principal component analysis found different clusters of honeys based on the presence of these specific markers. The results, although obviously only preliminary, suggest that the {sup 1}H NMR profile (with HPLC-MS analysis when necessary) can be used as a reference framework for identifying the botanical origin of honey.

A two dimensional finite difference time domain analysis of the quiet zone fields of an anechoic chamber

Science.gov (United States)

Ryan, Deirdre A.; Luebbers, Raymond J.; Nguyen, Truong X.; Kunz, Karl S.; Steich, David J.

1992-01-01

Prediction of anechoic chamber performance is a difficult problem. Electromagnetic anechoic chambers exist for a wide range of frequencies but are typically very large when measured in wavelengths. Three dimensional finite difference time domain (FDTD) modeling of anechoic chambers is possible with current computers but at frequencies lower than most chamber design frequencies. However, two dimensional FDTD (2D-FTD) modeling enables much greater detail at higher frequencies and offers significant insight into compact anechoic chamber design and performance. A major subsystem of an anechoic chamber for which computational electromagnetic analyses exist is the reflector. First, an analysis of the quiet zone fields of a low frequency anechoic chamber produced by a uniform source and a reflector in two dimensions using the FDTD method is presented. The 2D-FDTD results are compared with results from a three dimensional corrected physical optics calculation and show good agreement. Next, a directional source is substituted for the uniform radiator. Finally, a two dimensional anechoic chamber geometry, including absorbing materials, is considered, and the 2D-FDTD results for these geometries appear reasonable.

Analysis of one-dimensional nonequilibrium two-phase flow using control volume method

International Nuclear Information System (INIS)

Minato, Akihiko; Naitoh, Masanori

1987-01-01

A one-dimensional numerical analysis model was developed for prediction of rapid flow transient behavior involving boiling. This model was based on six conservation equations of time averaged parameters of gas and liquid behavior. These equations were solved by using a control volume method with an explicit time integration. This model did not use staggered mesh scheme, which had been commonly used in two-phase flow analysis. Because void fraction and velocity of each phase were defined at the same location in the present model, effects of void fraction on phase velocity calculation were treated directly without interpolation. Though non-staggered mesh scheme was liable to cause numerical instability with zigzag pressure field, stability was achieved by employing the Godunov method. In order to verify the present analytical model, Edwards' pipe blow down and Zaloudek's initially subcooled critical two-phase flow experiments were analyzed. Stable solutions were obtained for rarefaction wave propagation with boiling and transient two-phase flow behavior in a broken pipe by using this model. (author)

Completely two-dimensional model for analysis of characteristics of linear induction cylindrical pump

International Nuclear Information System (INIS)

Kirillov, I.R.; Obukhov, D.M.

2005-01-01

One introduces a completely two-dimensional mathematical model to calculate characteristics of induction magnetohydrodynamic (MHD) machines with a cylindrical channel. On the basis of the numerical analysis one obtained a pattern of liquid metal flow in a electromagnetic pump at presence of the MHD-instability characterized by initiation of large-scale vortices propagating longitudinally and azimuthally. Comparison of the basic calculated characteristics of pump with the experiment shows their adequate qualitative and satisfactory quantitative coincidence [ru

An educationally inspired illustration of two-dimensional Quantitative Microbiological Risk Assessment (QMRA) and sensitivity analysis.

Science.gov (United States)

Vásquez, G A; Busschaert, P; Haberbeck, L U; Uyttendaele, M; Geeraerd, A H

2014-11-03

Quantitative Microbiological Risk Assessment (QMRA) is a structured methodology used to assess the risk involved by ingestion of a pathogen. It applies mathematical models combined with an accurate exploitation of data sets, represented by distributions and - in the case of two-dimensional Monte Carlo simulations - their hyperparameters. This research aims to highlight background information, assumptions and truncations of a two-dimensional QMRA and advanced sensitivity analysis. We believe that such a detailed listing is not always clearly presented in actual risk assessment studies, while it is essential to ensure reliable and realistic simulations and interpretations. As a case-study, we are considering the occurrence of listeriosis in smoked fish products in Belgium during the period 2008-2009, using two-dimensional Monte Carlo and two sensitivity analysis methods (Spearman correlation and Sobol sensitivity indices) to estimate the most relevant factors of the final risk estimate. A risk estimate of 0.018% per consumption of contaminated smoked fish by an immunocompromised person was obtained. The final estimate of listeriosis cases (23) is within the actual reported result obtained for the same period and for the same population. Variability on the final risk estimate is determined by the variability regarding (i) consumer refrigerator temperatures, (ii) the reference growth rate of L. monocytogenes, (iii) the minimum growth temperature of L. monocytogenes and (iv) consumer portion size. Variability regarding the initial contamination level of L. monocytogenes tends to appear as a determinant of risk variability only when the minimum growth temperature is not included in the sensitivity analysis; when it is included the impact regarding the variability on the initial contamination level of L. monocytogenes is disappearing. Uncertainty determinants of the final risk indicated the need of gathering more information on the reference growth rate and the minimum

Selected topics from recent NMR studies of organolithium compounds

Directory of Open Access Journals (Sweden)

Günther Harald

1999-01-01

Full Text Available After a short introduction to NMR spectroscopy of alkali and alkaline earth metals the review concentrates on NMR investigations of organolithium compounds. The isotopic fingerprint method, which rests on deuterium-induced isotope shifts for 6Li resonances, is introduced and exemplified with applications from the aggregation behavior of cyclopropyllithium systems and mixed aggregate formation between methyllithium and lithium salts. In the following chapter, one- and two-dimensional pulse experiments, both for homo- and for heteronuclear spin systems are discussed. Finally, the structural aspects associated with benzyllithium are outlined and the formation of polylithium systems by lithium reduction of biphenylenes is described.

Surface representations of two- and three-dimensional fluid flow topology

Science.gov (United States)

Helman, James L.; Hesselink, Lambertus

1990-01-01

We discuss our work using critical point analysis to generate representations of the vector field topology of numerical flow data sets. Critical points are located and characterized in a two-dimensional domain, which may be either a two-dimensional flow field or the tangential velocity field near a three-dimensional body. Tangent curves are then integrated out along the principal directions of certain classes of critical points. The points and curves are linked to form a skeleton representing the two-dimensional vector field topology. When generated from the tangential velocity field near a body in a three-dimensional flow, the skeleton includes the critical points and curves which provide a basis for analyzing the three-dimensional structure of the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations to generate surfaces representing the topology of the associated flow separations.

In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes

International Nuclear Information System (INIS)

Sakai, Tomomi; Tochio, Hidehito; Tenno, Takeshi; Ito, Yutaka; Kokubo, Tetsuro; Hiroaki, Hidekazu; Shirakawa, Masahiro

2006-01-01

In-cell NMR is an application of solution NMR that enables the investigation of protein conformations inside living cells. We have measured in-cell NMR spectra in oocytes from the African clawed frog Xenopus laevis. 15 N-labeled ubiquitin, its derivatives and calmodulin were injected into Xenopus oocytes and two-dimensional 1 H- 15 N correlation spectra of the proteins were obtained. While the spectrum of wild-type ubiquitin in oocytes had rather fewer cross-peaks compared to its in vitro spectrum, ubiquitin derivatives that are presumably unable to bind to ubiquitin-interacting proteins gave a markedly larger number of cross-peaks. This observation suggests that protein-protein interactions between ubiquitin and ubiquitin-interacting proteins may cause NMR signal broadening, and hence spoil the quality of the in-cell HSQC spectra. In addition, we observed the maturation of ubiquitin precursor derivative in living oocytes using the in-cell NMR technique. This process was partly inhibited by pre-addition of ubiquitin aldehyde, a specific inhibitor for ubiquitin C-terminal hydrolase (UCH). Our work demonstrates the potential usefulness of in-cell NMR with Xenopus oocytes for the investigation of protein conformations and functions under intracellular environmental conditions

Two-dimensional PCA-based human gait identification

Science.gov (United States)

Chen, Jinyan; Wu, Rongteng

2012-11-01

It is very necessary to recognize person through visual surveillance automatically for public security reason. Human gait based identification focus on recognizing human by his walking video automatically using computer vision and image processing approaches. As a potential biometric measure, human gait identification has attracted more and more researchers. Current human gait identification methods can be divided into two categories: model-based methods and motion-based methods. In this paper a two-Dimensional Principal Component Analysis and temporal-space analysis based human gait identification method is proposed. Using background estimation and image subtraction we can get a binary images sequence from the surveillance video. By comparing the difference of two adjacent images in the gait images sequence, we can get a difference binary images sequence. Every binary difference image indicates the body moving mode during a person walking. We use the following steps to extract the temporal-space features from the difference binary images sequence: Projecting one difference image to Y axis or X axis we can get two vectors. Project every difference image in the difference binary images sequence to Y axis or X axis difference binary images sequence we can get two matrixes. These two matrixes indicate the styles of one walking. Then Two-Dimensional Principal Component Analysis(2DPCA) is used to transform these two matrixes to two vectors while at the same time keep the maximum separability. Finally the similarity of two human gait images is calculated by the Euclidean distance of the two vectors. The performance of our methods is illustrated using the CASIA Gait Database.

Covariance NMR Processing and Analysis for Protein Assignment.

Science.gov (United States)

Harden, Bradley J; Frueh, Dominique P

2018-01-01

During NMR resonance assignment it is often necessary to relate nuclei to one another indirectly, through their common correlations to other nuclei. Covariance NMR has emerged as a powerful technique to correlate such nuclei without relying on error-prone peak peaking. However, false-positive artifacts in covariance spectra have impeded a general application to proteins. We recently introduced pre- and postprocessing steps to reduce the prevalence of artifacts in covariance spectra, allowing for the calculation of a variety of 4D covariance maps obtained from diverse combinations of pairs of 3D spectra, and we have employed them to assign backbone and sidechain resonances in two large and challenging proteins. In this chapter, we present a detailed protocol describing how to (1) properly prepare existing 3D spectra for covariance, (2) understand and apply our processing script, and (3) navigate and interpret the resulting 4D spectra. We also provide solutions to a number of errors that may occur when using our script, and we offer practical advice when assigning difficult signals. We believe such 4D spectra, and covariance NMR in general, can play an integral role in the assignment of NMR signals.

Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba

OpenAIRE

Napolitano, José G.; Lankin, David C.; Chen, Shao-Nong; Pauli, Guido F.

2012-01-01

The complete and unambiguous 1H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive 1H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d6 were obtained through the examination of 1D 1H NMR and 2D 1H,1H-COSY data, in combination with 1H iterative Full Spin Analysis (HiFSA). The computational analysis of discrete spin systems allowed a ...

NMR-based approach to the analysis of radiopharmaceuticals: radiochemical purity, specific activity, and radioactive concentration values by proton and tritium NMR spectroscopy.

Science.gov (United States)

Schenk, David J; Dormer, Peter G; Hesk, David; Pollack, Scott R; Lavey, Carolee Flader

2015-06-15

Compounds containing tritium are widely used across the drug discovery and development landscape. These materials are widely utilized because they can be efficiently synthesized and produced at high specific activity. Results from internally calibrated (3)H and (1)H nuclear magnetic resonance (NMR) spectroscopy suggests that at least in some cases, this calibrated approach could supplement or potentially replace radio-high-performance liquid chromatography for radiochemical purity, dilution and scintillation counting for the measurement of radioactivity per volume, and liquid chromatography/mass spectrometry analysis for the determination of specific activity. In summary, the NMR-derived values agreed with those from the standard approaches to within 1% to 9% for solution count and specific activity. Additionally, the NMR-derived values for radiochemical purity deviated by less than 5%. A benefit of this method is that these values may be calculated at the same time that (3)H NMR analysis provides the location and distribution of tritium atoms within the molecule. Presented and discussed here is the application of this method, advantages and disadvantages of the approach, and a rationale for utilizing internally calibrated (1)H and (3)H NMR spectroscopy for specific activity, radioactive concentration, and radiochemical purity whenever acquiring (3)H NMR for tritium location. Copyright © 2015 John Wiley & Sons, Ltd.

Exploring high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for metabonomic analysis of apples.

Science.gov (United States)

Vermathen, Martina; Marzorati, Mattia; Vermathen, Peter

2012-01-01

Classical liquid-state high-resolution (HR) NMR spectroscopy has proved a powerful tool in the metabonomic analysis of liquid food samples like fruit juices. In this paper the application of (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to apple tissue is presented probing its potential for metabonomic studies. The (1)H HR-MAS NMR spectra are discussed in terms of the chemical composition of apple tissue and compared to liquid-state NMR spectra of apple juice. Differences indicate that specific metabolic changes are induced by juice preparation. The feasibility of HR-MAS NMR-based multivariate analysis is demonstrated by a study distinguishing three different apple cultivars by principal component analysis (PCA). Preliminary results are shown from subsequent studies comparing three different cultivation methods by means of PCA and partial least squares discriminant analysis (PLS-DA) of the HR-MAS NMR data. The compounds responsible for discriminating organically grown apples are discussed. Finally, an outlook of our ongoing work is given including a longitudinal study on apples.

Principal components analysis of protein structure ensembles calculated using NMR data

International Nuclear Information System (INIS)

Howe, Peter W.A.

2001-01-01

One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated structural variation across the population. PCA analysis has the additional advantage that it highlights regions of proteins which are varying across the population. To apply PCA, protein structures have to be reduced in complexity and this paper describes two different representations of protein structures which achieve this. The calculated structures of a 28 amino acid peptide are used to demonstrate the methods. The two different representations of protein structure are shown to give equivalent results, and correct results are obtained even though the ensemble of structures used as an example contains two different protein conformations. The PCA analysis also correctly identifies the structural differences between the two conformations

Application of tomographic techniques to two-dimensional surface analysis using the Harwell nuclear microprobe

International Nuclear Information System (INIS)

Huddleston, J.; Hutchinson, I.G.; Pierce, T.B.

1983-01-01

Nuclear methods of surface analysis are discussed briefly, and the circumstances are described in which a two-dimensional analysis of the sample surface is desirable to enable the surface composition to be mapped accurately. Tomographic techniques of data manipulation are outlined. Data acquisition in the present case is performed by moving the sample in a defined sequence of positions, at each of which analytical data are gathered by the proton microprobe. The method and equipment are outlined. Data processing leading to the reconstruction of the image is summarised. (U.K.)

NMR Techniques in Metabolomic Studies: A Quick Overview on Examples of Utilization.

Science.gov (United States)

Kruk, Joanna; Doskocz, Marek; Jodłowska, Elżbieta; Zacharzewska, Anna; Łakomiec, Joanna; Czaja, Kornelia; Kujawski, Jacek

2017-01-01

Metabolomics is a rapidly developing branch of science that concentrates on identifying biologically active molecules with potential biomarker properties. To define the best biomarkers for diseases, metabolomics uses both models (in vitro, animals) and human, as well as, various techniques such as mass spectroscopy, gas chromatography, liquid chromatography, infrared and UV-VIS spectroscopy and nuclear magnetic resonance. The last one takes advantage of the magnetic properties of certain nuclei, such as 1 H, 13 C, 31 P, 19 F, especially their ability to absorb and emit energy, what is crucial for analyzing samples. Among many spectroscopic NMR techniques not only one-dimensional (1D) techniques are known, but for many years two-dimensional (2D, for example, COSY, DOSY, JRES, HETCORE, HMQS), three-dimensional (3D, DART-MS, HRMAS, HSQC, HMBC) and solid-state NMR have been used. In this paper, authors taking apart fundamental division of nuclear magnetic resonance techniques intend to shown their wide application in metabolomic studies, especially in identifying biomarkers.

A two-dimensional Zn coordination polymer with a three-dimensional supramolecular architecture

Directory of Open Access Journals (Sweden)

Fuhong Liu

2017-10-01

Full Text Available The title compound, poly[bis{μ2-4,4′-bis[(1,2,4-triazol-1-ylmethyl]biphenyl-κ2N4:N4′}bis(nitrato-κOzinc(II], [Zn(NO32(C18H16N62]n, is a two-dimensional zinc coordination polymer constructed from 4,4′-bis[(1H-1,2,4-triazol-1-ylmethyl]-1,1′-biphenyl units. It was synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The ZnII cation is located on an inversion centre and is coordinated by two O atoms from two symmetry-related nitrate groups and four N atoms from four symmetry-related 4,4′-bis[(1H-1,2,4-triazol-1-ylmethyl]-1,1′-biphenyl ligands, forming a distorted octahedral {ZnN4O2} coordination geometry. The linear 4,4′-bis[(1H-1,2,4-triazol-1-ylmethyl]-1,1′-biphenyl ligand links two ZnII cations, generating two-dimensional layers parallel to the crystallographic (132 plane. The parallel layers are connected by C—H...O, C—H...N, C—H...π and π–π stacking interactions, resulting in a three-dimensional supramolecular architecture.

Quantitative produced water analysis using mobile 1H NMR

International Nuclear Information System (INIS)

Wagner, Lisabeth; Fridjonsson, Einar O; May, Eric F; Stanwix, Paul L; Graham, Brendan F; Carroll, Matthew R J; Johns, Michael L; Kalli, Chris

2016-01-01

Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1 H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1 H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1 H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1–30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography. (paper)

Automated NMR relaxation dispersion data analysis using NESSY

Directory of Open Access Journals (Sweden)

Gooley Paul R

2011-10-01

Full Text Available Abstract Background Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary. Results The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program. Conclusions NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.

Monitoring the functionalization of single-walled carbon nanotubes with chitosan and folic acid by two-dimensional diffusion-ordered nmr spectroscopy

DEFF Research Database (Denmark)

Castillo, John J.; Torres, Mary H.; Molina, Daniel R.

2012-01-01

A conjugate between single-walled carbon nanotubes, chitosan and folic acid has been prepared. It was characterized by diffusion ordered two-dimensional hydrogen-1 nuclear magnetic resonance and hydrogen-1 nuclear magnetic resonance spectroscopy which revealed the presence of a conjugate that was......A conjugate between single-walled carbon nanotubes, chitosan and folic acid has been prepared. It was characterized by diffusion ordered two-dimensional hydrogen-1 nuclear magnetic resonance and hydrogen-1 nuclear magnetic resonance spectroscopy which revealed the presence of a conjugate...... that was generated by the linkage between the carboxyl moiety of the folic acid and the amino group of the chitosan, which in turn was non-covalently bound to the single-walled carbon nanotubes. The obtained diffusion coefficient values demonstrated that free folic acid diffused more rapidly than the folic acid...... conjugated to single-walled carbon nanotubes-chitosan. The values of the proton signal of hydrogen-1 nuclear magnetic resonance spectroscopy and two-dimensional hydrogen-1 nuclear magnetic resonance spectroscopy further confirmed that the folic acid was conjugated to the chitosan, wrapping the single...

Variable-temperature NMR and conformational analysis of Oenothein B

International Nuclear Information System (INIS)

Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de

2014-01-01

Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

Variable-temperature NMR and conformational analysis of Oenothein B

Energy Technology Data Exchange (ETDEWEB)

Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de, [Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Instituto de Quimica

2014-02-15

Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

Complete sequence-specific 1H NMR assignments for human insulin

International Nuclear Information System (INIS)

Kline, A.D.; Justice, R.M. Jr.

1990-01-01

Solvent conditions where human insulin could be studied by high-resolution NMR were determined. Both low pH and addition of acetonitrile were required to overcome the protein's self-association and to obtain useful spectra. Two hundred eighty-six 1 H resonances were located and assigned to specific sites on the protein by using two-dimensional NMR methods. The presence and position of numerous d NN sequential NOE's indicate that the insulin conformation seen in crystallographic studies is largely retained under these solution conditions. Slowly exchanging protons were observed for seven backbone amide protons and were assigned to positions A15 and A16 and to positions B15-B19. These amides all occur within helical regions of the protein

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

Science.gov (United States)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high

Metabolic characterization of Palatinate German white wines according to sensory attributes, varieties, and vintages using NMR spectroscopy and multivariate data analyses

Energy Technology Data Exchange (ETDEWEB)

Ali, Kashif; Maltese, Federica [Leiden University, Division of Pharmacognosy, Section Metabolomics, Institute of Biology (Netherlands); Toepfer, Reinhard [Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants (Germany); Choi, Young Hae, E-mail: y.choi@chem.leidenuniv.nl; Verpoorte, Robert [Leiden University, Division of Pharmacognosy, Section Metabolomics, Institute of Biology (Netherlands)

2011-04-15

{sup 1}H NMR (nuclear magnetic resonance spectroscopy) has been used for metabolomic analysis of 'Riesling' and 'Mueller-Thurgau' white wines from the German Palatinate region. Diverse two-dimensional NMR techniques have been applied for the identification of metabolites, including phenolics. It is shown that sensory analysis correlates with NMR-based metabolic profiles of wine. {sup 1}H NMR data in combination with multivariate data analysis methods, like principal component analysis (PCA), partial least squares projections to latent structures (PLS), and bidirectional orthogonal projections to latent structures (O2PLS) analysis, were employed in an attempt to identify the metabolites responsible for the taste of wine, using a non-targeted approach. The high quality wines were characterized by elevated levels of compounds like proline, 2,3-butanediol, malate, quercetin, and catechin. Characterization of wine based on type and vintage was also done using orthogonal projections to latent structures (OPLS) analysis. 'Riesling' wines were characterized by higher levels of catechin, caftarate, valine, proline, malate, and citrate whereas compounds like quercetin, resveratrol, gallate, leucine, threonine, succinate, and lactate, were found discriminating for 'Mueller-Thurgau'. The wines from 2006 vintage were dominated by leucine, phenylalanine, citrate, malate, and phenolics, while valine, proline, alanine, and succinate were predominantly present in the 2007 vintage. Based on these results, it can be postulated the NMR-based metabolomics offers an easy and comprehensive analysis of wine and in combination with multivariate data analyses can be used to investigate the source of the wines and to predict certain sensory aspects of wine.

