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

Two dimensional NMR of liquids and oriented molecules

International Nuclear Information System (INIS)

Gochin, M.

1987-02-01

Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of 13 C and 1 H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface

Two dimensional NMR of liquids and oriented molecules

Energy Technology Data Exchange (ETDEWEB)

Gochin, M.

1987-02-01

Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of /sup 13/C and /sup 1/H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface.

Heteronuclear cross-polarization in multinuclear multidimensional NMR: Prospects for triple-resonance CP

Energy Technology Data Exchange (ETDEWEB)

Majumdar, A.; Zuiderweg, E.R.P. [Univ. of Michigan, Ann Arbor, MI (United States)

1994-12-01

Heteronuclear multiple-pulse-based Cross Polarization (HECP) between scalar coupled spins is gaining an important role in high-resolution multidimensional NMR of isotopically labeled biomolecules, especially in experiments involving net magnetization transfer. It has generally been observed that in these situations, the performance of HECP is superior to that of INEPT-based sequences. In particular, HECP-based three-dimensional HCCH spectroscopy is more efficient than the INEPT version of the same experiment. Differences in sensitivity have been intuitively attributed to relaxation effects and technical factors such as radiofrequency (rf) inhomogeneity We present theoretical analyses and computer simulations to probe the effects of these factors. Relaxation effects were treated phenomenologically; we found that relaxation differences are relatively small (up to 25%) between pulsed-free-precession (INEPT) and HECP-although always in favor of HECP. We explored the rf effects by employing a Gaussian distribution of rf amplitude over sample volume. We found that inhomogeneity effects significantly favor HECP over INEPT, especially under conditions of {open_quotes}matched {close_quotes} inhomogeneity in the two rf coils. The differences in favor of HECP indicate that an extension of HECP to triple resonance experiments (TRCP) in I -> S -> Q net transfers might yield better results relative to analogous INEPT-based net transfers. We theoretically analyze the possibilities of TRCP and find that transfer functions are critically dependent on the ratio J{sub IS}/J{sub SQ}. When J{sub IS} equals J{sub SQ}, we find that 100% transfer is possible for truly simultaneous TRCP and this transfer is obtained in a time 1.41 /J. The TRCP time requirement compares favorably with optimally concatenated INEPT-transfers, where net transfer I -> S -> Q is complete at 1.5 /J.

Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D H2BC and clean HMBC

DEFF Research Database (Denmark)

Meier, Sebastian; Petersen, Bent O.; Duus, Jens Øllgaard

2009-01-01

carbohydrates whose structure has been determined by NMR, not least due to the enhanced resolution offered by the third dimension in 3D H2BC and the improved spectral quality due to artifact suppression in clean HMBC. Hence these new experiments set the scene to take advantage of the sensitivity boost achieved...... by the latest generation of cold probes for NMR structure determination of even larger and more complex carbohydrates in solution.......The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of 13C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the 1H spins...

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

Two- and three-dimensional proton NMR studies of apo-neocarzinostatin

International Nuclear Information System (INIS)

Xiaolian Gao; Burkhart, W.

1991-01-01

Neocarzinostatin (NCS) is an antitumor protein from Streptomyces carzinostaticus that is identical in apo-protein sequence with mitomalcin (MMC) from Streptomyces malayensis. The authors describe the use of apo-NCS as a model system for applying combined two-and three-dimensional (2D and 3D) proton NMR spectroscopy to the structure determination of proteins without isotope labeling. Strategies aimed at accurately assigning overlapped 2D cross-peaks by using semiautomated combined 2D and 3D data analysis are developed. Using this approach, they have assigned 99% of the protons, including those of the side chains, and identified about 1,270 intra- and interresidue proton-proton interactions (fixed distances are not included) in apo-NCS. Comparing these results with those reported recently on 2D NMR studies of apo-NCS demonstrated advantages of proton 3D NMR spectroscopy in protein spectral assignments. They are able to obtain more complete proton resonance and secondary structural assignments and find several misassignments in the earlier report. Strategies utilized in this work should be useful for developing automation procedures for spectral assignments

Novel multi-dimensional heteronuclear NMR techniques for the study of 13C-O-acetylated oligosaccharides: Expanding the dimensions for carbohydrate structures

Energy Technology Data Exchange (ETDEWEB)

Jones, David N.M. [University of Colorado Health Sciences Center, Departments of Pharmacology (United States); Bendiak, Brad [University of Colorado Health Sciences Center, Departments of Cellular and Structural Biology (United States)