Metabolic characterization of Palatinate German white wines according to sensory attributes, varieties, and vintages using NMR spectroscopy and multivariate data analyses

International Nuclear Information System (INIS)

Ali, Kashif; Maltese, Federica; Toepfer, Reinhard; Choi, Young Hae; Verpoorte, Robert

2011-01-01

1 H NMR (nuclear magnetic resonance spectroscopy) has been used for metabolomic analysis of ‘Riesling’ and ‘Mueller-Thurgau’ white wines from the German Palatinate region. Diverse two-dimensional NMR techniques have been applied for the identification of metabolites, including phenolics. It is shown that sensory analysis correlates with NMR-based metabolic profiles of wine. 1 H NMR data in combination with multivariate data analysis methods, like principal component analysis (PCA), partial least squares projections to latent structures (PLS), and bidirectional orthogonal projections to latent structures (O2PLS) analysis, were employed in an attempt to identify the metabolites responsible for the taste of wine, using a non-targeted approach. The high quality wines were characterized by elevated levels of compounds like proline, 2,3-butanediol, malate, quercetin, and catechin. Characterization of wine based on type and vintage was also done using orthogonal projections to latent structures (OPLS) analysis. ‘Riesling’ wines were characterized by higher levels of catechin, caftarate, valine, proline, malate, and citrate whereas compounds like quercetin, resveratrol, gallate, leucine, threonine, succinate, and lactate, were found discriminating for ‘Mueller-Thurgau’. The wines from 2006 vintage were dominated by leucine, phenylalanine, citrate, malate, and phenolics, while valine, proline, alanine, and succinate were predominantly present in the 2007 vintage. Based on these results, it can be postulated the NMR-based metabolomics offers an easy and comprehensive analysis of wine and in combination with multivariate data analyses can be used to investigate the source of the wines and to predict certain sensory aspects of wine.

Application of NMR Spectroscopy in the Analysis of Petroleum Derivatives and Products

Directory of Open Access Journals (Sweden)

Parlov Vuković, J.

2012-11-01

Full Text Available Complex chemical composition and physical properties of oil and fuel make their complete cha racterization very difficult. Components present in oil and oil products differ in structure, size, po larity and functionality. The presence and structure of specific hydrocarbons in final products depend on the processing procedure and type of the fuel. In order to predict or improve fuel pro perties it is necessary to determine its composition. Thus, new and more sophisticated analytical methods and procedures are constantly being developed. NMR spectroscopy plays a significant role in analysis and identification of complex hydrocarbon mixtures of petroleum and petroleum products. In this review, we describe the application of NMR spectroscopy for analyzing gasoline and diesel fuels. Hence, by using NMR spectroscopy it is possible to determine gasoline composition and presence of benzene and oxygenates, as well as some important physical characteristics of gasoli ne such as the research octane number. An application of different NMR techniques made it pos sible to characterize diesel fuels and middle oil distillates from various refineries. Data so obtained can be used in combination with statistical methods to predict fuel properties and to monitor pro- duction processes in the petroleum industry. NMR spectroscopy has proven useful in analysis of FAME which has recently been used as an ecologically acceptable alternative fuel. Furthermore, techniques such as CP/MAS for characterization of solid state oil-geochemical samples are inclu- ded. Also, possibilities of using NMR spectroscopy in the analysis of polymeric additives are di- scussed.

Further studies on stability analysis of nonlinear Roesser-type two-dimensional systems

International Nuclear Information System (INIS)

Dai Xiao-Lin

2014-01-01

This paper is concerned with further relaxations of the stability analysis of nonlinear Roesser-type two-dimensional (2D) systems in the Takagi–Sugeno fuzzy form. To achieve the goal, a novel slack matrix variable technique, which is homogenous polynomially parameter-dependent on the normalized fuzzy weighting functions with arbitrary degree, is developed and the algebraic properties of the normalized fuzzy weighting functions are collected into a set of augmented matrices. Consequently, more information about the normalized fuzzy weighting functions is involved and the relaxation quality of the stability analysis is significantly improved. Moreover, the obtained result is formulated in the form of linear matrix inequalities, which can be easily solved via standard numerical software. Finally, a numerical example is provided to demonstrate the effectiveness of the proposed result. (general)

Further studies on stability analysis of nonlinear Roesser-type two-dimensional systems

Science.gov (United States)

Dai, Xiao-Lin

2014-04-01

This paper is concerned with further relaxations of the stability analysis of nonlinear Roesser-type two-dimensional (2D) systems in the Takagi-Sugeno fuzzy form. To achieve the goal, a novel slack matrix variable technique, which is homogenous polynomially parameter-dependent on the normalized fuzzy weighting functions with arbitrary degree, is developed and the algebraic properties of the normalized fuzzy weighting functions are collected into a set of augmented matrices. Consequently, more information about the normalized fuzzy weighting functions is involved and the relaxation quality of the stability analysis is significantly improved. Moreover, the obtained result is formulated in the form of linear matrix inequalities, which can be easily solved via standard numerical software. Finally, a numerical example is provided to demonstrate the effectiveness of the proposed result.

Surface Ship Shock Modeling and Simulation: Two-Dimensional Analysis

Directory of Open Access Journals (Sweden)

Young S. Shin

1998-01-01

Full Text Available The modeling and simulation of the response of a surface ship system to underwater explosion requires an understanding of many different subject areas. These include the process of underwater explosion events, shock wave propagation, explosion gas bubble behavior and bubble-pulse loading, bulk and local cavitation, free surface effect, fluid-structure interaction, and structural dynamics. This paper investigates the effects of fluid-structure interaction and cavitation on the response of a surface ship using USA-NASTRAN-CFA code. First, the one-dimensional Bleich-Sandler model is used to validate the approach, and second, the underwater shock response of a two-dimensional mid-section model of a surface ship is predicted with a surrounding fluid model using a constitutive equation of a bilinear fluid which does not allow transmission of negative pressures.

Authentication of beef versus horse meat using 60 MHz 1H NMR spectroscopy.

Science.gov (United States)

Jakes, W; Gerdova, A; Defernez, M; Watson, A D; McCallum, C; Limer, E; Colquhoun, I J; Williamson, D C; Kemsley, E K

2015-05-15

This work reports a candidate screening protocol to distinguish beef from horse meat based upon comparison of triglyceride signatures obtained by 60 MHz (1)H NMR spectroscopy. Using a simple chloroform-based extraction, we obtained classic low-field triglyceride spectra from typically a 10 min acquisition time. Peak integration was sufficient to differentiate samples of fresh beef (76 extractions) and horse (62 extractions) using Naïve Bayes classification. Principal component analysis gave a two-dimensional "authentic" beef region (p=0.001) against which further spectra could be compared. This model was challenged using a subset of 23 freeze-thawed training samples. The outcomes indicated that storing samples by freezing does not adversely affect the analysis. Of a further collection of extractions from previously unseen samples, 90/91 beef spectra were classified as authentic, and 16/16 horse spectra as non-authentic. We conclude that 60 MHz (1)H NMR represents a feasible high-throughput approach for screening raw meat. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural comparison of complexes of methotrexate analogues with Lactobacillus casei dihydrofolate reductase by two-dimensional 1H NMR at 500 MHz

International Nuclear Information System (INIS)

Hammond, S.J.; Birdsall, B.; Feeney, J.; Searle, M.S.; Roberts, G.C.K.; Cheung, H.T.A.

1987-01-01

The authors have used two-dimensional (2D) NMR methods to examine complexes of Lactobacillus casei dihydrofolate reductase and methotrexate (MTX) analogues having structural modifications of the benzoyl ring and also the glutamic acid moiety. Assignments of the 1 H signals in the spectra of the various complexes were made by comparison of their 2D spectra with those complexes containing methotrexate where we have previously assigned resonances from 32 of the 162 amino acid residues. In the complexes formed with the dihalomethotrexate analogues, the glutamic acid and pteridine ring moieties were shown to bind to the enzyme in a manner similar to that found in the methotrexate-enzyme complex. Perturbations in 1 H chemical shifts of protons in Phe-49, Leu-54, and Leu-27 and the methotrexate H7 and NMe protons were observed in the different complexes and were accounted for by changes in orientation of the benzoyl ring in the various complexes. Binding of oxidized or reduced coenzyme to the binary complexes did not result in different shifts for Leu-27, Leu-54, or Leu-19 protons, and thus, the orientation of the benzoyl ring of the methotrexate analogues is not perturbed greatly by the presence of either oxidized or reduced coenzyme. In the complex with the γ-monoamide analog, the 1 H signals of assigned residues in the protein had almost identical shifts with the corresponding protons in the methotrexate-enzyme complex for all residues except His-28 and, to a lesser extent, Leu-27. This indicates that while the His-28 interaction with the MTX γ-CO 2 - is no longer present in this complex with the γ-amide, there has not been a major change in the overall structure of the two complexes. This behavior contrasts to that of the α-amide complex where 1 H signals from protons in several amino acid residues are different compared with their values in the complex formed with methotrexate

Quantifying NMR relaxation correlation and exchange in articular cartilage with time domain analysis

Science.gov (United States)

Mailhiot, Sarah E.; Zong, Fangrong; Maneval, James E.; June, Ronald K.; Galvosas, Petrik; Seymour, Joseph D.

2018-02-01

Measured nuclear magnetic resonance (NMR) transverse relaxation data in articular cartilage has been shown to be multi-exponential and correlated to the health of the tissue. The observed relaxation rates are dependent on experimental parameters such as solvent, data acquisition methods, data analysis methods, and alignment to the magnetic field. In this study, we show that diffusive exchange occurs in porcine articular cartilage and impacts the observed relaxation rates in T1-T2 correlation experiments. By using time domain analysis of T2-T2 exchange spectroscopy, the diffusive exchange time can be quantified by measurements that use a single mixing time. Measured characteristic times for exchange are commensurate with T1 in this material and so impacts the observed T1 behavior. The approach used here allows for reliable quantification of NMR relaxation behavior in cartilage in the presence of diffusive fluid exchange between two environments.

Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

International Nuclear Information System (INIS)

Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

2003-01-01

NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

Science.gov (United States)

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data

Energy Technology Data Exchange (ETDEWEB)

Helmus, Jonathan J., E-mail: jjhelmus@gmail.com [Argonne National Laboratory, Environmental Science Division (United States); Jaroniec, Christopher P., E-mail: jaroniec@chemistry.ohio-state.edu [Ohio State University, Department of Chemistry and Biochemistry (United States)

2013-04-15

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.comhttp://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data

International Nuclear Information System (INIS)

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.comhttp://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Natural abundant solid state NMR studies in designed tripeptides for differentiation of multiple conformers.

Science.gov (United States)

Jayanthi, S; Chatterjee, Bhaswati; Raghothama, S

2009-10-01

Solid state NMR (SSNMR) experiments on heteronuclei in natural abundance are described for three synthetically designed tripeptides Piv-(L)Pro-(L)Pro-(L)Phe-OMe (1), Piv-(D)Pro-(L)Pro-(L)Phe-OMe (2), and Piv-(D)Pro-(L)Pro-(L)Phe-NHMe (3). These peptides exist in different conformation as shown by solution state NMR and single crystal X-ray analysis (Chatterjee et al., Chem Eur J 2008, 14, 6192). In this study, SSNMR has been used to probe the conformations of these peptides in their powder form. The (13)C spectrum of peptide (1) showed doubling of resonances corresponding to cis/cis form, unlike in solution where the similar doubling is attributed to cis/trans form. This has been confirmed by the chemical shift differences of C(beta) and C(gamma) carbon of Proline in peptide (1) both in solution and SSNMR. Peptide (2) and (3) provided single set of resonances which represented all trans form across the di-Proline segment. The results are in agreement with the X-ray analysis. Solid state (15)N resonances, especially from Proline residues provided additional information, which is normally not observable in solution state NMR. (1)H chemical shifts are also obtained from a two-dimensional heteronuclear correlation experiment between (1)H--(13)C. The results confirm the utility of NMR as a useful tool for identifying different conformers in peptides in the solid state. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 851-860, 2009.

Selective One-Dimensional Total Correlation Spectroscopy Nuclear Magnetic Resonance Experiments for a Rapid Identification of Minor Components in the Lipid Fraction of Milk and Dairy Products: Toward Spin Chromatography?

Science.gov (United States)

Papaemmanouil, Christina; Tsiafoulis, Constantinos G; Alivertis, Dimitrios; Tzamaloukas, Ouranios; Miltiadou, Despoina; Tzakos, Andreas G; Gerothanassis, Ioannis P

2015-06-10

We report a rapid, direct, and unequivocal spin-chromatographic separation and identification of minor components in the lipid fraction of milk and common dairy products with the use of selective one-dimensional (1D) total correlation spectroscopy (TOCSY) nuclear magnetic resonance (NMR) experiments. The method allows for the complete backbone spin-coupling network to be elucidated even in strongly overlapped regions and in the presence of major components from 4 × 10(2) to 3 × 10(3) stronger NMR signal intensities. The proposed spin-chromatography method does not require any derivatization steps for the lipid fraction, is selective with excellent resolution, is sensitive with quantitation capability, and compares favorably to two-dimensional (2D) TOCSY and gas chromatography-mass spectrometry (GC-MS) methods of analysis. The results of the present study demonstrated that the 1D TOCSY NMR spin-chromatography method can become a procedure of primary interest in food analysis and generally in complex mixture analysis.

Comparative {sup 1}H NMR-based metabonomic analysis of HIV-1 sera

Energy Technology Data Exchange (ETDEWEB)

Philippeos, C. [University of Johannesburg, Department of Biochemistry (South Africa); Steffens, F. E. [University of Pretoria, Department of Statistics (South Africa); Meyer, D. [University of Pretoria, Department of Biochemistry (South Africa)], E-mail: debra.meyer@up.ac.za

2009-07-15

{sup 1}H NMR spectroscopy of sera from HIV-1 infected and uninfected individuals was performed on 300 and 600 MHz instruments. The resultant spectra were automatically data reduced to 90 and 180 integral segments of equal length. Analysis of variance identified significant differences between the sample groups, especially for the samples analyzed on 600 MHz and reduced to fewer segments. Linear discriminant analysis correctly classified 100% of the samples analyzed on the 300 MHz NMR (reduced to 180 segments); an increase in instrument sensitivity resulted in lower percentages of correctly classified samples. Multinomial logistic regression (MLR) resulted in 100% correct classification of all samples from both instruments. Thus {sup 1}H-NMR metabonomics on either instrument distinguishes HIV-positive individuals using or not using anti retroviral therapy, but the sensitivity of the instrument impacts on data reduction. Furthermore, MLR is a novel multivariate statistical technique for improved classification of biological data analyzed in NMR.

Equilibrium: two-dimensional configurations

International Nuclear Information System (INIS)

Anon.

1987-01-01

In Chapter 6, the problem of toroidal force balance is addressed in the simplest, nontrivial two-dimensional geometry, that of an axisymmetric torus. A derivation is presented of the Grad-Shafranov equation, the basic equation describing axisymmetric toroidal equilibrium. The solutions to equations provide a complete description of ideal MHD equilibria: radial pressure balance, toroidal force balance, equilibrium Beta limits, rotational transform, shear, magnetic wall, etc. A wide number of configurations are accurately modeled by the Grad-Shafranov equation. Among them are all types of tokamaks, the spheromak, the reversed field pinch, and toroidal multipoles. An important aspect of the analysis is the use of asymptotic expansions, with an inverse aspect ratio serving as the expansion parameter. In addition, an equation similar to the Grad-Shafranov equation, but for helically symmetric equilibria, is presented. This equation represents the leading-order description low-Beta and high-Beta stellarators, heliacs, and the Elmo bumpy torus. The solutions all correspond to infinitely long straight helices. Bending such a configuration into a torus requires a full three-dimensional calculation and is discussed in Chapter 7

On the two-dimensional Saigo-Maeda fractional calculus asociated with two-dimensional Aleph TRANSFORM

Directory of Open Access Journals (Sweden)

Dinesh Kumar

2013-11-01

Full Text Available This paper deals with the study of two-dimensional Saigo-Maeda operators of Weyl type associated with Aleph function defined in this paper. Two theorems on these defined operators are established. Some interesting results associated with the H-functions and generalized Mittag-Leffler functions are deduced from the derived results. One dimensional analog of the derived results is also obtained.

Piperamides from Piper ottonoides by NMR and GC-MS based mixture analysis

Energy Technology Data Exchange (ETDEWEB)

Wolff, Thiago; Valente, Ligia M.M., E-mail: valente@iq.ufrj.br [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Química; Santos, Priscila F.P. [Centro Federal de Educação Tecnológica Celso Suckow da Fonseca (UnED/CEFET), Angra dos Reis, RJ (Brazil); Magalhães, Alvicler [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Departamento de Química Inorgânica; Tinoco, Luzineide W. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Instituto de Pesquisa em Produtos Naturais; Pereira, Rita C.A. [Embrapa Agroindústria Tropical, Fortaleza, CE (Brazil); Guimarães, Elsie F. [Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, RJ (Brazil)

2015-07-01

The species Piper ottonoides Yuncker (Piperaceae), known as 'joão-brandim', is a shrub that occurs in the Brazilian Amazon rainforest. Its roots and leaves are used in traditional medicine as local anesthetic to treat toothache and sore throat. In this study, the structural characterization in mixture of isobutyl amides present in semi-purified fractions from fruits, leaves, stems and roots of P. ottonoides was achieved by employing gas chromatography-mass spectrometry (GC-MS) and a combination of nuclear magnetic resonance (NMR) techniques ({sup 1}H, {sup 1}H-{sup 1}H COSY, {sup 1}H-{sup 13}CHSQC, {sup 1}H-{sup 13}CHMBC, TOCSY and {sup 1}H-{sup 1}H J-RES). The MS fragmentation patterns and the NMR chemical shifts, multiplicities, coupling constants and the signal correlations in the two-dimensional spectra were carefully analyzed also taking into account some key elements of differentiation among the compounds. The data set allowed identifying unequivocally the new amide N-isobutyl-7-(4'- methoxyphenyl)-2E,4E-heptadienamide, which we named ottonoidenamide as well as piperovatine and chingchengenamide A in all parts of the plant, the additional presence of pipercallosine and pipercallosidine in roots and of dihydropiperlonguminine in fruits and leaves. The presence of piperovatine and pipercallosine in P. ottonoides should be associated to its traditional use. (author)

Perspective of Dimensional Analysis in Medical Science

Directory of Open Access Journals (Sweden)

Kowalewski Wojciech

2017-09-01

Full Text Available This paper presents several applications of the dimensional analysis method to problems investigated in medical sciences. The method is used to analyze various complex processes without using formal laws governing the same. It is particularly suitable for a general analysis of fluid transfer (liquids and gases in the human body. This paper mainly serves as an overview of selected applications, mostly those emerging in the recent years, and includes a discussion of the mathematical fundamentals of dimensional analysis together followed by its critical analysis. Containing detailed calculations of two examples, the paper also serves as training material in the area of the computational method of the dimensional analysis algorithm.

An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus

International Nuclear Information System (INIS)

Huang Ribo; Du Qishi; Wang Chenghua; Chou, K.-C.

2008-01-01

The long-sought three-dimensional structure of the M2 proton channel of influenza A virus was successfully determined recently by the high-resolution NMR [J.R. Schnell, J.J. Chou, Structure and mechanism of the M2 proton channel of influenza A virus, Nature 451 (2008) 591-595]. Such a milestone work has provided a solid structural basis for studying drug-resistance problems. However, the action mechanism revealed from the NMR structure is completely different from the traditional view and hence prone to be misinterpreted as 'conflicting' with some previous biological functional studies. To clarify this kind of confusion, an in-depth analysis was performed for these functional studies, particularly for the mutations D44N, D44A and N44D on position 44, and the mutations on positions 27-38. The analyzed results have provided not only compelling evidences to further validate the NMR structure but also very useful clues for dealing with the drug-resistance problems and developing new effective drugs against H5N1 avian influenza virus, an impending threat to human beings.

Integration of fringe projection and two-dimensional digital image correlation for three-dimensional displacements measurements

Science.gov (United States)

Felipe-Sesé, Luis; López-Alba, Elías; Siegmann, Philip; Díaz, Francisco A.

2016-12-01

A low-cost approach for three-dimensional (3-D) full-field displacement measurement is applied for the analysis of large displacements involved in two different mechanical events. The method is based on a combination of fringe projection and two-dimensional digital image correlation (DIC) techniques. The two techniques have been employed simultaneously using an RGB camera and a color encoding method; therefore, it is possible to measure in-plane and out-of-plane displacements at the same time with only one camera even at high speed rates. The potential of the proposed methodology has been employed for the analysis of large displacements during contact experiments in a soft material block. Displacement results have been successfully compared with those obtained using a 3D-DIC commercial system. Moreover, the analysis of displacements during an impact test on a metal plate was performed to emphasize the application of the methodology for dynamics events. Results show a good level of agreement, highlighting the potential of FP + 2D DIC as low-cost alternative for the analysis of large deformations problems.

Mixture analysis by long-range J-resolved 2D NMR

International Nuclear Information System (INIS)

Ha, S.T.K.; Lee, R.W.K.; Wilkins, C.L.

1987-01-01

In most spectroscopic qualitative analyses chromatographic separations are done before identification. Unfortunately, this general approach has suffered from a number of shortcomings. Off-line chromatographic separation followed by spectroscopic analysis is time consuming and inefficient and on-line analysis suffers from mismatch of the material flow requirements between chromatographic columns and spectroscopic instruments. An alternative mixture identification procedure solely based upon use of edited 13 C NMR spectra and a 13 C NMR chemical shift data base is reported. This approach has been demonstrated in the analyses of several mixtures, including a mixture of amino acids and some isomers. In all cases, identifications of components of these mixtures are successful

Bispectral analysis of nonlinear compressional waves in a two-dimensional dusty plasma crystal

International Nuclear Information System (INIS)

Nosenko, V.; Goree, J.; Skiff, F.

2006-01-01

Bispectral analysis was used to study the nonlinear interaction of compressional waves in a two-dimensional strongly coupled dusty plasma. A monolayer of highly charged polymer microspheres was suspended in a plasma sheath. The microspheres interacted with a Yukawa potential and formed a triangular lattice. Two sinusoidal pump waves with different frequencies were excited in the lattice by pushing the particles with modulated Ar + laser beams. Coherent nonlinear interaction of the pump waves was shown to be the mechanism of generating waves at the sum, difference, and other combination frequencies. However, coherent nonlinear interaction was ruled out for certain combination frequencies, in particular, for the difference frequency below an excitation-power threshold, as predicted by theory

Spectral analysis and multigrid preconditioners for two-dimensional space-fractional diffusion equations

Science.gov (United States)

Moghaderi, Hamid; Dehghan, Mehdi; Donatelli, Marco; Mazza, Mariarosa

2017-12-01

Fractional diffusion equations (FDEs) are a mathematical tool used for describing some special diffusion phenomena arising in many different applications like porous media and computational finance. In this paper, we focus on a two-dimensional space-FDE problem discretized by means of a second order finite difference scheme obtained as combination of the Crank-Nicolson scheme and the so-called weighted and shifted Grünwald formula. By fully exploiting the Toeplitz-like structure of the resulting linear system, we provide a detailed spectral analysis of the coefficient matrix at each time step, both in the case of constant and variable diffusion coefficients. Such a spectral analysis has a very crucial role, since it can be used for designing fast and robust iterative solvers. In particular, we employ the obtained spectral information to define a Galerkin multigrid method based on the classical linear interpolation as grid transfer operator and damped-Jacobi as smoother, and to prove the linear convergence rate of the corresponding two-grid method. The theoretical analysis suggests that the proposed grid transfer operator is strong enough for working also with the V-cycle method and the geometric multigrid. On this basis, we introduce two computationally favourable variants of the proposed multigrid method and we use them as preconditioners for Krylov methods. Several numerical results confirm that the resulting preconditioning strategies still keep a linear convergence rate.