1999-10-15

Complex carbohydrates have critical roles in a wide variety of biological processes. An understanding of the molecular mechanisms that underlie these processes is essential in the development of novel oligosaccharide-based therapeutic strategies. Unfortunately, obtaining detailed structural information for larger oligosaccharides (>10 residues) can be exceedingly difficult, especially where the amount of sample available is limited. Here we demonstrate the application of {sup 13} C O-acetylation in combination with novel NMR experiments to obtain much of the information required to characterize the primary structure of oligosaccharides. (H)C{sub Me}COH-HEHAHA and H(C{sub Me})COH-HEHAHA experiments are presented that use heteronuclear Hartmann-Hahn transfer to correlate the acetyl groups with sugar ring protons in peracetylated oligosaccharides. The in-phase, pure absorption nature of the correlation peaks in these experiments allows measurement of both chemical shifts and, importantly, {sup 1}H-{sup 1}H coupling constants that are used to define the stereochemistry of the sugar ring. The (HC{sub Me})COH and (HC{sub Me})COH-RELAY experiments provide additional methods for obtaining chemical shift assignments for larger oligosaccharides to define the sites of glycosidic linkages from the patterns of acetylation.

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

The Three-Dimensional Solution Structure of the Src Homology Domain-2 of the Growth Factor Receptor-Bound Protein-2

International Nuclear Information System (INIS)

Senior, Mary M.; Frederick, Anne F.; Black, Stuart; Murgolo, Nicholas J.; Perkins, Louise M.; Wilson, Oswald; Snow, Mark E.; Wang Yusen

1998-01-01

A set of high-resolution three-dimensional solution structures of the Src homology region-2 (SH2) domain of the growth factor receptor-bound protein-2 was determined using heteronuclear NMR spectroscopy. The NMR data used in this study were collected on a stable monomeric protein solution that was free of protein aggregates and proteolysis. The solution structure was determined based upon a total of 1439 constraints, which included 1326 nuclear Overhauser effect distance constraints, 70 hydrogen bond constraints, and 43 dihedral angle constraints. Distance geometry-simulated annealing calculations followed by energy minimization yielded a family of 18 structures that converged to a root-mean-square deviation of 1.09 A for all backbone atoms and 0.40 A for the backbone atoms of the central β-sheet. The core structure of the SH2 domain contains an antiparallel β-sheet flanked by two parallel α-helices displaying an overall architecture that is similar to other known SH2 domain structures. This family of NMR structures is compared to the X-ray structure and to another family of NMR solution structures determined under different solution conditions

NMR of lignins

Science.gov (United States)

John Ralph; Larry L. Landucci

2010-01-01

This chapter will consider the basic aspects and findings of several forms of NMR spectroscopy, including separate discussions of proton, carbon, heteronuclear, and multidimensional NMR. Enhanced focus will be on 13C NMR, because of its qualitative and quantitative importance, followed by NMR’s contributions to our understanding of lignin...

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)

Exact quantum cross sections for a three dimensional angle dependent model for three body reactions.

Science.gov (United States)

Baer, M.; Kouri, D. J.

1971-01-01

Exact quantum mechanical reactive cross sections are reported for a three dimensional angle dependent model surface. The surface simulates an atom-heteronuclear diatom system A + BC leading to AB + C where atom B is much heavier than A or C. The molecules BC and AB are taken to be rotating vibrators which can dissociate. Results for two angle dependent potentials are given.

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.

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.

New strategy for stable-isotope-aided, multidimensional NMR spectroscopy of DNA oligomers

Energy Technology Data Exchange (ETDEWEB)

Ono, Okira; Tate, Shin-Ichi; Kainosho, Masatsune [Tokyo Metropolitan Univ., Tokyo (Japan)

1994-12-01

Nuclear Magnetic Resonance (NMR) is the most efficient method for determining the solution structures of biomolecules. By applying multidimensional heteronuclear NMR techniques to {sup 13}C/{sup 15}N-labeled proteins, we can determine the solution structures of proteins with molecular mass of 20 to 30kDa at an accuracy similar to that of x-ray crystallography. Improvements in NMR instrumentation and techniques as well as the development of protein engineering methods for labeling proteins have rapidly advanced multidimensional heteronuclear NMR of proteins. In contrast, multidimensional heteronuclear NMR studies of nucleic acids is less advanced because there were no efficient methods for preparing large amounts of labeled DNA/RNA oligomers. In this report, we focused on the chemical synthesis of DNA oligomers labeled at specific residue(s). RNA oligomers with specific labels, which are difficult to synthesize by the enzyme method, can be synthesized by the chemical method. The specific labels are useful for conformational analysis of larger molecules such as protein-nucleic acid complexes.

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

An improved synthesis of α-13C glycine and heteronuclear NMR studies of its incorporation into thioredoxin

International Nuclear Information System (INIS)

Wishart, D.S.; Sykes, B.D.; Richards, F.M.

1992-01-01

We present an improved method to easily prepare gram quantities of α- 13 C glycine beginning from K 13 CN. The four step synthesis involves the production of an N, N-diphenyl-cyanoformamidine intermediate through the coupling of cyanide to N, N-diphenylcarbodiimide. Subsequent reduction by LiAlH 4 and hydrolysis of the resulting amidine produces fully enriched α- 13 C labelled glycine with a 45-50% yield. This relatively fast and simple synthesis uses only commonly available compounds and requires no special equipment, making the process easy to perform in any well equipped biochemistry laboratory. We further demonstrate that the product may be used, without extensive purification, to specifically label bacterially expressed proteins (E. coli thioredoxin) through standard biosynthetic procedures. We also show that the 13 C glycine-labelled protein may be readily analyzed using commonly available heteronuclear NMR techniques. Complete assignments for all 9 glycines of native E. coli thoredoxin are presented. (Author)

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.

Heteronuclear long-range correlation, what’s new and how far can it take us?

DEFF Research Database (Denmark)

Sørensen, Ole W.

: A novel experiment for small-molecule and biomolecular NMR at natural isotopic abundance. Sebastian Meier, Andrew J. Benie, Jens Ø. Duus and Ole W. Sørensen, Journal of Magnetic Resonance, in press, doi:10.1016/j.jmr.2009.06.017 Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D...... H2BC and clean HMBC. Sebastian Meier, Bent O. Petersen, Jens Ø. Duus, Ole W. Sørensen. Carbohydrate Research, in press, doi:10.1016/j.carres.2009.08.013...

Quantum theory of NMR adiabatic pulses and their applications

International Nuclear Information System (INIS)

Ke, Y.

1993-01-01

Recently explosive developments of in vivo NMR spectroscopy (NMRS) and imaging (NMRI) in biological and medical sciences have resulted in the establishment of NMR as one of the most advanced major technique in life sciences. These developments have created huge demands for a variety of NMR adiabatic pulses with play a very important role in NMR experiments in vivo. In order to develop new NMR adiabatic pulses, a rigorous systematical quantum theory for this kind of pulses is greatly needed. Providing such a theory is one of the important goals of this dissertation. Quantum density matrix theory and product operator method have been used throughout this dissertation. Another goal, which is the major goal of this thesis research, is to use the quantum theory as a guide to develop new NMR adiabatic pulses and their applications. To fill this goal, a technique to construct a new type of adiabatic pulses, narrow band selective adiabatic pulses, has been invented, which is described through the example of constructing an adiabatic DANTE inversion pulse. This new adiabatic pulse is the first narrow band selective adiabatic pulses: Adiabatic homonuclear and heteronuclear spectral editing sequences. Unique to the first pulse sequence is a B 1 -field filter which is built by using two non-refocusing adiabatic full passage pulses to refocus the wanted signal and dephase unwanted signals. This extra filter greatly enhance the editing efficiency. Unlike commonly used heteronuclear spectral editing sequences which depend on the polarization transfer or spectral subtraction by phase cycling techniques, the second pulse sequences accomplishes the editing of heteronuclear J-coupled signals based on the fact that this sequence is transparent to the uncoupled spins and is equivalent a 90 degrees excitation pulse to the heteronuclear J-coupled spins. Experimental results have confirmed the ability of spectral editing with these two new sequences

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.

New sesquiterpenes from Euonymus europaeus (Celastraceae).

Science.gov (United States)

Descoins, Charles; Bazzocchi, Isabel López; Ravelo, Angel Gutiérrez

2002-02-01

A new sesquiterpene evoninate alkaloid (1), and two sesquiterpenes (2, 3) with a dihydro-beta-agarofuran skeleton, along with three known sesquiterpenes (4-6), were isolated from the seeds of Euonymus europaeus. Their structures were elucidated by high resolution mass analysis, and one- and two-dimensional (1D and 2D) NMR spectroscopy, including homonuclear and heteronuclear correlation [correlation spectroscopy (COSY), rotating frame Overhauser enhancement spectroscopy (ROESY), heteronuclear single quantum coherence (HSQC), and heteronuclear multiple bond correlation (HMBC)] experiments.