Energy Spectra of Vortex Distributions in Two-Dimensional Quantum Turbulence

Directory of Open Access Journals (Sweden)

Ashton S. Bradley

2012-10-01

Full Text Available We theoretically explore key concepts of two-dimensional turbulence in a homogeneous compressible superfluid described by a dissipative two-dimensional Gross-Pitaeveskii equation. Such a fluid supports quantized vortices that have a size characterized by the healing length ξ. We show that, for the divergence-free portion of the superfluid velocity field, the kinetic-energy spectrum over wave number k may be decomposed into an ultraviolet regime (k≫ξ^{-1} having a universal k^{-3} scaling arising from the vortex core structure, and an infrared regime (k≪ξ^{-1} with a spectrum that arises purely from the configuration of the vortices. The Novikov power-law distribution of intervortex distances with exponent -1/3 for vortices of the same sign of circulation leads to an infrared kinetic-energy spectrum with a Kolmogorov k^{-5/3} power law, which is consistent with the existence of an inertial range. The presence of these k^{-3} and k^{-5/3} power laws, together with the constraint of continuity at the smallest configurational scale k≈ξ^{-1}, allows us to derive a new analytical expression for the Kolmogorov constant that we test against a numerical simulation of a forced homogeneous, compressible, two-dimensional superfluid. The numerical simulation corroborates our analysis of the spectral features of the kinetic-energy distribution, once we introduce the concept of a clustered fraction consisting of the fraction of vortices that have the same sign of circulation as their nearest neighboring vortices. Our analysis presents a new approach to understanding two-dimensional quantum turbulence and interpreting similarities and differences with classical two-dimensional turbulence, and suggests new methods to characterize vortex turbulence in two-dimensional quantum fluids via vortex position and circulation measurements.

SDAR: a practical tool for graphical analysis of two-dimensional data

Directory of Open Access Journals (Sweden)

Weeratunga Saroja

2012-08-01

Full Text Available Abstract Background Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionally, more complex software packages typically require more time by the individual user to understand and operate. Practical and convenient graphical data analysis software in Java with a user-friendly interface are rare. Results We have developed SDAR, a Java application to analyse two-dimensional data with an intuitive graphical user interface. A smart ASCII parser allows import of data into SDAR without particular format requirements. The centre piece of SDAR is the Java class GraphPanel which provides methods for generic tasks of data visualisation. Data can be manipulated and analysed with respect to the most common operations experienced in an experimental biochemical laboratory. Images of the data plots can be generated in SVG-, TIFF- or PNG-format. Data exported by SDAR is annotated with commands compatible with the Grace software. Conclusion Since SDAR is implemented in Java, it is truly cross-platform compatible. The software is easy to install, and very convenient to use judging by experience in our own laboratories. It is freely available to academic users at http://www.structuralchemistry.org/pcsb/. To download SDAR, users will be asked for their name, institution and email address. A manual, as well as the source code of the GraphPanel class can also be downloaded from this site.

Use of optimized 1D TOCSY NMR for improved quantitation and metabolomic analysis of biofluids

Energy Technology Data Exchange (ETDEWEB)

Sandusky, Peter [Eckerd College, Department of Chemistry (United States); Appiah-Amponsah, Emmanuel; Raftery, Daniel, E-mail: raftery@purdue.edu [Purdue University, Department of Chemistry (United States)

2011-04-15

One dimensional selective TOCSY experiments have been shown to be advantageous in providing improved data inputs for principle component analysis (PCA) (Sandusky and Raftery 2005a, b). Better subpopulation cluster resolution in the observed scores plots results from the ability to isolate metabolite signals of interest via the TOCSY based filtering approach. This report reexamines the quantitative aspects of this approach, first by optimizing the 1D TOCSY experiment as it relates to the measurement of biofluid constituent concentrations, and second by comparing the integration of 1D TOCSY read peaks to the bucket integration of 1D proton NMR spectra in terms of precision and accuracy. This comparison indicates that, because of the extensive peak overlap that occurs in the 1D proton NMR spectra of biofluid samples, bucket integrals are often far less accurate as measures of individual constituent concentrations than 1D TOCSY read peaks. Even spectral fitting approaches have proven difficult in the analysis of significantly overlapped spectral regions. Measurements of endogenous taurine made over a sample population of human urine demonstrates that, due to background signals from other constituents, bucket integrals of 1D proton spectra routinely overestimate the taurine concentrations and distort its variation over the sample population. As a result, PCA calculations performed using data matrices incorporating 1D TOCSY determined taurine concentrations produce better scores plot subpopulation cluster resolution.

Use of optimized 1D TOCSY NMR for improved quantitation and metabolomic analysis of biofluids

International Nuclear Information System (INIS)

Sandusky, Peter; Appiah-Amponsah, Emmanuel; Raftery, Daniel

2011-01-01

One dimensional selective TOCSY experiments have been shown to be advantageous in providing improved data inputs for principle component analysis (PCA) (Sandusky and Raftery 2005a, b). Better subpopulation cluster resolution in the observed scores plots results from the ability to isolate metabolite signals of interest via the TOCSY based filtering approach. This report reexamines the quantitative aspects of this approach, first by optimizing the 1D TOCSY experiment as it relates to the measurement of biofluid constituent concentrations, and second by comparing the integration of 1D TOCSY read peaks to the bucket integration of 1D proton NMR spectra in terms of precision and accuracy. This comparison indicates that, because of the extensive peak overlap that occurs in the 1D proton NMR spectra of biofluid samples, bucket integrals are often far less accurate as measures of individual constituent concentrations than 1D TOCSY read peaks. Even spectral fitting approaches have proven difficult in the analysis of significantly overlapped spectral regions. Measurements of endogenous taurine made over a sample population of human urine demonstrates that, due to background signals from other constituents, bucket integrals of 1D proton spectra routinely overestimate the taurine concentrations and distort its variation over the sample population. As a result, PCA calculations performed using data matrices incorporating 1D TOCSY determined taurine concentrations produce better scores plot subpopulation cluster resolution.

Two-dimensional fluid-hammer analysis by the method of nearcharacteristics

International Nuclear Information System (INIS)

Shin, Y.W.; Kot, C.A.

1975-05-01

A numerical technique based on the method of nearcharacteristics is considered for solving propagation of fluid-hammer waves in a two-dimensional geometry. The solution is constructed by relating flow conditions by compatibility equations along lines called nearcharacteristics. Three choices are considered in the numerical scheme that are accurate within an error of the order of magnitude of the time step. Since the nearcharacteristics lie in the coordinate planes, the technique provides an efficient method requiring only simple interpolations in the initial plane. On the other hand, the nearcharacteristics fall outside the characteristics cone. Thus the solution procedure directly refers to conditions outside the true domain of dependence. The effect of this is studied through numerical calculation of a simple example problem and comparison with results obtained by a bicharacteristic method. Comparison is also made with existing analytical solutions and experiments. Furthermore, the three solution schemes considered are examined for numerical stability by the vonNeumann test. Two of the schemes were found to be unstable; the third yielded a stability criterion equivalent to that of the bicharacteristic formulation. The stability-analysis results were confirmed by numerical experimentation. (auth)

STRUYA a code for two-dimensional fluid flow analysis with and without structure coupling

International Nuclear Information System (INIS)

Katz, F.W.; Schlechtendahl, E.G.; Stoelting, K.

1979-11-01

STRUYA is a code for two-dimensional subsonic and supersonic flow analysis. Both Eulerian and Lagrangian grids are allowed. In the third dimension the flow domain may be bounded by a moving wall. The wall movement may be prescribed in a time-and space varying way or computed by a structural model. STRUYA offers a general scheme for adapting various structural models. As a standard feature it includes a cylindrical shell model (CYLDY2). (orig.) [de

Whole-core analysis by 13C NMR

International Nuclear Information System (INIS)

Vinegar, H.J.; Tutunjian, P.N.; Edelstein, W.A.; Roemer, P.B.

1991-01-01

This paper reports on a whole-core nuclear magnetic resonance (NMR) system that was used to obtain natural abundance 13 C spectra. The system enables rapid, nondestructive measurements of bulk volume of movable oil, aliphatic/aromatic ratio, oil viscosity, and organic vs. carbonate carbon. 13 C NMR can be used in cores where the 1 H NMR spectrum is too broad to resolve oil and water resonances separately. A 5 1/4-in. 13 C/ 1 H NMR coil was installed on a General Electric (GE) CSI-2T NMR imager/spectrometer. With a 4-in.-OD whole core, good 13 C signal/noise ratio (SNR) is obtained within minutes, while 1 H spectra are obtained in seconds. NMR measurements have been made of the 13 C and 1 H density of crude oils with a wide range of API gravities. For light- and medium-gravity oils, the 13 C and 1 H signal per unit volume is constant within about 3.5%. For heavy crudes, the 13 C and 1 H density measured by NMR is reduced by the shortening of spin-spin relaxation time. 13 C and 1 H NMR spin-lattice relaxation times were measured on a suite of Cannon viscosity standards, crude oils (4 to 60 degrees API), and alkanes (C 5 through C 16 ) with viscosities at 77 degrees F ranging from 0.5 cp to 2.5 x 10 7 cp. The 13 C and 1 H relaxation times show a similar correlation with viscosity from which oil viscosity can be estimated accurately for viscosities up to 100 cp. The 13 C surface relaxation rate for oils on water-wet rocks is very low. Nonproton decoupled 13 C NMR is shown to be insensitive to kerogen; thus, 13 C NMR measures only the movable hydrocarbon content of the cores. In carbonates, the 13 C spectrum also contains a carbonate powder pattern useful in quantifying inorganic carbon and distinguishing organic from carbonate carbon

A two-dimensional Zn coordination polymer with a three-dimensional supra-molecular architecture.

Science.gov (United States)

Liu, Fuhong; Ding, Yan; Li, Qiuyu; Zhang, Liping

2017-10-01

The title compound, poly[bis-{μ 2 -4,4'-bis-[(1,2,4-triazol-1-yl)meth-yl]biphenyl-κ 2 N 4 : N 4' }bis-(nitrato-κ O )zinc(II)], [Zn(NO 3 ) 2 (C 18 H 16 N 6 ) 2 ] n , is a two-dimensional zinc coordination polymer constructed from 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl units. It was synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The Zn II cation is located on an inversion centre and is coordinated by two O atoms from two symmetry-related nitrate groups and four N atoms from four symmetry-related 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligands, forming a distorted octa-hedral {ZnN 4 O 2 } coordination geometry. The linear 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligand links two Zn II cations, generating two-dimensional layers parallel to the crystallographic (132) plane. The parallel layers are connected by C-H⋯O, C-H⋯N, C-H⋯π and π-π stacking inter-actions, resulting in a three-dimensional supra-molecular architecture.

Two superconducting phases in CePt{sub 3}Si confirmed by NMR

Energy Technology Data Exchange (ETDEWEB)

Ueda, Koh-ichi; Motoyama, Gaku; Kohara, Takao, E-mail: ueda@sci.u-hyogo.ac.j [Graduate School of Material Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)

2009-03-01

Recent specific heat experiments in CePt{sub 3}Si of good quality gave an evidence of coexistence of two phases, which have distinct T{sub c} and T{sub n} for each phase. NMR spectrum of {sup 29}Si also showed a complicated line shape due to a co-existence of two phases below T{sub n}. One phase is an ordinary AF state and the other is a paramagnetic like phase, in which the internal field is somewhat small. The AF internal field deduced by NMR is expected to be parallel to the c-axis at Si site. With decreasing temperature below T{sub c}, 1/T{sub 1} measured at the satellite peak decreased rapidly followed by T{sup 3} with no enhancement just below T{sub c}.

On some classes of two-dimensional local models in discrete two-dimensional monatomic FPU lattice with cubic and quartic potential

International Nuclear Information System (INIS)

Quan, Xu; Qiang, Tian

2009-01-01

This paper discusses the two-dimensional discrete monatomic Fermi–Pasta–Ulam lattice, by using the method of multiple-scale and the quasi-discreteness approach. By taking into account the interaction between the atoms in the lattice and their nearest neighbours, it obtains some classes of two-dimensional local models as follows: two-dimensional bright and dark discrete soliton trains, two-dimensional bright and dark line discrete breathers, and two-dimensional bright and dark discrete breather. (condensed matter: structure, thermal and mechanical properties)

Authentication of beef versus horse meat using 60 MHz 1H NMR spectroscopy

Science.gov (United States)

Jakes, W.; Gerdova, A.; Defernez, M.; Watson, A.D.; McCallum, C.; Limer, E.; Colquhoun, I.J.; Williamson, D.C.; Kemsley, E.K.

2015-01-01

This work reports a candidate screening protocol to distinguish beef from horse meat based upon comparison of triglyceride signatures obtained by 60 MHz 1H NMR spectroscopy. Using a simple chloroform-based extraction, we obtained classic low-field triglyceride spectra from typically a 10 min acquisition time. Peak integration was sufficient to differentiate samples of fresh beef (76 extractions) and horse (62 extractions) using Naïve Bayes classification. Principal component analysis gave a two-dimensional “authentic” beef region (p = 0.001) against which further spectra could be compared. This model was challenged using a subset of 23 freeze–thawed training samples. The outcomes indicated that storing samples by freezing does not adversely affect the analysis. Of a further collection of extractions from previously unseen samples, 90/91 beef spectra were classified as authentic, and 16/16 horse spectra as non-authentic. We conclude that 60 MHz 1H NMR represents a feasible high-throughput approach for screening raw meat. PMID:25577043

Two-dimensional models

International Nuclear Information System (INIS)

Schroer, Bert; Freie Universitaet, Berlin

2005-02-01

It is not possible to compactly review the overwhelming literature on two-dimensional models in a meaningful way without a specific viewpoint; I have therefore tacitly added to the above title the words 'as theoretical laboratories for general quantum field theory'. I dedicate this contribution to the memory of J. A. Swieca with whom I have shared the passion of exploring 2-dimensional models for almost one decade. A shortened version of this article is intended as a contribution to the project 'Encyclopedia of mathematical physics' and comments, suggestions and critical remarks are welcome. (author)

Characterization of two minor saponins from Cordia piauhiensis by 1H and 13C NMR spectroscopy.

Science.gov (United States)

Santos, Renata P; Silveira, Edilberto R; Lemos, Telma Leda G; Viana, Francisco Arnaldo; Braz-Filho, Raimundo; Pessoa, Otília Deusdênia L

2005-06-01

A careful NMR analysis with full assignment of the 1H and 13C spectral data for two minor saponins isolated from stems of Cordia piauhiensis is reported. These saponins were isolated by high-performance liquid chromatography and characterized as 3beta-O-[alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl]pomolic acid 28-O-[beta-D-glucopyranosyl-(1 --> 6)-beta-D-glucopyranosyl] ester (1) and 3beta-O-[alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl]oleanolic acid 28-O-[beta-D-xylopyranosyl-(1 --> 2)-beta-D-glucopyranosyl-(1 --> 6)-beta-D-glucopyranosyl] ester (2). Their structures were established using a combination of 1D and 2D (1H, 1H-COSY, TOCSY, NOESY, gs-HMQC and gs-HMBC) NMR techniques, electrospray ionization mass spectrometry and chemical evidence. Copyright 2005 John Wiley & Sons, Ltd.

[Rapid analysis of suppositories by quantitative 1H NMR spectroscopy].

Science.gov (United States)

Abramovich, R A; Kovaleva, S A; Goriainov, S V; Vorob'ev, A N; Kalabin, G A

2012-01-01

Rapid analysis of suppositories with ibuprofen and arbidol by quantitative 1H NMR spectroscopy was performed. Optimal conditions for the analysis were developed. The results are useful for design of rapid methods for quality control of suppositories with different components

Ultrahigh-Resolution Magnetic Resonance in Inhomogeneous Magnetic Fields: Two-Dimensional Long-Lived-Coherence Correlation Spectroscopy

Science.gov (United States)

Chinthalapalli, Srinivas; Bornet, Aurélien; Segawa, Takuya F.; Sarkar, Riddhiman; Jannin, Sami; Bodenhausen, Geoffrey

2012-07-01

A half-century quest for improving resolution in Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) has enabled the study of molecular structures, biological interactions, and fine details of anatomy. This progress largely relied on the advent of sophisticated superconducting magnets that can provide stable and homogeneous fields with temporal and spatial variations below ΔB0/B0LLC-COSY) opens the way to overcome both inhomogeneous and homogeneous broadening, which arise from local variations in static fields and fluctuating dipole-dipole interactions, respectively. LLC-COSY makes it possible to obtain ultrahigh resolution two-dimensional spectra, with linewidths on the order of Δν=0.1 to 1 Hz, even in very inhomogeneous fields (ΔB0/B0>10ppm or 5000 Hz at 9.7 T), and can improve resolution by a factor up to 9 when the homogeneous linewidths are determined by dipole-dipole interactions. The resulting LLC-COSY spectra display chemical shift differences and scalar couplings in two orthogonal dimensions, like in “J spectroscopy.” LLC-COSY does not require any sophisticated gradient switching or frequency-modulated pulses. Applications to in-cell NMR and to magnetic resonance spectroscopy (MRS) of selected volume elements in MRI appear promising, particularly when susceptibility variations tend to preclude high resolution.

NMR studies at high magnetic fields of LiVGe_2O_6, a quasi one-dimensional spin S=1 system

Science.gov (United States)

Vonlanthen, P.; Tanaka, K. B.; Clark, W. G.; Gavilano, J. L.; Ott, H. R.; Millet, P.; Mila, F.; Kuhns, P.; Reyes, A. P.; Moulton, W. G.

2001-03-01

We report ^7Li NMR studies of LiVGe_2O_6, a quasi one-dimensional spin S=1 system. Our measurements include NMR spectra, the spin-lattice relaxation rate, T_1-1, and the spin-spin relaxation rate, T_2-1, obtained at magnetic fields (B) of 9 and 23 T and temperatures (T) over the range 1.8 - 300 K. The 9 T NMR spectra show a continuous transfer of spectral weight from a paramagnetic phase to an antiferromagnetic one in a narrow temperature range of about 2 K around the transition temperature TN ≈ 25 K. Both phases coexist in this range. Below 10 K, well into the antiferromagnetic phase, the T_1-1 measurements are consistent with electron spin excitations across an energy gap (Δ) with Δ/k_B≈ 14 K at 9 T and 11 K at about 23 T; i.e., applying a large B slightly reduces Δ. Changing B from 9 to 23 T increases TN by 1 K. Thus, TN is influenced only marginally by B up to 23 Tesla. The UCLA part of the work was supported by NSF Grants DMR-9705369 and DMR-0072524.

Discrete breathers in a two-dimensional Fermi-Pasta-Ulam lattice

International Nuclear Information System (INIS)

Butt, Imran A; Wattis, Jonathan A D

2006-01-01

Using asymptotic methods, we investigate whether discrete breathers are supported by a two-dimensional Fermi-Pasta-Ulam lattice. A scalar (one-component) two-dimensional Fermi-Pasta-Ulam lattice is shown to model the charge stored within an electrical transmission lattice. A third-order multiple-scale analysis in the semi-discrete limit fails, since at this order, the lattice equations reduce to the (2 + 1)-dimensional cubic nonlinear Schroedinger (NLS) equation which does not support stable soliton solutions for the breather envelope. We therefore extend the analysis to higher order and find a generalized (2 + 1)-dimensional NLS equation which incorporates higher order dispersive and nonlinear terms as perturbations. We find an ellipticity criterion for the wave numbers of the carrier wave. Numerical simulations suggest that both stationary and moving breathers are supported by the system. Calculations of the energy show the expected threshold behaviour whereby the energy of breathers does not go to zero with the amplitude; we find that the energy threshold is maximized by stationary breathers, and becomes arbitrarily small as the boundary of the domain of ellipticity is approached

Two-dimensional beam profiles and one-dimensional projections

Science.gov (United States)

Findlay, D. J. S.; Jones, B.; Adams, D. J.

2018-05-01

One-dimensional projections of improved two-dimensional representations of transverse profiles of particle beams are proposed for fitting to data from harp-type monitors measuring beam profiles on particle accelerators. Composite distributions, with tails smoothly matched on to a central (inverted) parabola, are shown to give noticeably better fits than single gaussian and single parabolic distributions to data from harp-type beam profile monitors all along the proton beam transport lines to the two target stations on the ISIS Spallation Neutron Source. Some implications for inferring beam current densities on the beam axis are noted.

DNP-enhanced solid-state NMR spectroscopy of active pharmaceutical ingredients.

Science.gov (United States)

Zhao, Li; Pinon, Arthur C; Emsley, Lyndon; Rossini, Aaron J

2017-11-28

Solid-state NMR spectroscopy has become a valuable tool for the characterization of both pure and formulated active pharmaceutical ingredients (APIs). However, NMR generally suffers from poor sensitivity that often restricts NMR experiments to nuclei with favorable properties, concentrated samples, and acquisition of one-dimensional (1D) NMR spectra. Here, we review how dynamic nuclear polarization (DNP) can be applied to routinely enhance the sensitivity of solid-state NMR experiments by one to two orders of magnitude for both pure and formulated APIs. Sample preparation protocols for relayed DNP experiments and experiments on directly doped APIs are detailed. Numerical spin diffusion models illustrate the dependence of relayed DNP enhancements on the relaxation properties and particle size of the solids and can be used for particle size determination when the other factors are known. We then describe the advanced solid-state NMR experiments that have been enabled by DNP and how they provide unique insight into the molecular and macroscopic structure of APIs. For example, with large sensitivity gains provided by DNP, natural isotopic abundance, 13 C- 13 C double-quantum single-quantum homonuclear correlation NMR spectra of pure APIs can be routinely acquired. DNP also enables solid-state NMR experiments with unreceptive quadrupolar nuclei such as 2 H, 14 N, and 35 Cl that are commonly found in APIs. Applications of DNP-enhanced solid-state NMR spectroscopy for the molecular level characterization of low API load formulations such as commercial tablets and amorphous solid dispersions are described. Future perspectives for DNP-enhanced solid-state NMR experiments on APIs are briefly discussed. Copyright © 2017 John Wiley & Sons, Ltd.

Development of Two-Dimensional NMR

Indian Academy of Sciences (India)

IAS Admin

time domain, allowing the application of multiple pulses and giving rise to the subject ... case of saturation, change the intensity of 'nearest-neighbours-in- space' by .... and I reached Zürich to work in the 'joint' project for one year. I was given a ...

Iterative Two- and One-Dimensional Methods for Three-Dimensional Neutron Diffusion Calculations

International Nuclear Information System (INIS)

Lee, Hyun Chul; Lee, Deokjung; Downar, Thomas J.

2005-01-01

Two methods are proposed for solving the three-dimensional neutron diffusion equation by iterating between solutions of the two-dimensional (2-D) radial and one-dimensional (1-D) axial solutions. In the first method, the 2-D/1-D equations are coupled using a current correction factor (CCF) with the average fluxes of the lower and upper planes and the axial net currents at the plane interfaces. In the second method, an analytic expression for the axial net currents at the interface of the planes is used for planar coupling. A comparison of the new methods is made with two previously proposed methods, which use interface net currents and partial currents for planar coupling. A Fourier convergence analysis of the four methods was performed, and results indicate that the two new methods have at least three advantages over the previous methods. First, the new methods are unconditionally stable, whereas the net current method diverges for small axial mesh size. Second, the new methods provide better convergence performance than the other methods in the range of practical mesh sizes. Third, the spectral radii of the new methods asymptotically approach zero as the mesh size increases, while the spectral radius of the partial current method approaches a nonzero value as the mesh size increases. Of the two new methods proposed here, the analytic method provides a smaller spectral radius than the CCF method, but the CCF method has several advantages over the analytic method in practical applications

[Analysis of total proteins in the seed of almond (Prunus dulcis) by two-dimensional electrophoresis].

Science.gov (United States)

Li, Dong-dong; He, Shao-heng

2004-07-01

To analyse the total proteins in the seeds of almond (Prunus dulcis), one of the popular ingestent allergens in China, by two-dimensional electrophoresis. The total proteins of the seeds were extracted by trichloracetic acid (TCA) method, and then separated by isoelectric focusing as first dimension and SDS-PAGE as the second dimension. The spots of proteins were visualized by staining with Coomassie Brilliant Blue R-250. After analysis with software (ImageMaster 2D), 188 different proteins were detected. The isoelectric points (pI) for approximately 28% of total proteins were between 4.5-5.5, and the relative molecular mass (M(r)) of approximately 62% total proteins were between (20-25)x10(3). This was the first high-resolution, two-dimensional protein map of the seed of almond (Prunus dulcis) in China. Our finding has laid a solid foundation for further identification, characterization, gene cloning and standardization of allergenic proteins in the seed of almond (Prunus dulcis).

Metabolomic differentiation of maca (Lepidium meyenii) accessions cultivated under different conditions using NMR and chemometric analysis.

Science.gov (United States)

Zhao, Jianping; Avula, Bharathi; Chan, Michael; Clément, Céline; Kreuzer, Michael; Khan, Ikhlas A

2012-01-01

To gain insights on the effects of color type, cultivation history, and growing site on the composition alterations of maca (Lepidium meyenii Walpers) hypocotyls, NMR profiling combined with chemometric analysis was applied to investigate the metabolite variability in different maca accessions. Maca hypocotyls with different colors (yellow, pink, violet, and lead-colored) cultivated at different geographic sites and different areas were examined for differences in metabolite expression. Differentiations of the maca accessions grown under the different cultivation conditions were determined by principle component analyses (PCAs) which were performed on the datasets derived from their ¹H NMR spectra. A total of 16 metabolites were identified by NMR analysis, and the changes in metabolite levels in relation to the color types and growing conditions of maca hypocotyls were evaluated using univariate statistical analysis. In addition, the changes of the correlation pattern among the metabolites identified in the maca accessions planted at the two different sites were examined. The results from both multivariate and univariate analysis indicated that the planting site was the major determining factor with regards to metabolite variations in maca hypocotyls, while the color of maca accession seems to be of minor importance in this respect. © Georg Thieme Verlag KG Stuttgart · New York.

Crystallinity and compositional changes in carbonated apatites: Evidence from 31P solid-state NMR, Raman, and AFM analysis

Science.gov (United States)

McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M. Banaszak; Tecklenburg, Mary M. J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

2013-10-01

Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and 31P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse 31P NMR linewidth and inverse Raman PO43-ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3-10.3 wt% CO32- range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the 31P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals.

FPGA Implementation of one-dimensional and two-dimensional cellular automata

International Nuclear Information System (INIS)

D'Antone, I.

1999-01-01

This report describes the hardware implementation of one-dimensional and two-dimensional cellular automata (CAs). After a general introduction to the cellular automata, we consider a one-dimensional CA used to implement pseudo-random techniques in built-in self test for VLSI. Due to the increase in digital ASIC complexity, testing is becoming one of the major costs in the VLSI production. The high electronics complexity, used in particle physics experiments, demands higher reliability than in the past time. General criterions are given to evaluate the feasibility of the circuit used for testing and some quantitative parameters are underlined to optimize the architecture of the cellular automaton. Furthermore, we propose a two-dimensional CA that performs a peak finding algorithm in a matrix of cells mapping a sub-region of a calorimeter. As in a two-dimensional filtering process, the peaks of the energy clusters are found in one evolution step. This CA belongs to Wolfram class II cellular automata. Some quantitative parameters are given to optimize the architecture of the cellular automaton implemented in a commercial field programmable gate array (FPGA)

Lie algebra contractions on two-dimensional hyperboloid

International Nuclear Information System (INIS)

Pogosyan, G. S.; Yakhno, A.

2010-01-01

The Inoenue-Wigner contraction from the SO(2, 1) group to the Euclidean E(2) and E(1, 1) group is used to relate the separation of variables in Laplace-Beltrami (Helmholtz) equations for the four corresponding two-dimensional homogeneous spaces: two-dimensional hyperboloids and two-dimensional Euclidean and pseudo-Euclidean spaces. We show how the nine systems of coordinates on the two-dimensional hyperboloids contracted to the four systems of coordinates on E 2 and eight on E 1,1 . The text was submitted by the authors in English.

Quasi-two-dimensional holography

International Nuclear Information System (INIS)

Kutzner, J.; Erhard, A.; Wuestenberg, H.; Zimpfer, J.

1980-01-01

The acoustical holography with numerical reconstruction by area scanning is memory- and time-intensive. With the experiences by the linear holography we tried to derive a scanning for the evaluating of the two-dimensional flaw-sizes. In most practical cases it is sufficient to determine the exact depth extension of a flaw, whereas the accuracy of the length extension is less critical. For this reason the applicability of the so-called quasi-two-dimensional holography is appropriate. The used sound field given by special probes is divergent in the inclined plane and light focussed in the perpendicular plane using cylindrical lenses. (orig.) [de

Two-dimensional boundary-value problem for ion-ion diffusion

International Nuclear Information System (INIS)

Tuszewski, M.; Lichtenberg, A.J.

1977-01-01

Like-particle diffusion is usually negligible compared with unlike-particle diffusion because it is two orders higher in spatial derivatives. When the ratio of the ion gyroradius to the plasma transverse dimension is of the order of the fourth root of the mass ratio, previous one-dimensional analysis indicated that like-particle diffusion is significant. A two-dimensional boundary-value problem for ion-ion diffusion is investigated. Numerical solutions are found with models for which the nonlinear partial differential equation reduces to an ordinary fourth-order differential equation. These solutions indicate that the ion-ion losses are higher by a factor of six for a slab geometry, and by a factor of four for circular geometry, than estimated from dimensional analysis. The solutions are applied to a multiple mirror experiment stabilized with a quadrupole magnetic field which generates highly elliptical flux surfaces. It is found that the ion-ion losses dominate the electron-ion losses and that these classical radial losses contribute to a significant decrease of plasma lifetime, in qualitiative agreement with the experimental results

Topology optimization of two-dimensional waveguides

DEFF Research Database (Denmark)

Jensen, Jakob Søndergaard; Sigmund, Ole

2003-01-01

In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss.......In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss....

Traditional Semiconductors in the Two-Dimensional Limit.

Science.gov (United States)

Lucking, Michael C; Xie, Weiyu; Choe, Duk-Hyun; West, Damien; Lu, Toh-Ming; Zhang, S B

2018-02-23

Interest in two-dimensional materials has exploded in recent years. Not only are they studied due to their novel electronic properties, such as the emergent Dirac fermion in graphene, but also as a new paradigm in which stacking layers of distinct two-dimensional materials may enable different functionality or devices. Here, through first-principles theory, we reveal a large new class of two-dimensional materials which are derived from traditional III-V, II-VI, and I-VII semiconductors. It is found that in the ultrathin limit the great majority of traditional binary semiconductors studied (a series of 28 semiconductors) are not only kinetically stable in a two-dimensional double layer honeycomb structure, but more energetically stable than the truncated wurtzite or zinc-blende structures associated with three dimensional bulk. These findings both greatly increase the landscape of two-dimensional materials and also demonstrate that in the double layer honeycomb form, even ordinary semiconductors, such as GaAs, can exhibit exotic topological properties.

Structure resolution of Ba5Al3F19 and Iivestigation of fluorine ion dynamics by synchrotron powder diffraction, variable-temperature solid-state NMR, and quantum computations

International Nuclear Information System (INIS)

Martineau, C.; Fayon, F.; Suchomel, M.R.; Allix, M.; Massiot, D.; Taulelle, F.

2011-01-01

The room temperature structure of Ba 5 Al 3 F 19 has been solved using electron microscopy and synchrotron powder diffraction data. One-dimensional (1D) 27 Al and ultrafast magic-angle-spinning (MAS) 19 F NMR spectra have been recorded and are in agreement with the proposed structural model for Ba 5 Al 3 F 19 . The 19 F isotropic chemical shift and 27 Al quadrupolar parameters have been calculated using the CASTEP code from the experimental and density functional theory geometry-optimized structures. After optimization, the calculated NMR parameters of both the 19 F and 27 Al nuclei show improved consistency with the experimental values, demonstrating that the geometry optimization step is necessary to obtain more accurate and reliable structural data. This also enables a complete and unambiguous assignment of the 19 F MAS NMR spectrum of Ba 5 Al 3 F 19 . Variable-temperature 1D MAS 19 F NMR experiments have been carried out, showing the occurrence of fluorine ion mobility. Complementary insights were obtained from both two-dimensional (2D) exchange and 2D double-quantum dipolar recoupling NMR experiments, and a detailed analysis of the anionic motion in Ba 5 Al 3 F 19 is proposed, including the distinction between reorientational processes and chemical exchange involving bond breaking and re-formation.

Scale-free crystallization of two-dimensional complex plasmas: Domain analysis using Minkowski tensors

Science.gov (United States)

Böbel, A.; Knapek, C. A.; Räth, C.

2018-05-01

Experiments of the recrystallization processes in two-dimensional complex plasmas are analyzed to rigorously test a recently developed scale-free phase transition theory. The "fractal-domain-structure" (FDS) theory is based on the kinetic theory of Frenkel. It assumes the formation of homogeneous domains, separated by defect lines, during crystallization and a fractal relationship between domain area and boundary length. For the defect number fraction and system energy a scale-free power-law relation is predicted. The long-range scaling behavior of the bond-order correlation function shows clearly that the complex plasma phase transitions are not of the Kosterlitz, Thouless, Halperin, Nelson, and Young type. Previous preliminary results obtained by counting the number of dislocations and applying a bond-order metric for structural analysis are reproduced. These findings are supplemented by extending the use of the bond-order metric to measure the defect number fraction and furthermore applying state-of-the-art analysis methods, allowing a systematic testing of the FDS theory with unprecedented scrutiny: A morphological analysis of lattice structure is performed via Minkowski tensor methods. Minkowski tensors form a complete family of additive, motion covariant and continuous morphological measures that are sensitive to nonlinear properties. The FDS theory is rigorously confirmed and predictions of the theory are reproduced extremely well. The predicted scale-free power-law relation between defect fraction number and system energy is verified for one more order of magnitude at high energies compared to the inherently discontinuous bond-order metric. It is found that the fractal relation between crystalline domain area and circumference is independent of the experiment, the particular Minkowski tensor method, and the particular choice of parameters. Thus, the fractal relationship seems to be inherent to two-dimensional phase transitions in complex plasmas. Minkowski

Sufficient Controllability Condition for Affine Systems with Two-Dimensional Control and Two-Dimensional Zero Dynamics

Directory of Open Access Journals (Sweden)

D. A. Fetisov

2015-01-01

Full Text Available The controllability conditions are well known if we speak about linear stationary systems: a linear stationary system is controllable if and only if the dimension of the state vector is equal to the rank of the controllability matrix. The concept of the controllability matrix is extended to affine systems, but relations between affine systems controllability and properties of this matrix are more complicated. Various controllability conditions are set for affine systems, but they deal as usual either with systems of some special form or with controllability in some small neighborhood of the concerned point. An affine system is known to be controllable if the system is equivalent to a system of a canonical form, which is defined and regular in the whole space of states. In this case, the system is said to be feedback linearizable in the space of states. However there are examples, which illustrate that a system can be controllable even if it is not feedback linearizable in any open subset in the space of states. In this article we deal with such systems.Affine systems with two-dimensional control are considered. The system in question is assumed to be equivalent to a system of a quasicanonical form with two-dimensional zero dynamics which is defined and regular in the whole space of states. Therefore the controllability of the original system is equivalent to the controllability of the received system of a quasicanonical form. In this article the sufficient condition for an available solution of the terminal problem is proven for systems of a quasicanonical form with two-dimensional control and two-dimensional zero dynamics. The condition is valid in the case of an arbitrary time interval and arbitrary initial and finite states of the system. Therefore the controllability condition is set for systems of a quasicanonical form with two-dimensional control and two-dimensional zero dynamics. An example is given which illustrates how the proved

Two-dimensional condensation of physi-sorbed methane on layer-like halides

International Nuclear Information System (INIS)

Nardon, Yves

1972-01-01

Two-dimensional condensation of methane in physi-sorbed layers has been studied from sets of stepped isotherms of methane on the cleavage plane of layer-like halides (FeCl 2 , CdCl 2 , NiBr 2 , CdBr 2 , FeI 2 , CaI 2 , CaI 2 and PbI 2 ) in most cases prepared by sublimation in a rapid current of inert gas. The vertical parts of the steps of adsorption isotherms correspond to the formation of successive monomolecular layers by two-dimensional condensation. Thermodynamic analysis of experimental results, has mainly emphasized the important effect of the potential relief of adsorbent surfaces, on both the structure of the physi-sorbed layers and the two-dimensional critical temperature. From its entropy, we conclude that the first layer is a (111) plane of f.c.c.: methane which becomes more loosely packed as the dimensional compatibility of the lattices of the adsorbent and adsorbate becomes poorer. Experimental values of the two-dimensional critical temperatures in the first, second and third layers have been determined, and interpreted on the following basis. An expansion of the layer induces a lowering of the two-dimensional critical temperature by decreasing the lateral interaction energy, while a localisation of the adsorbed molecules in potential wells, when possible, induces a rise of the two-dimensional critical temperature. (author) [fr

Structural study of ethyl 3-methyl-9-oxo-3-azabicyclo63.3.19nonane-1-carboxylate by two-dimensional NMR spectroscopy

Science.gov (United States)

Arias-Pérez, M. S.; Alejo, A.; Gálvez, E.; Pérez, S. M.; Santos, M. J.

1995-04-01

Ethyl 3-methyl-9-oxo-3-azabicyclo[3.3.1]nonane-1-carboxylate has been studied by 1H, 13C and 2D NMR spectroscopy in order to establish its conformational behaviour. The combined use of COSY and 1H- 13C correlation spectra helped in the unambiguous and complete assignment of the bicyclic carbon and proton resonances. It is found that the piperidone ring displays a slightly fattened chair conformation with the N-methyl group in the equatorial position, while a twist-chair form seems to be favoured for the cyclohexanone one. Two preferred orientations migth be proposed for the ethoxycarbonyl moiety.

Two-dimensional profiling of Xanthomonas campestris pv. viticola ...

African Journals Online (AJOL)

However, the analysis of the 2D-PAGE gel images revealed a larger number of spots in the lysis method when compared to the others. Taking ... Keywords: Bacterial canker, Vitis vinifera, proteomics, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis (2D-PAGE).

NMR structure of the first Ig module of mouse FGFR1

DEFF Research Database (Denmark)

Kiselyov, V.V.; Bock, Elisabeth Marianne; Berezin, V.

2006-01-01

of this module. We describe here the NMR structure of the Ig1 module of mouse FGFR1. The three-dimensional fold of the module belongs to the intermediate Ig subgroup and can be described as a beta-barrel consisting of two beta-sheets. One sheet is formed by A', G, F, C, and C', and the other by A, B, B', E...

The Hydrodynamic Study of the Swimming Gliding: a Two-Dimensional Computational Fluid Dynamics (CFD) Analysis.

Science.gov (United States)

Marinho, Daniel A; Barbosa, Tiago M; Rouboa, Abel I; Silva, António J

2011-09-01

Nowadays the underwater gliding after the starts and the turns plays a major role in the overall swimming performance. Hence, minimizing hydrodynamic drag during the underwater phases should be a main aim during swimming. Indeed, there are several postures that swimmers can assume during the underwater gliding, although experimental results were not conclusive concerning the best body position to accomplish this aim. Therefore, the purpose of this study was to analyse the effect in hydrodynamic drag forces of using different body positions during gliding through computational fluid dynamics (CFD) methodology. For this purpose, two-dimensional models of the human body in steady flow conditions were studied. Two-dimensional virtual models had been created: (i) a prone position with the arms extended at the front of the body; (ii) a prone position with the arms placed alongside the trunk; (iii) a lateral position with the arms extended at the front and; (iv) a dorsal position with the arms extended at the front. The drag forces were computed between speeds of 1.6 m/s and 2 m/s in a two-dimensional Fluent(®) analysis. The positions with the arms extended at the front presented lower drag values than the position with the arms aside the trunk. The lateral position was the one in which the drag was lower and seems to be the one that should be adopted during the gliding after starts and turns.

Interpretations of NMR images

International Nuclear Information System (INIS)

Shi, J.Z.; McFarland, W.D.; Chen, S.S.; Sadhu, V.K.

1986-01-01

Two color display schemes are generally considered in medical images: pseudo-color and color composite. Psuedo-color technique maps the intensity means of a single monochrome image into a three dimensional color space, the gray level is thus replaced by the assigned color. Such a psuedo-color assignment is somewhat arbitrary but may be advantageous if the monochrome image is composed of simple intensity patterns. A good example of psuedo-color application is in nuclear medicine: The change of gray levels can be simply determined and the isocounts from two regions with different surroundings can be readily recognized. However, the use of psuedo-color in CT or MR imaging is controversial because it does not give additional information and may exaggerate insignificant gray scale differences. The color composite technique maps three parametric image data into a three dimensional color space, and thus three monochrome images are merged to form a single color image. The color composite technique increases the number of ways information can be displayed and provides both quantitative and qualitative data about the object or event represented. This paper describes the application of color composite in NMR images

A Lagrangian analysis of a two-dimensional airfoil with vortex shedding

Energy Technology Data Exchange (ETDEWEB)

Lipinski, Doug; Cardwell, Blake; Mohseni, Kamran [Department of Aerospace Engineering Sciences, University of Colorado, Boulder, CO 80309-0429 (United States)], E-mail: Mohseni@colorado.edu

2008-08-29

Using invariant material manifolds and flow topology, the flow behavior and structure of flow around a two-dimensional Eppler 387 airfoil is examined with an emphasis on vortex shedding and the time-dependent reattachment profile. The examination focuses on low Reynolds number (Re = 60 000) flow at several angles of attack. Using specialized software, we identify invariant manifolds in the flow and use these structures to illuminate the process of vortex formation and the periodic behavior of the reattachment profile. Our analysis concludes with a topological view of the flow, including fixed points and a discussion of phase plots and the frequency spectrum of several key points in the flow. The behavior of invariant manifolds directly relates to the flow topology and illuminates some aspects seen in phase space during vortex shedding. Furthermore, it highlights the reattachment behavior in ways not seen before.

A Lagrangian analysis of a two-dimensional airfoil with vortex shedding

International Nuclear Information System (INIS)

Lipinski, Doug; Cardwell, Blake; Mohseni, Kamran

2008-01-01

Using invariant material manifolds and flow topology, the flow behavior and structure of flow around a two-dimensional Eppler 387 airfoil is examined with an emphasis on vortex shedding and the time-dependent reattachment profile. The examination focuses on low Reynolds number (Re = 60 000) flow at several angles of attack. Using specialized software, we identify invariant manifolds in the flow and use these structures to illuminate the process of vortex formation and the periodic behavior of the reattachment profile. Our analysis concludes with a topological view of the flow, including fixed points and a discussion of phase plots and the frequency spectrum of several key points in the flow. The behavior of invariant manifolds directly relates to the flow topology and illuminates some aspects seen in phase space during vortex shedding. Furthermore, it highlights the reattachment behavior in ways not seen before

Human muscle proteins: analysis by two-dimensional electrophoresis

Energy Technology Data Exchange (ETDEWEB)

Giometti, C.S.; Danon, M.J.; Anderson, N.G.

1983-09-01

Proteins from single frozen sections of human muscle were separated by two-dimensional gel electrophoresis and detected by fluorography or Coomassie Blue staining. The major proteins were identical in different normal muscles obtained from either sex at different ages, and in Duchenne and myotonic dystrophy samples. Congenital myopathy denervation atrophy, polymyositis, and Becker's muscular dystrophy samples, however, showed abnormal myosin light chain compositions, some with a decrease of fast-fiber myosin light chains and others with a decrease of slow-fiber light chains. These protein alterations did not correlate with any specific disease, and may be cause by generalized muscle-fiber damage.

3D Reconstruction of NMR Images by LabVIEW

Directory of Open Access Journals (Sweden)

Peter IZAK

2007-01-01

Full Text Available This paper introduces the experiment of 3D reconstruction NMR images via virtual instrumentation - LabVIEW. The main idea is based on marching cubes algorithm and image processing implemented by module of Vision assistant. The two dimensional images shot by the magnetic resonance device provide information about the surface properties of human body. There is implemented algorithm which can be used for 3D reconstruction of magnetic resonance images in biomedical application.

Phosphorus-31 NMR analysis of gold plating baths

Energy Technology Data Exchange (ETDEWEB)

Smith, R.E.

1992-03-01

This report describes the nuclear magnetic resonance (NMR) analysis of gold plating baths in the Micro-Miniature Electronic Assembly department of Allied-Signal Inc., Kansas City Division (KCD). The baths were analyzed for phosphorylated components. In freshly prepared gold plating baths in this department the principle compound observed is aminotrimethyl-phosphonate, or ATMP. As the bath is used in production, the ATMP breaks down; and new compounds, aminodimethylphosphonate (ADMP), aminomonomethylphosphonate, (AMMP), and inorganic phosphate (H{sub 2}PO{sub 4}{sup {minus}}), are formed. The NMR method has been used for almost three years to monitor the concentrations of the ATMP and breakdown products. In a previous report, results from January through October 1988 were reported. In this report, results from November 1988 through January 1991 are given.

Two-dimensional flexible nanoelectronics

Science.gov (United States)

Akinwande, Deji; Petrone, Nicholas; Hone, James

2014-12-01

2014/2015 represents the tenth anniversary of modern graphene research. Over this decade, graphene has proven to be attractive for thin-film transistors owing to its remarkable electronic, optical, mechanical and thermal properties. Even its major drawback--zero bandgap--has resulted in something positive: a resurgence of interest in two-dimensional semiconductors, such as dichalcogenides and buckled nanomaterials with sizeable bandgaps. With the discovery of hexagonal boron nitride as an ideal dielectric, the materials are now in place to advance integrated flexible nanoelectronics, which uniquely take advantage of the unmatched portfolio of properties of two-dimensional crystals, beyond the capability of conventional thin films for ubiquitous flexible systems.

Two-dimensional nonlinear analysis of steel linear and anchorage systems for post-tensioned concrete containment buildings

International Nuclear Information System (INIS)

Wedellsborg, B.W.

1981-01-01

This paper presents a two-dimensional nonlinear analysis method applicable to floor, wall, and containment dome liner analysis for continuous line anchor liner systems. The procedure initially involve obtaining the strain input data for each load case at each liner panel from available load data. This load input is then mapped for the entire liner, and an optimum pattern of inward deflected liner panels is then selected for each particular load case in order to obtain maximum liner system response. In-plane axial and shear sresses are calculated at critical points, and safety factors based on ASME Section III Division 2 Criteria against postulated and actually observed failure modes are evaluated. Modifications on the ASME criteria on safety factors based on biaxial strain capacity are proposed. The method has been used for analyzing an actual containment liner system with welded continuous orthogonal line anchors. Complete two-dimensional liner displacement and stress response were obtained and mapped for each load case. The response indicated the existence of several potential high stress regions in the dome and wall liners, and new types of response modes were predicted. (orig./HP)

Comparison of Two- and Three-Dimensional Methods for Analysis of Trunk Kinematic Variables in the Golf Swing.

Science.gov (United States)

Smith, Aimée C; Roberts, Jonathan R; Wallace, Eric S; Kong, Pui; Forrester, Stephanie E

2016-02-01

Two-dimensional methods have been used to compute trunk kinematic variables (flexion/extension, lateral bend, axial rotation) and X-factor (difference in axial rotation between trunk and pelvis) during the golf swing. Recent X-factor studies advocated three-dimensional (3D) analysis due to the errors associated with two-dimensional (2D) methods, but this has not been investigated for all trunk kinematic variables. The purpose of this study was to compare trunk kinematic variables and X-factor calculated by 2D and 3D methods to examine how different approaches influenced their profiles during the swing. Trunk kinematic variables and X-factor were calculated for golfers from vectors projected onto the global laboratory planes and from 3D segment angles. Trunk kinematic variable profiles were similar in shape; however, there were statistically significant differences in trunk flexion (-6.5 ± 3.6°) at top of backswing and trunk right-side lateral bend (8.7 ± 2.9°) at impact. Differences between 2D and 3D X-factor (approximately 16°) could largely be explained by projection errors introduced to the 2D analysis through flexion and lateral bend of the trunk and pelvis segments. The results support the need to use a 3D method for kinematic data calculation to accurately analyze the golf swing.

Bayesian Peak Picking for NMR Spectra

KAUST Repository

Cheng, Yichen

2014-02-01

Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

NMR imaging of the cardiovascular system

International Nuclear Information System (INIS)

Canby, R.C.; Evanochko, W.T.; Pohost, G.M.

1986-01-01

Proton nuclear magnetic resonance (NMR) imaging permits high-resolution tomographic and three-dimensional images of the human body to be obtained without exposure to ionizing radiation. Such imaging not only yields anatomic resolution comparable to X-ray examinations but also provides a potential means to discriminate between healthy tissue and diseased tissue. This potential is based on certain NMR properties known as relaxation times, which determine, in part, the signal intensity in an image. These properties are related to such factors as the sizes and concentrations of proteins and mobile lipids and the compartmentalization of the protons of water. Although NMR imaging (also called magnetic resonance imaging, MRI) is becoming widely available for clinical use, application to the cardiovascular system, though promising, remains primarily a research tool. Gated proton NMR imaging can generate cardiac images with excellent morphologic detail and contrast; however, its ultimate importance as a cardiovascular diagnostic modality will depend on the development of several unique applications. These applications are discussed in this paper

Structural investigation of e-beam cured epoxy resins through solid state NMR

International Nuclear Information System (INIS)

Alessi, Sabina; Spinella, Alberto; Caponetti, Eugenio; Dispenza, Clelia; Spadaro, Giuseppe

2012-01-01

In this paper the network structure of e-beam cured DGEBF based epoxy resins is investigated. Two epoxy systems, having different reactivity and cured in different process conditions, were analyzed through solid state NMR spectroscopy. The analysis shows that the more reactive system has higher cross-linking density and higher uniformity of network distribution. Similar information were obtained, in a previous work, on the same systems through dynamic mechanical thermal analysis. It is worth noting that unlike DMTA tests, which interfere with the molecular structure of the analyzed material, due to the heating during the analysis itself, more reliable information, without any artefact, are obtained by solid state NMR, carried out at constant room temperature. - Highlights: ► The structure of two e-beam cured epoxy systems is investigated through solid state NMR. ► The aim is to have direct information about the structure without inducing modifications. ► The different molecular structures are able to emphasize the response of solid state NMR. ► T 1 H, T 1ρ H and T CH measurements indicate different cross-linking degrees. ► The NMR results are in agreement with DMTA analysis performed in a previous paper.

A stock market forecasting model combining two-directional two-dimensional principal component analysis and radial basis function neural network.

Science.gov (United States)

Guo, Zhiqiang; Wang, Huaiqing; Yang, Jie; Miller, David J

2015-01-01

In this paper, we propose and implement a hybrid model combining two-directional two-dimensional principal component analysis ((2D)2PCA) and a Radial Basis Function Neural Network (RBFNN) to forecast stock market behavior. First, 36 stock market technical variables are selected as the input features, and a sliding window is used to obtain the input data of the model. Next, (2D)2PCA is utilized to reduce the dimension of the data and extract its intrinsic features. Finally, an RBFNN accepts the data processed by (2D)2PCA to forecast the next day's stock price or movement. The proposed model is used on the Shanghai stock market index, and the experiments show that the model achieves a good level of fitness. The proposed model is then compared with one that uses the traditional dimension reduction method principal component analysis (PCA) and independent component analysis (ICA). The empirical results show that the proposed model outperforms the PCA-based model, as well as alternative models based on ICA and on the multilayer perceptron.

Multi dimensional analysis of Design Basis Events using MARS-LMR

International Nuclear Information System (INIS)

Woo, Seung Min; Chang, Soon Heung

2012-01-01

the multi-dimensional analysis. In particular, we can see the reverse and mixing flow phenomena in LOHS better than TOP and LOF, which affect the peak temperature in the one dimensional analysis at 330 s but is not observed in the multi-dimensional analysis. In addition, the different temperatures at the central line of fuel and cladding are shown due to different mass flow in the core. The two PDRCs show the almost same results in one and multi-dimensional analysis, respectively. However, in the comparison between the one and multi-dimension, the heat removal capability of PDRC in the multi-dimensional analysis is better than the one dimensional analysis at the beginning of calculation. The aspects change at the ending of calculation due to the different mass flow in PDRC and over flow sodium temperature. In wrap up, the sodium temperatures of the core in the one dimensional analysis are generally higher than the multidimensional analysis. The temperature peak point in the one dimensional analysis under LOHS does not show in the multi-dimensional analysis, because the reverse and mixing flow pattern between the hot pool and the core outlet region. Even thought there are some different results between the two different dimensional analyses, we can say that the KALIMER-600 system has the safety margins.

Chemical shift-dependent apparent scalar couplings: An alternative concept of chemical shift monitoring in multi-dimensional NMR experiments

International Nuclear Information System (INIS)

Kwiatkowski, Witek; Riek, Roland

2003-01-01

The paper presents an alternative technique for chemical shift monitoring in a multi-dimensional NMR experiment. The monitored chemical shift is coded in the line-shape of a cross-peak through an apparent residual scalar coupling active during an established evolution period or acquisition. The size of the apparent scalar coupling is manipulated with an off-resonance radio-frequency pulse in order to correlate the size of the coupling with the position of the additional chemical shift. The strength of this concept is that chemical shift information is added without an additional evolution period and accompanying polarization transfer periods. This concept was incorporated into the three-dimensional triple-resonance experiment HNCA, adding the information of 1 H α chemical shifts. The experiment is called HNCA coded HA, since the chemical shift of 1 H α is coded in the line-shape of the cross-peak along the 13 C α dimension

NMR study of 1,4-dihydropyridine derivatives endowed with long alkyl and functionalized chains

Energy Technology Data Exchange (ETDEWEB)

Suarez, Margarita; Salfran, Esperanza; Rodriguez, Hortensia; Coro, Julieta, E-mail: msuarez@fq.uh.c [Universidad de La Habana (Cuba). Facultad de Quimica. Lab. de Sintesis Organica; Molero, Dolores; Saez, Elena [Universidad Complutense, Madrid (Spain). CAI-RMN; Martinez-Alvarez, Roberto; Martin, Nazario [Universidad Complutense, Madrid (Spain). Facultad de Quimica. Dept. de Quimica Organica I

2011-07-01

The {sup 1}H , {sup 13}C and {sup 15}N NMR spectroscopic data for 1,4-dihydropyridine endowed with long alkyl and functionalized chain on C-3 and C-5, have been fully assigned by combination of one- and two dimensional experiments (DEPT, HMBC, HMQC, COSY, nOe). (author)

Comprehensive NMR analysis of compositional changes of black garlic during thermal processing.

Science.gov (United States)

Liang, Tingfu; Wei, Feifei; Lu, Yi; Kodani, Yoshinori; Nakada, Mitsuhiko; Miyakawa, Takuya; Tanokura, Masaru

2015-01-21

Black garlic is a processed food product obtained by subjecting whole raw garlic to thermal processing that causes chemical reactions, such as the Maillard reaction, which change the composition of the garlic. In this paper, we report a nuclear magnetic resonance (NMR)-based comprehensive analysis of raw garlic and black garlic extracts to determine the compositional changes resulting from thermal processing. (1)H NMR spectra with a detailed signal assignment showed that 38 components were altered by thermal processing of raw garlic. For example, the contents of 11 l-amino acids increased during the first step of thermal processing over 5 days and then decreased. Multivariate data analysis revealed changes in the contents of fructose, glucose, acetic acid, formic acid, pyroglutamic acid, cycloalliin, and 5-(hydroxymethyl)furfural (5-HMF). Our results provide comprehensive information on changes in NMR-detectable components during thermal processing of whole garlic.

Approximate solutions for the two-dimensional integral transport equation. Solution of complex two-dimensional transport problems

International Nuclear Information System (INIS)

Sanchez, Richard.

1980-11-01

This work is divided into two parts: the first part deals with the solution of complex two-dimensional transport problems, the second one (note CEA-N-2166) treats the critically mixed methods of resolution. A set of approximate solutions for the isotropic two-dimensional neutron transport problem has been developed using the interface current formalism. The method has been applied to regular lattices of rectangular cells containing a fuel pin, cladding, and water, or homogenized structural material. The cells are divided into zones that are homogeneous. A zone-wise flux expansion is used to formulate a direct collision probability problem within a cell. The coupling of the cells is effected by making extra assumptions on the currents entering and leaving the interfaces. Two codes have been written: CALLIOPE uses a cylindrical cell model and one or three terms for the flux expansion, and NAUSICAA uses a two-dimensional flux representation and does a truly two-dimensional calculation inside each cell. In both codes, one or three terms can be used to make a space-independent expansion of the angular fluxes entering and leaving each side of the cell. The accuracies and computing times achieved with the different approximations are illustrated by numerical studies on two benchmark problems and by calculations performed in the APOLLO multigroup code [fr

Two dimensional neutral transport analysis in tokamak plasma

International Nuclear Information System (INIS)

Shimizu, Katsuhiro; Azumi, Masafumi

1987-02-01

Neutral particle influences the particle and energy balance, and play an important role on sputtering impurity and the charge exchange loss of neutral beam injection. In order to study neutral particle behaviour including the effects of asymmetric source and divertor configuration, the two dimensional neutral transport code has been developed using the Monte-Carlo techniques. This code includes the calculation of the H α radiation intensity based on the collisional-radiation model. The particle confinement time of the joule heated plasma in JT-60 tokamak is evaluated by comparing the calculated H α radiation intensity with the experimental data. The effect of the equilibrium on the neutral density profile in high-β plasma is also investigated. (author)

Two Dimensional Electrophoresis of Galactosidase Relating to the Disappearance of Bombyx Lectin Activity

OpenAIRE

カトウ, ヤスオ; Yasuo, Kato

2004-01-01

"Two dimensional polyacrylamide gel electroporesis (2 D-PAGE) analysis on the haemolymph of Bombyx mori was performed using the Mini-PROTEAN mini tube gel two dimensional polyacrylamide gel electrophoresis system (Bio-Rad Laboratories, Inc.). The result on various electrophoretical conditions using the haemolymph-protein showed the possibility that the haemolymph-protein was separated actually by means of this method. Moreover, the result of 2 D-PAGE analysis on Fraction II obtained by gel fi...

Two-Dimensional Nonlinear Finite Element Analysis of CMC Microstructures

Science.gov (United States)

Mital, Subodh K.; Goldberg, Robert K.; Bonacuse, Peter J.

2012-01-01

A research program has been developed to quantify the effects of the microstructure of a woven ceramic matrix composite and its variability on the effective properties and response of the material. In order to characterize and quantify the variations in the microstructure of a five harness satin weave, chemical vapor infiltrated (CVI) SiC/SiC composite material, specimens were serially sectioned and polished to capture images that detailed the fiber tows, matrix, and porosity. Open source quantitative image analysis tools were then used to isolate the constituents, from which two dimensional finite element models were generated which approximated the actual specimen section geometry. A simplified elastic-plastic model, wherein all stress above yield is redistributed to lower stress regions, is used to approximate the progressive damage behavior for each of the composite constituents. Finite element analyses under in-plane tensile loading were performed to examine how the variability in the local microstructure affected the macroscopic stress-strain response of the material as well as the local initiation and progression of damage. The macroscopic stress-strain response appeared to be minimally affected by the variation in local microstructure, but the locations where damage initiated and propagated appeared to be linked to specific aspects of the local microstructure.

Two-dimensional topological field theories coupled to four-dimensional BF theory

International Nuclear Information System (INIS)

Montesinos, Merced; Perez, Alejandro

2008-01-01

Four-dimensional BF theory admits a natural coupling to extended sources supported on two-dimensional surfaces or string world sheets. Solutions of the theory are in one to one correspondence with solutions of Einstein equations with distributional matter (cosmic strings). We study new (topological field) theories that can be constructed by adding extra degrees of freedom to the two-dimensional world sheet. We show how two-dimensional Yang-Mills degrees of freedom can be added on the world sheet, producing in this way, an interactive (topological) theory of Yang-Mills fields with BF fields in four dimensions. We also show how a world sheet tetrad can be naturally added. As in the previous case the set of solutions of these theories are contained in the set of solutions of Einstein's equations if one allows distributional matter supported on two-dimensional surfaces. These theories are argued to be exactly quantizable. In the context of quantum gravity, one important motivation to study these models is to explore the possibility of constructing a background-independent quantum field theory where local degrees of freedom at low energies arise from global topological (world sheet) degrees of freedom at the fundamental level

Poincare' maps of impulsed oscillators and two-dimensional dynamics

International Nuclear Information System (INIS)

Lupini, R.; Lenci, S.; Gardini, L.; Urbino Univ.

1996-01-01

The Poincare' map of one-dimensional linear oscillators subject to periodic, non-linear and time-delayed impulses is shown to reduce to a family of plane maps with possible non-uniqueness of the inverse. By restricting the analysis to a convenient form of the impulse function, a variety of interesting dynamical behaviours in this family are pointed out, including multistability and homoclinic bifurcations. Critical curves of two-dimensional endomorphisms are used to identify the structure of absorbing areas and their bifurcations

Extinction maps toward the Milky Way bulge: Two-dimensional and three-dimensional tests with apogee

Energy Technology Data Exchange (ETDEWEB)

Schultheis, M. [Université de Nice Sophia-Antipolis, CNRS, Observatoire de Côte d' Azur, Laboratoire Lagrange, 06304 Nice Cedex 4 (France); Zasowski, G. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Allende Prieto, C. [Instituto de Astrofísica de Canarias, Calle Vía Láctea s/n, E-38205 La Laguna, Tenerife (Spain); Anders, F.; Chiappini, C. [Leibniz-Institut für Astrophysik Potsdam (AIP), D-14482 Potsdam (Germany); Beaton, R. L.; García Pérez, A. E.; Majewski, S. R. [Department of Astronomy, University of Virginia, Charlottesville, VA 22904 (United States); Beers, T. C. [National Optical Astronomy Observatory, Tucson, AZ 85719 (United States); Bizyaev, D. [Apache Point Observatory, Sunspot, NM 88349 (United States); Frinchaboy, P. M. [Department of Physics and Astronomy, Texas Christian University, TCU Box 298840, Fort Worth, TX 76129 (United States); Ge, J. [Astronomy Department, University of Florida, Gainesville, FL 32611 (United States); Hearty, F.; Schneider, D. P. [Department of Astronomy and Astrophysics, The Pennsylvania State University, University Park, PA 16802 (United States); Holtzman, J. [New Mexico State University, Las Cruces, NM 88003 (United States); Muna, D. [Department of Astronomy, The Ohio State University, Columbus, OH 43210 (United States); Nidever, D. [Department of Astronomy, University of Michigan, Ann Arbor, MI 48109 (United States); Shetrone, M., E-mail: mathias.schultheis@oca.eu, E-mail: gail.zasowski@gmail.com [McDonald Observatory, The University of Texas at Austin, Austin, TX 78712 (United States)

2014-07-01

Galactic interstellar extinction maps are powerful and necessary tools for Milky Way structure and stellar population analyses, particularly toward the heavily reddened bulge and in the midplane. However, due to the difficulty of obtaining reliable extinction measures and distances for a large number of stars that are independent of these maps, tests of their accuracy and systematics have been limited. Our goal is to assess a variety of photometric stellar extinction estimates, including both two-dimensional and three-dimensional extinction maps, using independent extinction measures based on a large spectroscopic sample of stars toward the Milky Way bulge. We employ stellar atmospheric parameters derived from high-resolution H-band Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectra, combined with theoretical stellar isochrones, to calculate line-of-sight extinction and distances for a sample of more than 2400 giants toward the Milky Way bulge. We compare these extinction values to those predicted by individual near-IR and near+mid-IR stellar colors, two-dimensional bulge extinction maps, and three-dimensional extinction maps. The long baseline, near+mid-IR stellar colors are, on average, the most accurate predictors of the APOGEE extinction estimates, and the two-dimensional and three-dimensional extinction maps derived from different stellar populations along different sightlines show varying degrees of reliability. We present the results of all of the comparisons and discuss reasons for the observed discrepancies. We also demonstrate how the particular stellar atmospheric models adopted can have a strong impact on this type of analysis, and discuss related caveats.

Extinction maps toward the Milky Way bulge: Two-dimensional and three-dimensional tests with apogee

International Nuclear Information System (INIS)

Schultheis, M.; Zasowski, G.; Allende Prieto, C.; Anders, F.; Chiappini, C.; Beaton, R. L.; García Pérez, A. E.; Majewski, S. R.; Beers, T. C.; Bizyaev, D.; Frinchaboy, P. M.; Ge, J.; Hearty, F.; Schneider, D. P.; Holtzman, J.; Muna, D.; Nidever, D.; Shetrone, M.

2014-01-01

Galactic interstellar extinction maps are powerful and necessary tools for Milky Way structure and stellar population analyses, particularly toward the heavily reddened bulge and in the midplane. However, due to the difficulty of obtaining reliable extinction measures and distances for a large number of stars that are independent of these maps, tests of their accuracy and systematics have been limited. Our goal is to assess a variety of photometric stellar extinction estimates, including both two-dimensional and three-dimensional extinction maps, using independent extinction measures based on a large spectroscopic sample of stars toward the Milky Way bulge. We employ stellar atmospheric parameters derived from high-resolution H-band Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectra, combined with theoretical stellar isochrones, to calculate line-of-sight extinction and distances for a sample of more than 2400 giants toward the Milky Way bulge. We compare these extinction values to those predicted by individual near-IR and near+mid-IR stellar colors, two-dimensional bulge extinction maps, and three-dimensional extinction maps. The long baseline, near+mid-IR stellar colors are, on average, the most accurate predictors of the APOGEE extinction estimates, and the two-dimensional and three-dimensional extinction maps derived from different stellar populations along different sightlines show varying degrees of reliability. We present the results of all of the comparisons and discuss reasons for the observed discrepancies. We also demonstrate how the particular stellar atmospheric models adopted can have a strong impact on this type of analysis, and discuss related caveats.

The Application of Canonical Correlation to Two-Dimensional Contingency Tables

Directory of Open Access Journals (Sweden)

Alberto F. Restori

2010-03-01

Full Text Available This paper re-introduces and demonstrates the use of Mickey’s (1970 canonical correlation method in analyzing large two-dimensional contingency tables. This method of analysis supplements the traditional analysis using the Pearson chi-square. Examples and a MATLAB source listing are provided.

Two-dimensional heat flow analysis applied to heat sterilization of ponderosa pine and Douglas-fir square timbers

Science.gov (United States)

William T. Simpson

2004-01-01

Equations for a two-dimensional finite difference heat flow analysis were developed and applied to ponderosa pine and Douglas-fir square timbers to calculate the time required to heat the center of the squares to target temperature. The squares were solid piled, which made their surfaces inaccessible to the heating air, and thus surface temperatures failed to attain...

Beginning Introductory Physics with Two-Dimensional Motion

Science.gov (United States)

Huggins, Elisha

2009-01-01

During the session on "Introductory College Physics Textbooks" at the 2007 Summer Meeting of the AAPT, there was a brief discussion about whether introductory physics should begin with one-dimensional motion or two-dimensional motion. Here we present the case that by starting with two-dimensional motion, we are able to introduce a considerable…

Two-dimensional thermofield bosonization

International Nuclear Information System (INIS)

Amaral, R.L.P.G.; Belvedere, L.V.; Rothe, K.D.

2005-01-01

The main objective of this paper was to obtain an operator realization for the bosonization of fermions in 1 + 1 dimensions, at finite, non-zero temperature T. This is achieved in the framework of the real-time formalism of Thermofield Dynamics. Formally, the results parallel those of the T = 0 case. The well-known two-dimensional Fermion-Boson correspondences at zero temperature are shown to hold also at finite temperature. To emphasize the usefulness of the operator realization for handling a large class of two-dimensional quantum field-theoretic problems, we contrast this global approach with the cumbersome calculation of the fermion-current two-point function in the imaginary-time formalism and real-time formalisms. The calculations also illustrate the very different ways in which the transmutation from Fermi-Dirac to Bose-Einstein statistics is realized

Two-dimensional impurity transport calculations for a high recycling divertor

International Nuclear Information System (INIS)

Brooks, J.N.

1986-04-01

Two dimensional analysis of impurity transport in a high recycling divertor shows asymmetric particle fluxes to the divertor plate, low helium pumping efficiency, and high scrapeoff zone shielding for sputtered impurities

High-resolution nuclear magnetic resonance measurements in inhomogeneous magnetic fields: A fast two-dimensional J-resolved experiment

Energy Technology Data Exchange (ETDEWEB)

Huang, Yuqing; Cai, Shuhui; Yang, Yu; Sun, Huijun; Lin, Yanqin, E-mail: linyq@xmu.edu.cn, E-mail: chenz@xmu.edu.cn; Chen, Zhong, E-mail: linyq@xmu.edu.cn, E-mail: chenz@xmu.edu.cn [Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005 (China); Lin, Yung-Ya [Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 (United States)

2016-03-14

High spectral resolution in nuclear magnetic resonance (NMR) is a prerequisite for achieving accurate information relevant to molecular structures and composition assignments. The continuous development of superconducting magnets guarantees strong and homogeneous static magnetic fields for satisfactory spectral resolution. However, there exist circumstances, such as measurements on biological tissues and heterogeneous chemical samples, where the field homogeneity is degraded and spectral line broadening seems inevitable. Here we propose an NMR method, named intermolecular zero-quantum coherence J-resolved spectroscopy (iZQC-JRES), to face the challenge of field inhomogeneity and obtain desired high-resolution two-dimensional J-resolved spectra with fast acquisition. Theoretical analyses for this method are given according to the intermolecular multiple-quantum coherence treatment. Experiments on (a) a simple chemical solution and (b) an aqueous solution of mixed metabolites under externally deshimmed fields, and on (c) a table grape sample with intrinsic field inhomogeneity from magnetic susceptibility variations demonstrate the feasibility and applicability of the iZQC-JRES method. The application of this method to inhomogeneous chemical and biological samples, maybe in vivo samples, appears promising.

NMR and Chemometric Characterization of Vacuum Residues and Vacuum Gas Oils from Crude Oils of Different Origin

Directory of Open Access Journals (Sweden)

Jelena Parlov Vuković

2015-03-01

Full Text Available NMR spectroscopy in combination with statistical methods was used to study vacuum residues and vacuum gas oils from 32 crude oils of different origin. Two chemometric metodes were applied. Firstly, principal component analysis on complete spectra was used to perform classification of samples and clear distinction between vacuum residues and vacuum light and heavy gas oils were obtained. To quantitatively predict the composition of asphaltenes, principal component regression models using areas of resonance signals spaned by 11 frequency bins of the 1H NMR spectra were build. The first 5 principal components accounted for more than 94 % of variations in the input data set and coefficient of determination for correlation between measured and predicted values was R2 = 0.7421. Although this value is not significant, it shows the underlying linear dependence in the data. Pseudo two-dimensional DOSY NMR experiments were used to assess the composition and structural properties of asphaltenes in a selected crude oil and its vacuum residue on the basis of their different hydrodynamic behavior and translational diffusion coefficients. DOSY spectra showed the presence of several asphaltene aggregates differing in size and interactions they formed. The obtained results have shown that NMR techniques in combination with chemometrics are very useful to analyze vacuum residues and vacuum gas oils. Furthermore, we expect that our ongoing investigation of asphaltenes from crude oils of different origin will elucidate in more details composition, structure and properties of these complex molecular systems.

On the detection of corrosion pit interactions using two-dimensional spectral analysis

International Nuclear Information System (INIS)

Jarrah, Adil; Nianga, Jean-Marie; Iost, Alain; Guillemot, Gildas; Najjar, Denis

2010-01-01

A statistical methodology for detecting pits interactions based on a two-dimensional spectral analysis is presented. This method can be used as a tool for the exploratory analysis of spatial point patterns and can be advanced as an alternative of classical methods based on distance. One of the major advantages of the spectral analysis approach over the use of classical methods is its ability to reveal more details about the spatial structure like the scale for which pits corrosion can be considered as independent. Furthermore, directional components of pattern can be investigated. The method is validated in a first time using numerical simulations on random, regular and aggregated structures. The density of pits, used in the numerical simulations, corresponds to that assessed from a corroded aluminium sheet. In a second time, this method is applied to verify the independence of the corrosion pits observed on the aforementioned aluminium sheet before applying the Gumbel theory to determine the maximum pit depth. Indeed, the property of independence is a prerequisite of the Gumbel theory which is one of the most frequently used in the field of safety and reliability.

Piezoelectricity in Two-Dimensional Materials

KAUST Repository

Wu, Tao

2015-02-25

Powering up 2D materials: Recent experimental studies confirmed the existence of piezoelectricity - the conversion of mechanical stress into electricity - in two-dimensional single-layer MoS2 nanosheets. The results represent a milestone towards embedding low-dimensional materials into future disruptive technologies. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.

Two-dimensional correlation spectroscopy in polymer study

Science.gov (United States)

Park, Yeonju; Noda, Isao; Jung, Young Mee

2015-01-01

This review outlines the recent works of two-dimensional correlation spectroscopy (2DCOS) in polymer study. 2DCOS is a powerful technique applicable to the in-depth analysis of various spectral data of polymers obtained under some type of perturbation. The powerful utility of 2DCOS combined with various analytical techniques in polymer studies and noteworthy developments of 2DCOS used in this field are also highlighted. PMID:25815286

Fractal analysis on a classical hard-wall billiard with openings using a two-dimensional set of initial conditions

International Nuclear Information System (INIS)

Ree, Suhan

2003-01-01

Fractal analysis is performed to measure the chaoticity of a classical hard-wall billiard with openings. We use the circular billiard with a straight cut with two openings, and a two-dimensional (2D) set of initial conditions that produce all possible trajectories of a particle injected from one opening. We numerically compute the fractal dimension of singular points of the function that maps an initial condition to the number of collisions with the wall before the exit, using the box-counting algorithm that uses uniformly distributed points inside the 2D set of initial conditions. Finally, the classical chaotic properties are observed while the parameters of the billiard are varied, and the results are compared with those with the one-dimensional set of initial conditions

Spectral line shapes in linear absorption and two-dimensional spectroscopy with skewed frequency distributions

NARCIS (Netherlands)

Farag, Marwa H.; Hoenders, Bernhard J.; Knoester, Jasper; Jansen, Thomas L. C.

2017-01-01

The effect of Gaussian dynamics on the line shapes in linear absorption and two-dimensional correlation spectroscopy is well understood as the second-order cumulant expansion provides exact spectra. Gaussian solvent dynamics can be well analyzed using slope line analysis of two-dimensional

Spin Choreography: Basic Steps in High Resolution NMR (by Ray Freeman)

Science.gov (United States)

Minch, Michael J.

1998-02-01

There are three orientations that NMR courses may take. The traditional molecular structure course focuses on the interpretation of spectra and the use of chemical shifts, coupling constants, and nuclear Overhauser effects (NOE) to sort out subtle details of structure and stereochemistry. Courses can also focus on the fundamental quantum mechanics of observable NMR parameters and processes such a spin-spin splitting and relaxation. More recently there are courses devoted to the manipulation of nuclear spins and the basic steps of one- and two-dimensional NMR experiments. Freeman's book is directed towards the latter audience. Modern NMR methods offer a myriad ways to extract information about molecular structure and motion by observing the behavior of nuclear spins under a variety of conditions. In Freeman's words: "We can lead the spins through an intricate dance, carefully programmed in advance, to enhance, simplify, correlate, decouple, edit or assign NMR spectra." This is a carefully written, well-illustrated account of how this dance is choreographed by pulse programming, double resonance, and gradient effects. Although well written, this book is not an easy read; every word counts. It is recommended for graduate courses that emphasize the fundamentals of magnetic resonance. It is not a text on interpretation of spectra.

Two-dimensional confinement of heavy fermions

International Nuclear Information System (INIS)

Shishido, Hiroaki; Shibauchi, Takasada; Matsuda, Yuji; Terashima, Takahito

2010-01-01

Metallic systems with the strongest electron correlations are realized in certain rare-earth and actinide compounds whose physics are dominated by f-electrons. These materials are known as heavy fermions, so called because the effective mass of the conduction electrons is enhanced via correlation effects up to as much as several hundreds times the free electron mass. To date the electronic structure of all heavy-fermion compounds is essentially three-dimensional. Here we report on the first realization of a two-dimensional heavy-fermion system, where the dimensionality is adjusted in a controllable fashion by fabricating heterostructures using molecular beam epitaxy. The two-dimensional heavy fermion system displays striking deviations from the standard Fermi liquid low-temperature electronic properties. (author)

Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

International Nuclear Information System (INIS)

Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

2002-01-01

The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

Positional enrichment by proton analysis (PEPA). A one-dimensional "1H-NMR approach for "1"3C stable isotope tracer studies in metabolomics

International Nuclear Information System (INIS)

Vinaixa, Maria; Yanes, Oscar; Rodriguez, Miguel A.; Capellades, Jordi; Aivio, Suvi; Stracker, Travis H.; Gomez, Josep; Canyellas, Nicolau

2017-01-01

A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of "1"3C-satellite peaks using 1D-"1H-NMR spectra. In comparison with "1"3C-NMR, TOCSY and HSQC, PEPA improves sensitivity, accelerates the elucidation of "1"3C positions in labeled metabolites and the quantification of the percentage of stable isotope enrichment. Altogether, PEPA provides a novel framework for extending the high-throughput of "1H-NMR metabolic profiling to stable isotope tracing in metabolomics, facilitating and complementing the information derived from 2D-NMR experiments and expanding the range of isotopically enriched metabolites detected in cellular extracts. (copyright 2017 The Authors. Published by Wiley-VCH Verlag GmbH and Co. KGaA.)

Unlike twins: an NMR comparison of two α-synuclein polymorphs featuring different toxicity.

Directory of Open Access Journals (Sweden)

Julia Gath

Full Text Available We structurally compare, using solid-state NMR, two different polymorphs of α-synuclein which, as established recently, display contrasting biochemical properties, toxicity, and tropism for cells. We show that both forms, which can each be produced as a pure polymorph, are greatly different in secondary structure. While β-sheets are the dominating secondary structure elements for both polymorphs, they are markedly divergent in terms of number of elements, as well as their distribution. We demonstrate that all identified β-sheets feature an in-register parallel stacking for both polymorphs. The two forms show a different molecular arrangement in the unit cell and distinct dynamic features, while sharing a highly flexible C-terminal domain. The use of reproducible, well-identified conditions for sample preparation and the recording of identical NMR experiments allows for a direct comparison of the results.

Two-dimensional topological photonics

Science.gov (United States)

Khanikaev, Alexander B.; Shvets, Gennady

2017-12-01

Originating from the studies of two-dimensional condensed-matter states, the concept of topological order has recently been expanded to other fields of physics and engineering, particularly optics and photonics. Topological photonic structures have already overturned some of the traditional views on wave propagation and manipulation. The application of topological concepts to guided wave propagation has enabled novel photonic devices, such as reflection-free sharply bent waveguides, robust delay lines, spin-polarized switches and non-reciprocal devices. Discrete degrees of freedom, widely used in condensed-matter physics, such as spin and valley, are now entering the realm of photonics. In this Review, we summarize the latest advances in this highly dynamic field, with special emphasis on the experimental work on two-dimensional photonic topological structures.

Structures of two-dimensional three-body systems

International Nuclear Information System (INIS)

Ruan, W.Y.; Liu, Y.Y.; Bao, C.G.

1996-01-01

Features of the structure of L = 0 states of a two-dimensional three-body model system have been investigated. Three types of permutation symmetry of the spatial part, namely symmetric, antisymmetric, and mixed, have been considered. A comparison has been made between the two-dimensional system and the corresponding three-dimensional one. The effect of symmetry on microscopic structures is emphasized. (author)

Zakharov-Shabat-Mikhailov scheme of construction of two-dimensional completely integrable field theories

International Nuclear Information System (INIS)

Chudnovsky, D.V.; Columbia Univ., New York; Chudnovsky, G.V.; Columbia Univ., New York

1980-01-01

General algebraic and analytic formalism for derivation and solution of general two dimensional field theory equations of Zakharov-Shabat-Mikhailov type is presented. The examples presented show that this class of equations covers most of the known two-dimensional completely integrable equations. Possible generalizations for four dimensional systems require detailed analysis of Baecklund transformation of these equations. Baecklund transformation is presented in the form of Riemann problem and one special case of dual symmetry is worked out. (orig.)

Parent heparin and daughter LMW heparin correlation analysis using LC-MS and NMR

Energy Technology Data Exchange (ETDEWEB)

Liu, Xinyue, E-mail: liux22@rpi.edu [National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, 250100 (China); Department of Chemistry and Chemical Biology, Department of Chemical and Biological Engineering, Department of Biology, Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States); St Ange, Kalib, E-mail: stangk2@rpi.edu [Department of Chemistry and Chemical Biology, Department of Chemical and Biological Engineering, Department of Biology, Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States); Wang, Xiaohua, E-mail: wangx35@rpi.edu [Department of Chemistry and Chemical Biology, Department of Chemical and Biological Engineering, Department of Biology, Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States); School of Computer and Information, Hefei University of Technology, Hefei (China); Lin, Lei, E-mail: Linl5@rpi.edu [Department of Chemistry and Chemical Biology, Department of Chemical and Biological Engineering, Department of Biology, Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States); Zhang, Fuming, E-mail: zhangf2@rpi.edu [Department of Chemistry and Chemical Biology, Department of Chemical and Biological Engineering, Department of Biology, Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States); and others

2017-04-08

Heparin is a structurally complex, polysaccharide anticoagulant derived from livestock, primarily porcine intestinal tissues. Low molecular weight (LMW) heparins are derived through the controlled partial depolymerization of heparin. Increased manufacturing and regulatory concerns have provided the motivation for the development of more sophisticated analytical methods for determining both their structure and pedigree. A strategy, for the comprehensive comparison of parent heparins and their LMW heparin daughters, is described that relies on the analysis of monosaccharide composition, disaccharide composition, and oligosaccharide composition. Liquid chromatography-mass spectrometry is rapid, robust, and amenable to automated processing and interpretation of both top-down and bottom-up analyses. Nuclear magnetic resonance spectroscopy provides complementary top-down information on the chirality of the uronic acid residues and glucosamine substitution. Principal component analysis (PCA) was applied to the normalized abundance of oligosaccharides, calculated in the bottom-up analysis, to show parent and daughter correlation in oligosaccharide composition. Using these approaches, six pairs of parent heparins and their daughter generic enoxaparins from two different manufacturers were comprehensively analyzed. Enoxaparin is the most widely used LMW heparin and is prepared through controlled chemical β-eliminative cleavage of porcine intestinal heparin. Lovenox{sup ®}, the innovator version of enoxaparin marketed in the US, was analyzed as a reference for the daughter LMW heparins. The results, show similarities between LMW heparins from two different manufacturers with Lovenox{sup ®}, excellent lot-to-lot consistency of products from each manufacturer, and detects a correlation between each parent heparin and daughter LMW heparin. - Highlights: • Low molecular weight heparins prepared from different heparin parents were analyzed. • An integrated analytical

Parent heparin and daughter LMW heparin correlation analysis using LC-MS and NMR

International Nuclear Information System (INIS)

Liu, Xinyue; St Ange, Kalib; Wang, Xiaohua; Lin, Lei; Zhang, Fuming

2017-01-01

Heparin is a structurally complex, polysaccharide anticoagulant derived from livestock, primarily porcine intestinal tissues. Low molecular weight (LMW) heparins are derived through the controlled partial depolymerization of heparin. Increased manufacturing and regulatory concerns have provided the motivation for the development of more sophisticated analytical methods for determining both their structure and pedigree. A strategy, for the comprehensive comparison of parent heparins and their LMW heparin daughters, is described that relies on the analysis of monosaccharide composition, disaccharide composition, and oligosaccharide composition. Liquid chromatography-mass spectrometry is rapid, robust, and amenable to automated processing and interpretation of both top-down and bottom-up analyses. Nuclear magnetic resonance spectroscopy provides complementary top-down information on the chirality of the uronic acid residues and glucosamine substitution. Principal component analysis (PCA) was applied to the normalized abundance of oligosaccharides, calculated in the bottom-up analysis, to show parent and daughter correlation in oligosaccharide composition. Using these approaches, six pairs of parent heparins and their daughter generic enoxaparins from two different manufacturers were comprehensively analyzed. Enoxaparin is the most widely used LMW heparin and is prepared through controlled chemical β-eliminative cleavage of porcine intestinal heparin. Lovenox"®, the innovator version of enoxaparin marketed in the US, was analyzed as a reference for the daughter LMW heparins. The results, show similarities between LMW heparins from two different manufacturers with Lovenox"®, excellent lot-to-lot consistency of products from each manufacturer, and detects a correlation between each parent heparin and daughter LMW heparin. - Highlights: • Low molecular weight heparins prepared from different heparin parents were analyzed. • An integrated analytical approach relied

New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

International Nuclear Information System (INIS)

Xiong, Kecai; Liu, Wei; Teat, Simon J.; An, Litao; Wang, Hao; Emge, Thomas J.; Li, Jing

2015-01-01

Two new hybrid lead halides (H 2 BDA)[PbI 4 ] (1) (H 2 BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI 3 ] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively. - Graphical abstract: Two new hybrid lead halides built on one-dimensional edge-sharing double chains and two-dimensional corner-sharing perovskite layers are synthesized and their structural and electronic properties are analyzed. - Highlights: • Two new hybrid lead iodides are designed, synthesized, and characterized. • They are closely related to, but different from, perovskite structures. • The electronic properties of both compounds are analyzed by DFT calculations

New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

Energy Technology Data Exchange (ETDEWEB)

Xiong, Kecai; Liu, Wei [Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 (United States); Teat, Simon J. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); An, Litao; Wang, Hao; Emge, Thomas J. [Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 (United States); Li, Jing, E-mail: jingli@rutgers.edu [Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 (United States)

2015-10-15

Two new hybrid lead halides (H{sub 2}BDA)[PbI{sub 4}] (1) (H{sub 2}BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI{sub 3}] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively. - Graphical abstract: Two new hybrid lead halides built on one-dimensional edge-sharing double chains and two-dimensional corner-sharing perovskite layers are synthesized and their structural and electronic properties are analyzed. - Highlights: • Two new hybrid lead iodides are designed, synthesized, and characterized. • They are closely related to, but different from, perovskite structures. • The electronic properties of both compounds are analyzed by DFT calculations.

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms.

Science.gov (United States)

Appel, R D; Vargas, J R; Palagi, P M; Walther, D; Hochstrasser, D F

1997-12-01

After two generations of software systems for the analysis of two-dimensional electrophoresis (2-DE) images, a third generation of such software packages has recently emerged that combines state-of-the-art graphical user interfaces with comprehensive spot data analysis capabilities. A key characteristic common to most of these software packages is that many of their tools are implementations of algorithms that resulted from research areas such as image processing, vision, artificial intelligence or machine learning. This article presents the main algorithms implemented in the Melanie II 2-D PAGE software package. The applications of these algorithms, embodied as the feature of the program, are explained in an accompanying article (R. D. Appel et al.; Electrophoresis 1997, 18, 2724-2734).

Two-dimensional liquid chromatography consisting of twelve second-dimension columns for comprehensive analysis of intact proteins.

Science.gov (United States)

Ren, Jiangtao; Beckner, Matthew A; Lynch, Kyle B; Chen, Huang; Zhu, Zaifang; Yang, Yu; Chen, Apeng; Qiao, Zhenzhen; Liu, Shaorong; Lu, Joann J

2018-05-15

A comprehensive two-dimensional liquid chromatography (LCxLC) system consisting of twelve columns in the second dimension was developed for comprehensive analysis of intact proteins in complex biological samples. The system consisted of an ion-exchange column in the first dimension and the twelve reverse-phase columns in the second dimension; all thirteen columns were monolithic and prepared inside 250 µm i.d. capillaries. These columns were assembled together through the use of three valves and an innovative configuration. The effluent from the first dimension was continuously fractionated and sequentially transferred into the twelve second-dimension columns, while the second-dimension separations were carried out in a series of batches (six columns per batch). This LCxLC system was tested first using standard proteins followed by real-world samples from E. coli. Baseline separation was observed for eleven standard proteins and hundreds of peaks were observed for the real-world sample analysis. Two-dimensional liquid chromatography, often considered as an effective tool for mapping proteins, is seen as laborious and time-consuming when configured offline. Our online LCxLC system with increased second-dimension columns promises to provide a solution to overcome these hindrances. Copyright © 2018 Elsevier B.V. All rights reserved.

Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

Directory of Open Access Journals (Sweden)

Yang Liu

2016-01-01

Full Text Available Quantitative nuclear magnetic resonance (qNMR is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR and only a few fluorine qNMR (19F qNMR were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes.

Two dimensional nonlinear spectral estimation techniques for breast cancer localization

International Nuclear Information System (INIS)

Stathaki, P.T.; Constantinides, A.G.

1994-01-01

In this paper the problem of image texture analysis in the presence of noise is examined from a higher-order statistical perspective. The approach taken involves the use of two dimensional second order Volterra filters where the filter weights are derived from third order cumulants of the two dimensional signal. The specific application contained in this contribution is in mammography, an area in which it is difficult to discern the appropriate features. The paper describes the fundamental issues of the various components of the approach. The results of the entire texture modelling, classification and segmentation scheme contained in this paper are very encouraging

X-ray imaging device for one-dimensional and two-dimensional radioscopy

International Nuclear Information System (INIS)

1978-01-01

The X-ray imaging device for the selectable one-dimensional or two-dimensional pictures of objects illuminated by X-rays, comprising an X-ray source, an X-ray screen, and an opto-electrical picture development device placed behind the screen, is characterized by an anamorphotic optical system, which is positioned with a one-dimensional illumination between the X-ray screen and the opto-electrical device and that a two-dimensional illumination will be developed, and that in view of the lens system which forms part of the opto-electrical device, there is placed an X-ray screen in a specified beam direction so that a magnified image may be formed by equalisation of the distance between the X-ray screen and the lens system. (G.C.)

Hamiltonian formalism of two-dimensional Vlasov kinetic equation.

Science.gov (United States)

Pavlov, Maxim V

2014-12-08

In this paper, the two-dimensional Benney system describing long wave propagation of a finite depth fluid motion and the multi-dimensional Russo-Smereka kinetic equation describing a bubbly flow are considered. The Hamiltonian approach established by J. Gibbons for the one-dimensional Vlasov kinetic equation is extended to a multi-dimensional case. A local Hamiltonian structure associated with the hydrodynamic lattice of moments derived by D. J. Benney is constructed. A relationship between this hydrodynamic lattice of moments and the two-dimensional Vlasov kinetic equation is found. In the two-dimensional case, a Hamiltonian hydrodynamic lattice for the Russo-Smereka kinetic model is constructed. Simple hydrodynamic reductions are presented.

Novel target design algorithm for two-dimensional optical storage (TwoDOS)

NARCIS (Netherlands)

Huang, Li; Chong, T.C.; Vijaya Kumar, B.V.K.; Kobori, H.

2004-01-01

In this paper we introduce the Hankel transform based channel model of Two-Dimensional Optical Storage (TwoDOS) system. Based on this model, the two-dimensional (2D) minimum mean-square error (MMSE) equalizer has been derived and applied to some simple but common cases. The performance of the 2D

Structure determination of two new indole-diterpenoids from Penicillium sp. CM-7 by NMR spectroscopy.

Science.gov (United States)

Zhang, Yu-Hong; Huang, Sheng-Dong; Pan, Hua-Qi; Bian, Xi-Qing; Wang, Zai-Ying; Han, Ai-Hong; Bai, Jiao

2014-06-01

Two new indole-diterpenoids 4b-deoxy-1'-O-acetylpaxilline (1) and 4b-deoxypenijanthine A (2) were isolated from the fermentation broth and the mycelia of the soil fungus Penicillium sp. CM-7, along with three known structurally related compounds, 1'-O-acetylpaxilline (3), paspaline (4) and 3-deoxo-4b-deoxypaxilline (5). The structures of compounds 1 and 2 were elucidated by extensive spectroscopic methods, especially 2D NMR, and their absolute configurations were suggested on the basis of the circular dichroism spectral analysis and the NOESY data. Copyright © 2014 John Wiley & Sons, Ltd.

Application of NMR Screening Methods with 19F Detection to Fluorinated Compounds Bound to Proteins

Directory of Open Access Journals (Sweden)

Kazuo Furihata

2017-12-01

Full Text Available The combinational use of one-dimensional (1D NMR-based screening techniques with 1H and 19F detections were applied to a human serum albumin–diflunisal complex. Since most NMR screening methods observe 1H spectra, the overlapped 1H signals were unavailable in the binding epitope mapping. However, the NMR experiments with 19F detection can be used as an effective complementary method. For the purpose of identifying the 1H and 19F binding epitopes of diflunisal, this paper carries out a combinatorial analysis using 1H{1H} and 19F{1H} saturation transfer difference experiments. The differences of the 1H-inversion recovery rates with and without target irradiation are also analyzed for a comprehensive interpretation of binding epitope mapping.

Two-dimensional analysis of human lymphocyte proteins. III. Preliminary report on a marker for the early detection and diagnosis of infectious mononucleosis

International Nuclear Information System (INIS)

Willard, K.E.

1982-01-01

Two-dimensional gel electrophoretic patterns of human peripheral blood leukocytes from 12 patients with infectious mononucleosis were prepared by use of the ISO-DALT system. Before the two-dimensional separation, the leukocytes were purified by Ficoll-Paque gradient centrifugation and labeled overnight with [ 35 S] methionine. Quantitative increases in two proteins were detected in the patterns of infected leukocytes from the patients as compared with controls. Fluorescence-activated cell sorting of leukocytes from normal human peripheral blood before subsequent two-dimensional gel analysis revealed that the dramatic increase in one of these proteins (Inmono:2) could be due to shifts in the population ratios of lymphocytes, monocytes, and granulocytes. In contrast, the appearance in the infected leukocytes of a second protein, Inmono:1, could not be accounted for by cell-population shifts. Increased amounts of these two proteins have been found in every patient studied who had clinically detectable infectious mononucleosis. In addition, a patient who displayed symptoms of infectious mononucleosis but who did not have a positive result in the MONOSPOT test (Ortho) until three weeks after our analysis also demonstrated increased relative amounts of these proteins in his leukocyte pattern

Two-dimensional ferroelectrics

Energy Technology Data Exchange (ETDEWEB)

Blinov, L M; Fridkin, Vladimir M; Palto, Sergei P [A.V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russian Federaion (Russian Federation); Bune, A V; Dowben, P A; Ducharme, Stephen [Department of Physics and Astronomy, Behlen Laboratory of Physics, Center for Materials Research and Analysis, University of Nebraska-Linkoln, Linkoln, NE (United States)

2000-03-31

The investigation of the finite-size effect in ferroelectric crystals and films has been limited by the experimental conditions. The smallest demonstrated ferroelectric crystals had a diameter of {approx}200 A and the thinnest ferroelectric films were {approx}200 A thick, macroscopic sizes on an atomic scale. Langmuir-Blodgett deposition of films one monolayer at a time has produced high quality ferroelectric films as thin as 10 A, made from polyvinylidene fluoride and its copolymers. These ultrathin films permitted the ultimate investigation of finite-size effects on the atomic thickness scale. Langmuir-Blodgett films also revealed the fundamental two-dimensional character of ferroelectricity in these materials by demonstrating that there is no so-called critical thickness; films as thin as two monolayers (1 nm) are ferroelectric, with a transition temperature near that of the bulk material. The films exhibit all the main properties of ferroelectricity with a first-order ferroelectric-paraelectric phase transition: polarization hysteresis (switching); the jump in spontaneous polarization at the phase transition temperature; thermal hysteresis in the polarization; the increase in the transition temperature with applied field; double hysteresis above the phase transition temperature; and the existence of the ferroelectric critical point. The films also exhibit a new phase transition associated with the two-dimensional layers. (reviews of topical problems)

Calculation of two-dimensional thermal transients by the finite element method

International Nuclear Information System (INIS)

Fontoura Rodrigues, J.L.A. da; Barcellos, C.S. de

1981-01-01

The linear heat conduction through anisotropic and/or heterogeneous matter, in either two-dimensional fields with any kind of geometry or three-dimensional fields with axial symmetry is analysed. It only accepts time-independent boundary conditions and it is possible to have internal heat generation. The solution is obtained by modal analysis employing the finite element method under Galerkin formulation. (Author) [pt

Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

Science.gov (United States)

Kupka, Teobald; Wieczorek, Piotr P.

2016-01-01

In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data

Directory of Open Access Journals (Sweden)

Dommisse Roger

2011-10-01

Full Text Available Abstract Background Nuclear magnetic resonance spectroscopy (NMR is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. Results We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA. The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. Conclusions The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

Science.gov (United States)

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down

Two-dimensional nonlinear transient heat transfer analysis of variable section pin fins

Energy Technology Data Exchange (ETDEWEB)

Malekzadeh, P. [Department of Mechanical Engineering, School of Engineering, Persian Gulf University, Boushehr 75168 (Iran); Rahideh, H. [Department of Chemical Engineering, School of Engineering, Persian Gulf University, Boushehr 75168 (Iran)

2009-04-15

The two-dimensional nonlinear transient heat transfer analysis of variable cross section pin-fins is studied using the incremental differential quadrature method (IDQM) as a simple, accurate, and computationally efficient numerical tool. The formulations are general so that it can easily be used for arbitrary continuously varying cross section pin fins with the spatial-temperature dependent thermal parameters. On all external surfaces of the pin fin, the convective-radiative condition is considered. The effects of two different types of boundary conditions at the base of pin fin are investigated: time and spatial dependent temperature, and the convection heat transfer. The thermal conductivity of the pin fin is assumed to vary as a linear function of the temperature. The accuracy of the method is demonstrated by comparing its results with those generated by finite difference method. It is shown that using few grid points, results in excellent agreements with those of FDM are obtained. Less computational efforts of the method with respect to finite difference method is shown. (author)

Two-Dimensional Materials for Sensing: Graphene and Beyond

Directory of Open Access Journals (Sweden)

Seba Sara Varghese

2015-09-01

Full Text Available Two-dimensional materials have attracted great scientific attention due to their unusual and fascinating properties for use in electronics, spintronics, photovoltaics, medicine, composites, etc. Graphene, transition metal dichalcogenides such as MoS2, phosphorene, etc., which belong to the family of two-dimensional materials, have shown great promise for gas sensing applications due to their high surface-to-volume ratio, low noise and sensitivity of electronic properties to the changes in the surroundings. Two-dimensional nanostructured semiconducting metal oxide based gas sensors have also been recognized as successful gas detection devices. This review aims to provide the latest advancements in the field of gas sensors based on various two-dimensional materials with the main focus on sensor performance metrics such as sensitivity, specificity, detection limit, response time, and reversibility. Both experimental and theoretical studies on the gas sensing properties of graphene and other two-dimensional materials beyond graphene are also discussed. The article concludes with the current challenges and future prospects for two-dimensional materials in gas sensor applications.

Thermal and structural analysis of a cryogenic conduction cooling system for a HTS NMR magnet

Energy Technology Data Exchange (ETDEWEB)

In, Se Hwan; Hong, Yong Jun; Yeom, Han Kil; Ko, Hyo Bong; Park, Seong Je [Korea Institute of Machinery and Materials, Daejeon (Korea, Republic of)

2016-03-15

The superconducting NMR magnets have used cryogen such as liquid helium for their cooling. The conduction cooling method using cryocoolers, however, makes the cryogenic cooling system for NMR magnets more compact and user-friendly than the cryogen cooling method. This paper describes the thermal and structural analysis of a cryogenic conduction cooling system for a 400 MHz HTS NMR magnet, focusing on the magnet assembly. The highly thermo-conductive cooling plates between HTS double pancake coils are used to transfer the heat generated in coils, namely Joule heating at lap splice joints, to thermal link blocks and finally the cryocooler. The conduction cooling structure of the HTS magnet assembly preliminarily designed is verified by thermal and structural analysis. The orthotropic thermal properties of the HTS coil, thermal contact resistance and radiation heat load are considered in the thermal analysis. The thermal analysis confirms the uniform temperature distribution for the present thermal design of the NMR magnet within 0.2 K. The mechanical stress and the displacement by the electromagnetic force and the thermal contraction are checked to verify structural stability. The structural analysis indicates that the mechanical stress on each component of the magnet is less than its material yield strength and the displacement is acceptable in comparison with the magnet dimension.

New on-line separation workflow of microbial metabolites via hyphenation of analytical and preparative comprehensive two-dimensional liquid chromatography.

Science.gov (United States)

Yan, Xia; Wang, Li-Juan; Wu, Zhen; Wu, Yun-Long; Liu, Xiu-Xiu; Chang, Fang-Rong; Fang, Mei-Juan; Qiu, Ying-Kun

2016-10-15

Microbial metabolites represent an important source of bioactive natural products, but always exhibit diverse of chemical structures or complicated chemical composition with low active ingredients content. Traditional separation methods rely mainly on off-line combination of open-column chromatography and preparative high performance liquid chromatography (HPLC). However, the multi-step and prolonged separation procedure might lead to exposure to oxygen and structural transformation of metabolites. In the present work, a new two-dimensional separation workflow for fast isolation and analysis of microbial metabolites from Chaetomium globosum SNSHI-5, a cytotoxic fungus derived from extreme environment. The advantage of this analytical comprehensive two-dimensional liquid chromatography (2D-LC) lies on its ability to analyze the composition of the metabolites, and to optimize the separation conditions for the preparative 2D-LC. Furthermore, gram scale preparative 2D-LC separation of the crude fungus extract could be performed on a medium-pressure liquid chromatograph×preparative high-performance liquid chromatography system, under the optimized condition. Interestingly, 12 cytochalasan derivatives, including two new compounds named cytoglobosin Ab (3) and isochaetoglobosin Db (8), were successfully obtained with high purity in a short period of time. The structures of the isolated metabolites were comprehensively characterized by HR ESI-MS and NMR. To be highlighted, this is the first report on the combination of analytical and preparative 2D-LC for the separation of microbial metabolites. The new workflow exhibited apparent advantages in separation efficiency and sample treatment capacity compared with conventional methods. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional Parallel Factor Analysis for Functions of One- and Two-dimensional Arguments

NARCIS (Netherlands)

Choi, Ji Yeh; Hwang, Heungsun; Timmerman, Marieke

Parallel factor analysis (PARAFAC) is a useful multivariate method for decomposing three-way data that consist of three different types of entities simultaneously. This method estimates trilinear components, each of which is a low-dimensional representation of a set of entities, often called a mode,

Autonomous driving in NMR.

Science.gov (United States)

Perez, Manuel

2017-01-01

The automatic analysis of NMR data has been a much-desired endeavour for the last six decades, as it is the case with any other analytical technique. This need for automation has only grown as advances in hardware; pulse sequences and automation have opened new research areas to NMR and increased the throughput of data. Full automatic analysis is a worthy, albeit hard, challenge, but in a world of artificial intelligence, instant communication and big data, it seems that this particular fight is happening with only one technique at a time (let this be NMR, MS, IR, UV or any other), when the reality of most laboratories is that there are several types of analytical instrumentation present. Data aggregation, verification and elucidation by using complementary techniques (e.g. MS and NMR) is a desirable outcome to pursue, although a time-consuming one if performed manually; hence, the use of automation to perform the heavy lifting for users is required to make the approach attractive for scientists. Many of the decisions and workflows that could be implemented under automation will depend on the two-way communication with databases that understand analytical data, because it is desirable not only to query these databases but also to grow them in as much of an automatic manner as possible. How these databases are designed, set up and the data inside classified will determine what workflows can be implemented. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Two-dimensional calculus

CERN Document Server

Osserman, Robert

2011-01-01

The basic component of several-variable calculus, two-dimensional calculus is vital to mastery of the broader field. This extensive treatment of the subject offers the advantage of a thorough integration of linear algebra and materials, which aids readers in the development of geometric intuition. An introductory chapter presents background information on vectors in the plane, plane curves, and functions of two variables. Subsequent chapters address differentiation, transformations, and integration. Each chapter concludes with problem sets, and answers to selected exercises appear at the end o

Phase transitions in two-dimensional systems

International Nuclear Information System (INIS)

Salinas, S.R.A.

1983-01-01

Some experiences are related using synchrotron radiation beams, to characterize solid-liquid (fusion) and commensurate solid-uncommensurate solid transitions in two-dimensional systems. Some ideas involved in the modern theories of two-dimensional fusion are shortly exposed. The systems treated consist of noble gases (Kr,Ar,Xe) adsorbed in the basal plane of graphite and thin films formed by some liquid crystal shells. (L.C.) [pt

Experimental study on two-dimensional film flow with local measurement methods

Energy Technology Data Exchange (ETDEWEB)

Yang, Jin-Hwa, E-mail: evo03@snu.ac.kr [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Cho, Hyoung-Kyu [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Kim, Seok [Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Euh, Dong-Jin, E-mail: djeuh@kaeri.re.kr [Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Park, Goon-Cherl [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of)

2015-12-01

Highlights: • An experimental study on the two-dimensional film flow with lateral air injection was performed. • The ultrasonic thickness gauge was used to measure the local liquid film thickness. • The depth-averaged PIV (Particle Image Velocimetry) method was applied to measure the local liquid film velocity. • The uncertainty of the depth-averaged PIV was quantified with a validation experiment. • Characteristics of two-dimensional film flow were classified following the four different flow patterns. - Abstract: In an accident condition of a nuclear reactor, multidimensional two-phase flows may occur in the reactor vessel downcomer and reactor core. Therefore, those have been regarded as important issues for an advanced thermal-hydraulic safety analysis. In particular, the multi-dimensional two-phase flow in the upper downcomer during the reflood phase of large break loss of coolant accident appears with an interaction between a downward liquid and a transverse gas flow, which determines the bypass flow rate of the emergency core coolant and subsequently, the reflood coolant flow rate. At present, some thermal-hydraulic analysis codes incorporate multidimensional modules for the nuclear reactor safety analysis. However, their prediction capability for the two-phase cross flow in the upper downcomer has not been validated sufficiently against experimental data based on local measurements. For this reason, an experimental study was carried out for the two-phase cross flow to clarify the hydraulic phenomenon and provide local measurement data for the validation of the computational tools. The experiment was performed in a 1/10 scale unfolded downcomer of Advanced Power Reactor 1400 (APR1400). Pitot tubes, a depth-averaged PIV method and ultrasonic thickness gauge were applied for local measurement of the air velocity, the liquid film velocity and the liquid film thickness, respectively. The uncertainty of the depth-averaged PIV method for the averaged

Experimental study on two-dimensional film flow with local measurement methods

International Nuclear Information System (INIS)

Yang, Jin-Hwa; Cho, Hyoung-Kyu; Kim, Seok; Euh, Dong-Jin; Park, Goon-Cherl

2015-01-01

Highlights: • An experimental study on the two-dimensional film flow with lateral air injection was performed. • The ultrasonic thickness gauge was used to measure the local liquid film thickness. • The depth-averaged PIV (Particle Image Velocimetry) method was applied to measure the local liquid film velocity. • The uncertainty of the depth-averaged PIV was quantified with a validation experiment. • Characteristics of two-dimensional film flow were classified following the four different flow patterns. - Abstract: In an accident condition of a nuclear reactor, multidimensional two-phase flows may occur in the reactor vessel downcomer and reactor core. Therefore, those have been regarded as important issues for an advanced thermal-hydraulic safety analysis. In particular, the multi-dimensional two-phase flow in the upper downcomer during the reflood phase of large break loss of coolant accident appears with an interaction between a downward liquid and a transverse gas flow, which determines the bypass flow rate of the emergency core coolant and subsequently, the reflood coolant flow rate. At present, some thermal-hydraulic analysis codes incorporate multidimensional modules for the nuclear reactor safety analysis. However, their prediction capability for the two-phase cross flow in the upper downcomer has not been validated sufficiently against experimental data based on local measurements. For this reason, an experimental study was carried out for the two-phase cross flow to clarify the hydraulic phenomenon and provide local measurement data for the validation of the computational tools. The experiment was performed in a 1/10 scale unfolded downcomer of Advanced Power Reactor 1400 (APR1400). Pitot tubes, a depth-averaged PIV method and ultrasonic thickness gauge were applied for local measurement of the air velocity, the liquid film velocity and the liquid film thickness, respectively. The uncertainty of the depth-averaged PIV method for the averaged

Correlation between two-dimensional video analysis and subjective assessment in evaluating knee control among elite female team handball players

DEFF Research Database (Denmark)

Stensrud, Silje; Myklebust, Grethe; Kristianslund, Eirik

2011-01-01

. The present study investigated the correlation between a two-dimensional (2D) video analysis and subjective assessment performed by one physiotherapist in evaluating knee control. We also tested the correlation between three simple clinical tests using both methods. A cohort of 186 female elite team handball...

Two-dimensional polyacrylamide gel electrophoresis of intracellular proteins

International Nuclear Information System (INIS)

Ojima, N.; Sakamoto, T.; Yamashita, M.

1996-01-01

Since two-dimensional electrophoresis was established by O'Farrell for analysis of intracellular proteins of Escherichia coli, it has been applied to separation of proteins of animal cells and tissues, and especially to identification of stress proteins. Using this technique, proteins are separated by isoelectric focusing containing 8 m urea in the first dimension and by SDS-PAGE in the second dimension. The gels are stained with Coomassie Blue R-250 dye, followed by silver staining. In the case of radio-labeled proteins, the gels are dried and then autoradiographed. In order to identify a specific protein separated by two-dimensional electrophoresis, a technique determining the N-terminal amino acid sequence of the protein has been developed recently. After the proteins in the gel were electrotransferred to a polyvinylidene difluoride membrane, the membrane was stained for protein with Commassie Blue and a stained membrane fragment was applied to a protein sequencer. Our recent studies demonstrated that fish cells newly synthesized various proteins in response to heat shock, cold nd osmotic stresses. For example, when cellular proteins extracted from cold-treated rainbow trout cells were subjected to two-dimensional gel electrophoresis, the 70 kDa protein was found to be synthesized during the cold-treatment. N-Terminal sequence analysis showed that the cold-inducible protein was a homolog of mammalian valosin-containing protein and yeast cell division cycle gene product CDC48p. Furthermore, the sequence data were useful for preparing PCR primers and a rabbit antibody against a synthetic peptide to analyze a role for the protein in the function of trout cells and mechanisms for regulation

Reduction of multi-dimensional laboratory data to a two-dimensional plot: a novel technique for the identification of laboratory error.

Science.gov (United States)

Kazmierczak, Steven C; Leen, Todd K; Erdogmus, Deniz; Carreira-Perpinan, Miguel A

2007-01-01

The clinical laboratory generates large amounts of patient-specific data. Detection of errors that arise during pre-analytical, analytical, and post-analytical processes is difficult. We performed a pilot study, utilizing a multidimensional data reduction technique, to assess the utility of this method for identifying errors in laboratory data. We evaluated 13,670 individual patient records collected over a 2-month period from hospital inpatients and outpatients. We utilized those patient records that contained a complete set of 14 different biochemical analytes. We used two-dimensional generative topographic mapping to project the 14-dimensional record to a two-dimensional space. The use of a two-dimensional generative topographic mapping technique to plot multi-analyte patient data as a two-dimensional graph allows for the rapid identification of potentially anomalous data. Although we performed a retrospective analysis, this technique has the benefit of being able to assess laboratory-generated data in real time, allowing for the rapid identification and correction of anomalous data before they are released to the physician. In addition, serial laboratory multi-analyte data for an individual patient can also be plotted as a two-dimensional plot. This tool might also be useful for assessing patient wellbeing and prognosis.

A Two-Temperature Open-Source CFD Model for Hypersonic Reacting Flows, Part Two: Multi-Dimensional Analysis †

OpenAIRE

Vincent Casseau; Daniel E. R. Espinoza; Thomas J. Scanlon; Richard E. Brown

2016-01-01

hy2Foam is a newly-coded open-source two-temperature computational fluid dynamics (CFD) solver that has previously been validated for zero-dimensional test cases. It aims at (1) giving open-source access to a state-of-the-art hypersonic CFD solver to students and researchers; and (2) providing a foundation for a future hybrid CFD-DSMC (direct simulation Monte Carlo) code within the OpenFOAM framework. This paper focuses on the multi-dimensional verification of hy2Foam and firstly describes th...

NMR spectroscopy using liquid crystal solvents

CERN Document Server

Emsley, JW

2013-01-01

NMR Spectroscopy using Liquid Crystal Solvents covers the importance of using a liquid crystal solvent in NMR to derive nuclear dipolar spin-spin coupling constants. This book is composed of ten chapters, and begins with a brief description of the features and benefits of liquid crystal in NMR spectroscopic analysis. The succeeding chapters deal with the mode of operation of nuclear spin Hamiltonian for partially oriented molecules and the analysis of NMR spectra of partially oriented molecules, as well as the determination of rigid molecule structure. These topics are followed by discussions

Two-dimensional study of shock breakout at the rear face of laser irradiated metallic targets

Energy Technology Data Exchange (ETDEWEB)

Cottet, F.; Marty, L.; Hallouin, M.; Romain, J.P.; Virmont, J.; Fabbro, R.; Faral, B.

1988-11-01

The two-dimensional propagation dynamics of laser-driven shock waves in solids is studied through the analysis of the shock breakout at the rear face of the target for a set of materials and laser intensities. The laser shock simulations were carried out by means of a two-dimensional hydrodynamics code in which the laser-ablation pressure is replaced by an equivalent pressure pulse. It is shown that the two-dimensional code is a very useful tool to analyze laser-shock experiments where two-dimensional effects arise from a finite laser-spot size or a heterogeneous energy deposition.

Two-dimensional study of shock breakout at the rear face of laser irradiated metallic targets

International Nuclear Information System (INIS)

Cottet, F.; Marty, L.; Hallouin, M.; Romain, J.P.; Virmont, J.; Fabbro, R.; Faral, B.

1988-01-01

The two-dimensional propagation dynamics of laser-driven shock waves in solids is studied through the analysis of the shock breakout at the rear face of the target for a set of materials and laser intensities. The laser shock simulations were carried out by means of a two-dimensional hydrodynamics code in which the laser-ablation pressure is replaced by an equivalent pressure pulse. It is shown that the two-dimensional code is a very useful tool to analyze laser-shock experiments where two-dimensional effects arise from a finite laser-spot size or a heterogeneous energy deposition

PVT Degradation Studies: NMR Analysis

Energy Technology Data Exchange (ETDEWEB)

Cho, Herman M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kouzes, Richard T. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2017-06-06

Under certain environmental conditions, polyvinyl toluene (PVT) plastic scintillator has been observed to undergo internal fogging. Nuclear magnetic resonance spectroscopy has been used to elucidate the state of water inside the PVT. The deuterium NMR results show that water absorbed by PVT under warm, humid conditions enters several distinct environments, and when the PVT is transferred from incubation to ambient temperature and humidity the water is lost on a time scale of a few hours from these samples. Most of the deuterium NMR peaks can be assigned to bulk liquid water, but almost 35% of the detected signal intensity is contained in a resonance that resembles spectra of water contained in nanometer-scale pores in mesoporous carbon.

A two-dimensional finite element method for analysis of solid body contact problems in fuel rod mechanics

International Nuclear Information System (INIS)

Nissen, K.L.

1988-06-01

Two computer codes for the analysis of fuel rod behavior have been developed. Fuel rod mechanics is treated by a two-dimensional, axisymmetric finite element method. The program KONTAKT is used for detailed examinations on fuel rod sections, whereas the second program METHOD2D allows instationary calculations of whole fuel rods. The mechanical contact of fuel and cladding during heating of the fuel rod is very important for it's integrity. Both computer codes use a Newton-Raphson iteration for the solution of the nonlinear solid body contact problem. A constitutive equation is applied for the dependency of contact pressure on normal approach of the surfaces which are assumed to be rough. If friction is present on the contacting surfaces, Coulomb's friction law is used. Code validation is done by comparison with known analytical solutions for special problems. Results of the contact algorithm for an elastic ball pressing against a rigid surface are confronted with Hertzian theory. Influences of fuel-pellet geometry as well as influences of discretisation of displacements and stresses of a single fuel pellet are studied. Contact of fuel and cladding is calculated for a fuel rod section with two fuel pellets. The influence of friction forces between fuel and cladding on their axial expansion is demonstrated. By calculation of deformations and temperatures during an instationary fuel rod experiment of the CABRI-series the feasibility of two-dimensional finite element analysis of whole fuel rods is shown. (orig.) [de

Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

Energy Technology Data Exchange (ETDEWEB)

Qu, Yi; Feng, Ju; Deng, Shuang; Cao, Li; Zhang, Qibin; Zhao, Rui; Zhang, Zhaorui; Jiang, Yuxuan; Zink, Erika M.; Baker, Scott E.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Hu, Jian Z.; Wu, Si

2014-11-19

Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.

13C NMR and EPR spectroscopic evaluation of oil shale mined soil recuperation

International Nuclear Information System (INIS)

Santos, J.V. dos; Mangrich, A.S.; Pereira, B.F.; Pillon, C.N.; Bonagamba, T.J.

2013-01-01

In this work, native forest soil (NFS) organic matter (SOM) sample and SOM samples from a neighboring forest soil area of an oil shale mine which is being rehabilitated for thirty years (RFS) were analyzed. X-band electron paramagnetic resonance (EPR) and solid-state 13 C nuclear magnetic resonance (NMR) spectroscopies were used to evaluate the soil reclamation of the Brazilian oil shale mining process. Two-dimensional heterospectral correlation studies of the results obtained from EPRand 13 C NMR were used to obtain information about SOM structures and their interactions with residual paramagnetic metal ion. The signal of the residual metallic oxycation, VO 2+ correlated positively with uronic acid-type hydrophilic organic structures, determined from the 13 C NMR spectra, and correlated negatively with the organic free radical (OFR) signal associated with oxygen atoms (g = 2.0042). The hydrophobic aromatic structures correlate positively with the EPR OFR signal associated with carbon atoms (g = 2.0022). The data from the two spectroscopic magnetic techniques show that the used recuperation process is effective. (author)

Two-dimensional thermal modeling of power monolithic microwave integrated circuits (MMIC's)

Science.gov (United States)

Fan, Mark S.; Christou, Aris; Pecht, Michael G.

1992-01-01

Numerical simulations of the two-dimensional temperature distributions for a typical GaAs MMIC circuit are conducted, aiming at understanding the heat conduction process of the circuit chip and providing temperature information for device reliability analysis. The method used is to solve the two-dimensional heat conduction equation with a control-volume-based finite difference scheme. In particular, the effects of the power dissipation and the ambient temperature are examined, and the criterion for the worst operating environment is discussed in terms of the allowed highest device junction temperature.

Two dimensional nonlinear spectral estimation techniques for breast cancer localization

Energy Technology Data Exchange (ETDEWEB)

Stathaki, P T; Constantinides, A G [Signal Processing Section, Department of Electrical and Electronic Engineering, Imperial College, Exhibition Road, London SW7 2BT, UK (United Kingdom)

1994-12-31

In this paper the problem of image texture analysis in the presence of noise is examined from a higher-order statistical perspective. The approach taken involves the use of two dimensional second order Volterra filters where the filter weights are derived from third order cumulants of the two dimensional signal. The specific application contained in this contribution is in mammography, an area in which it is difficult to discern the appropriate features. The paper describes the fundamental issues of the various components of the approach. The results of the entire texture modelling, classification and segmentation scheme contained in this paper are very encouraging. 7 refs, 2 figs.

Structure determination of the single glycan of rabbit serotransferrin by methylation analysis and 360 MHz 1H NMR spectroscopy

International Nuclear Information System (INIS)

Leger, D.; Tordera, V.; Spik, G.; Dorland, L.; Haverkamp, J.; Vliegenthart, J.F.G.

1978-01-01

The glycopeptide fraction of rabbit serotransferrin (STF) has been investigated applying an original method for the determination of glycan primary structure combining monosaccharide determination, permethylation and 360 MHz 1 H NMR. It is concluded that the highly purified rabbit transferrin contains only 1 glycan chain/molecule. A heterogeneity of the glycan moiety in the sialic acid residues was observed on isolation by paper electrophoresis of a disialylglycopeptide G-1 and a monosialylglycopeptide 2. The primary structure of glycopeptide G-1 deduced on the basis of the data of carbohydrate composition, permethylation analysis and 360 MHz 1 H NMR spectroscopy is identical to the primary structure of human serotransferrin glycan and the glycopeptide G-2 was shown by 1 H NMR spectroscopy, to be a mixture of two isomeric monosialylglycopeptides. (Auth.)

NMR characterization of weak interactions between RhoGDI2 and fragment screening hits.

Science.gov (United States)

Liu, Jiuyang; Gao, Jia; Li, Fudong; Ma, Rongsheng; Wei, Qingtao; Wang, Aidong; Wu, Jihui; Ruan, Ke

2017-01-01

The delineation of intrinsically weak interactions between novel targets and fragment screening hits has long limited the pace of hit-to-lead evolution. Rho guanine-nucleotide dissociation inhibitor 2 (RhoGDI2) is a novel target that lacks any chemical probes for the treatment of tumor metastasis. Protein-observed and ligand-observed NMR spectroscopy was used to characterize the weak interactions between RhoGDI2 and fragment screening hits. We identified three hits of RhoGDI2 using streamlined NMR fragment-based screening. The binding site residues were assigned using non-uniformly sampled C α - and H α -based three dimensional NMR spectra. The molecular docking to the proposed geranylgeranyl binding pocket of RhoGDI2 was guided by NMR restraints of chemical shift perturbations and ligand-observed transferred paramagnetic relaxation enhancement. We further validated the weak RhoGDI2-hit interactions using mutagenesis and structure-affinity analysis. Weak interactions between RhoGDI2 and fragment screening hits were delineated using an integrated NMR approach. Binders to RhoGDI2 as a potential anti-cancer target have been first reported, and their weak interactions were depicted using NMR spectroscopy. Our work highlights the powerfulness and the versatility of the integrative NMR techniques to provide valuable structural insight into the intrinsically weak interactions between RhoGDI2 and the fragment screening hits, which could hardly be conceived using other biochemical techniques. Copyright © 2016 Elsevier B.V. All rights reserved.

Reliability of ^1^H NMR analysis for assessment of lipid oxidation at frying temperatures

Science.gov (United States)

The reliability of a method using ^1^H NMR analysis for assessment of oil oxidation at a frying temperature was examined. During heating and frying at 180 °C, changes of soybean oil signals in the ^1^H NMR spectrum including olefinic (5.16-5.30 ppm), bisallylic (2.70-2.88 ppm), and allylic (1.94-2.1...

Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.

Science.gov (United States)

Feng, Yingang

2017-01-01

The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy.

Advances in solid-state NMR of cellulose.

Science.gov (United States)

Foston, Marcus

2014-06-01

Nuclear magnetic resonance (NMR) spectroscopy is a well-established analytical and enabling technology in biofuel research. Over the past few decades, lignocellulosic biomass and its conversion to supplement or displace non-renewable feedstocks has attracted increasing interest. The application of solid-state NMR spectroscopy has long been seen as an important tool in the study of cellulose and lignocellulose structure, biosynthesis, and deconstruction, especially considering the limited number of effective solvent systems and the significance of plant cell wall three-dimensional microstructure and component interaction to conversion yield and rate profiles. This article reviews common and recent applications of solid-state NMR spectroscopy methods that provide insight into the structural and dynamic processes of cellulose that control bulk properties and biofuel conversion. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Recent advances in analysis of petroleum geological samples by comprehensive two-dimensional gas chromatography].

Science.gov (United States)

Gao, Xuanbo; Chang, Zhenyang; Dai, Wei; Tong, Ting; Zhang, Wanfeng; He, Sheng; Zhu, Shukui

2014-10-01

Abundant geochemical information can be acquired by analyzing the chemical compositions of petroleum geological samples. The information obtained from the analysis provides scientifical evidences for petroleum exploration. However, these samples are complicated and can be easily influenced by physical (e. g. evaporation, emulsification, natural dispersion, dissolution and sorption), chemical (photodegradation) and biological (mainly microbial degradation) weathering processes. Therefore, it is very difficult to analyze the petroleum geological samples and they cannot be effectively separated by traditional gas chromatography/mass spectrometry. A newly developed separation technique, comprehensive two-dimensional gas chromatography (GC x GC), has unique advantages in complex sample analysis, and recently it has been applied to petroleum geological samples. This article mainly reviews the research progres- ses in the last five years, the main problems and the future research about GC x GC applied in the area of petroleum geology.

Positional enrichment by proton analysis (PEPA). A one-dimensional {sup 1}H-NMR approach for {sup 13}C stable isotope tracer studies in metabolomics

Energy Technology Data Exchange (ETDEWEB)

Vinaixa, Maria; Yanes, Oscar [Department of Electronic Engineering-Universitat Rovira i Virgili, Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Reus (Spain); Rodriguez, Miguel A.; Capellades, Jordi [Universitat Rovira i Virgili, Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Reus (Spain); Aivio, Suvi; Stracker, Travis H. [Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (Spain); Gomez, Josep; Canyellas, Nicolau [Department of Electronic Engineering-, Universitat Rovira i Virgili, Tarragona (Spain)

2017-03-20

A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of {sup 13}C-satellite peaks using 1D-{sup 1}H-NMR spectra. In comparison with {sup 13}C-NMR, TOCSY and HSQC, PEPA improves sensitivity, accelerates the elucidation of {sup 13}C positions in labeled metabolites and the quantification of the percentage of stable isotope enrichment. Altogether, PEPA provides a novel framework for extending the high-throughput of {sup 1}H-NMR metabolic profiling to stable isotope tracing in metabolomics, facilitating and complementing the information derived from 2D-NMR experiments and expanding the range of isotopically enriched metabolites detected in cellular extracts. (copyright 2017 The Authors. Published by Wiley-VCH Verlag GmbH and Co. KGaA.)

1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

International Nuclear Information System (INIS)

Moore, J.M.; Chazin, W.J.; Wright, P.E.; Powls, R.

1988-01-01

Two-dimensional 1 H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight β-strands, one short segment of helix, five reverse turns, and five loops. The β-strands may be arranged into two βsheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key β-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified

Multi-dimensional two-fluid flow computation. An overview

International Nuclear Information System (INIS)

Carver, M.B.

1992-01-01

This paper discusses a repertoire of three-dimensional computer programs developed to perform critical analysis of single-phase, two-phase and multi-fluid flow in reactor components. The basic numerical approach to solving the governing equations common to all the codes is presented and the additional constitutive relationships required for closure are discussed. Particular applications are presented for a number of computer codes. (author). 12 refs

On two-dimensionalization of three-dimensional turbulence in shell models

DEFF Research Database (Denmark)

Chakraborty, Sagar; Jensen, Mogens Høgh; Sarkar, A.

2010-01-01

Applying a modified version of the Gledzer-Ohkitani-Yamada (GOY) shell model, the signatures of so-called two-dimensionalization effect of three-dimensional incompressible, homogeneous, isotropic fully developed unforced turbulence have been studied and reproduced. Within the framework of shell m......-similar PDFs for longitudinal velocity differences are also presented for the rotating 3D turbulence case....

Two-dimensional turbulent convection

Science.gov (United States)

Mazzino, Andrea

2017-11-01

We present an overview of the most relevant, and sometimes contrasting, theoretical approaches to Rayleigh-Taylor and mean-gradient-forced Rayleigh-Bénard two-dimensional turbulence together with numerical and experimental evidences for their support. The main aim of this overview is to emphasize that, despite the different character of these two systems, especially in relation to their steadiness/unsteadiness, turbulent fluctuations are well described by the same scaling relationships originated from the Bolgiano balance. The latter states that inertial terms and buoyancy terms balance at small scales giving rise to an inverse kinetic energy cascade. The main difference with respect to the inverse energy cascade in hydrodynamic turbulence [R. H. Kraichnan, "Inertial ranges in two-dimensional turbulence," Phys. Fluids 10, 1417 (1967)] is that the rate of cascade of kinetic energy here is not constant along the inertial range of scales. Thanks to the absence of physical boundaries, the two systems here investigated turned out to be a natural physical realization of the Kraichnan scaling regime hitherto associated with the elusive "ultimate state of thermal convection" [R. H. Kraichnan, "Turbulent thermal convection at arbitrary Prandtl number," Phys. Fluids 5, 1374-1389 (1962)].

Two-dimensional finite element neutron diffusion analysis using hierarchic shape functions

International Nuclear Information System (INIS)

Carpenter, D.C.

1997-01-01

Recent advances have been made in the use of p-type finite element method (FEM) for structural and fluid dynamics problems that hold promise for reactor physics problems. These advances include using hierarchic shape functions, element-by-element iterative solvers and more powerful mapping techniques. Use of the hierarchic shape functions allows greater flexibility and efficiency in implementing energy-dependent flux expansions and incorporating localized refinement of the solution space. The irregular matrices generated by the p-type FEM can be solved efficiently using element-by-element conjugate gradient iterative solvers. These solvers do not require storage of either the global or local stiffness matrices and can be highly vectorized. Mapping techniques based on blending function interpolation allow exact representation of curved boundaries using coarse element grids. These features were implemented in a developmental two-dimensional neutron diffusion program based on the use of hierarchic shape functions (FEM2DH). Several aspects in the effective use of p-type analysis were explored. Two choices of elemental preconditioning were examined--the proper selection of the polynomial shape functions and the proper number of functions to use. Of the five shape function polynomials tested, the integral Legendre functions were the most effective. The serendipity set of functions is preferable over the full tensor product set. Two global preconditioners were also examined--simple diagonal and incomplete Cholesky. The full effectiveness of the finite element methodology was demonstrated on a two-region, two-group cylindrical problem but solved in the x-y coordinate space, using a non-structured element grid. The exact, analytic eigenvalue solution was achieved with FEM2DH using various combinations of element grids and flux expansions

Two-dimensional wavelet transform for reliability-guided phase unwrapping in optical fringe pattern analysis.

Science.gov (United States)

Li, Sikun; Wang, Xiangzhao; Su, Xianyu; Tang, Feng

2012-04-20

This paper theoretically discusses modulus of two-dimensional (2D) wavelet transform (WT) coefficients, calculated by using two frequently used 2D daughter wavelet definitions, in an optical fringe pattern analysis. The discussion shows that neither is good enough to represent the reliability of the phase data. The differences between the two frequently used 2D daughter wavelet definitions in the performance of 2D WT also are discussed. We propose a new 2D daughter wavelet definition for reliability-guided phase unwrapping of optical fringe pattern. The modulus of the advanced 2D WT coefficients, obtained by using a daughter wavelet under this new daughter wavelet definition, includes not only modulation information but also local frequency information of the deformed fringe pattern. Therefore, it can be treated as a good parameter that represents the reliability of the retrieved phase data. Computer simulation and experimentation show the validity of the proposed method.

Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

Energy Technology Data Exchange (ETDEWEB)

Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D., E-mail: jdfv2009@gmail.com [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Grupo de Ressonância Magnética Nuclear e Química Medicinal

2017-07-01

This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

International Nuclear Information System (INIS)

Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D.

2017-01-01

This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

NMR studies of two spliced leader RNAs using isotope labeling

Energy Technology Data Exchange (ETDEWEB)

Lapham, J.; Crothers, D.M. [Yale Univ., New Haven, CT (United States)

1994-12-01

Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions between the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.

Calculation of two-dimensional thermal transients by the method of finite elements

International Nuclear Information System (INIS)

Fontoura Rodrigues, J.L.A. da.

1980-08-01

The unsteady linear heat conduction analysis throught anisotropic and/or heterogeneous matter, in either two-dimensional fields with any kind of geometry or three-dimensional fields with axial symmetry is presented. The boundary conditions and the internal heat generation are supposed time - independent. The solution is obtained by modal analysis employing the finite element method under Galerkin formulation. Optionally, it can be used with a reduced resolution method called Stoker Economizing Method wich allows a decrease on the program processing costs. (Author) [pt

Comparison between the efficacy of two cleanup methods for the 1H NMR analysis of food samples contaminated with Cypermethrin

International Nuclear Information System (INIS)

Silva, M.M.; Figueroa-Villar, J.D.; Aguiar, A.P.; Riehl, C.A.S.

2004-01-01

This work aimed to study the use of 1 H NMR for the identification of cypermethrin in cooked foods. 1 H NMR is not commonly used in these cases, because food samples ready for consumption have complex substances, mainly lipids, which usually interfere with the identification of cypermethrin. Thus, we drew a comparison between the most applied method for the treatment of those samples and an alternative route that made possible the use of 1 H NMR in the identification of cypermethrin in a matrix consisting of rice, bean, and chicken, which allows the Forensic work for such cases.(author)