Isotope labeling for NMR studies of macromolecular structure and interactions

International Nuclear Information System (INIS)

Wright, P.E.

1994-01-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform 13 C, 15 N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific 13 C and 15 N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions

Isotope labeling for NMR studies of macromolecular structure and interactions

Energy Technology Data Exchange (ETDEWEB)

Wright, P.E. [Scripps Research Institute, La Jolla, CA (United States)

1994-12-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

Three-dimensional biomedical imaging

International Nuclear Information System (INIS)

Robb, R.A.

1985-01-01

Scientists in biomedical imaging provide researchers, physicians, and academicians with an understanding of the fundamental theories and practical applications of three-dimensional biomedical imaging methodologies. Succinct descriptions of each imaging modality are supported by numerous diagrams and illustrations which clarify important concepts and demonstrate system performance in a variety of applications. Comparison of the different functional attributes, relative advantages and limitations, complementary capabilities, and future directions of three-dimensional biomedical imaging modalities are given. Volume 1: Introductions to Three-Dimensional Biomedical Imaging Photoelectronic-Digital Imaging for Diagnostic Radiology. X-Ray Computed Tomography - Basic Principles. X-Ray Computed Tomography - Implementation and Applications. X-Ray Computed Tomography: Advanced Systems and Applications in Biomedical Research and Diagnosis. Volume II: Single Photon Emission Computed Tomography. Position Emission Tomography (PET). Computerized Ultrasound Tomography. Fundamentals of NMR Imaging. Display of Multi-Dimensional Biomedical Image Information. Summary and Prognostications

NMR longitudinal relaxation enhancement in metal halides by heteronuclear polarization exchange during magic-angle spinning

Energy Technology Data Exchange (ETDEWEB)

Shmyreva, Anna A. [Center for Magnetic Resonance, St. Petersburg State University, St. Petersburg 198504 (Russian Federation); Safdari, Majid; Furó, István [Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm (Sweden); Dvinskikh, Sergey V., E-mail: sergeid@kth.se [Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm (Sweden); Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034 (Russian Federation)

2016-06-14

Orders of magnitude decrease of {sup 207}Pb and {sup 199}Hg NMR longitudinal relaxation times T{sub 1} upon magic-angle-spinning (MAS) are observed and systematically investigated in solid lead and mercury halides MeX{sub 2} (Me = Pb, Hg and X = Cl, Br, I). In lead(II) halides, the most dramatic decrease of T{sub 1} relative to that in a static sample is in PbI{sub 2}, while it is smaller but still significant in PbBr{sub 2}, and not detectable in PbCl{sub 2}. The effect is magnetic-field dependent but independent of the spinning speed in the range 200–15 000 Hz. The observed relaxation enhancement is explained by laboratory-frame heteronuclear polarization exchange due to crossing between energy levels of spin-1/2 metal nuclei and adjacent quadrupolar-spin halogen nuclei. The enhancement effect is also present in lead-containing organometal halide perovskites. Our results demonstrate that in affected samples, it is the relaxation data recorded under non-spinning conditions that characterize the local properties at the metal sites. A practical advantage of fast relaxation at slow MAS is that spectral shapes with orientational chemical shift anisotropy information well retained can be acquired within a shorter experimental time.

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

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.

Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

International Nuclear Information System (INIS)

Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V.

2016-01-01

Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental data obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees

Development of Two-Dimensional NMR

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Development of Two-Dimensional NMR: Strucure Determination of Biomolecules in Solution. Anil Kumar. General Article Volume 20 Issue 11 November 2015 pp 995-1002 ...

Heteronuclear relaxation in time-dependent spin systems: 15N-T1ρ dispersion during adiabatic fast passage

International Nuclear Information System (INIS)

Konrat, Robert; Tollinger, Martin

1999-01-01

A novel NMR experiment comprising adiabatic fast passage techniques for the measurement of heteronuclear self-relaxation rates in fully 15N-enriched proteins is described. Heteronuclear self-relaxation is monitored by performing adiabatic fast passage (AFP) experiments at variable adiabaticity (e.g., variation of RF spin-lock field intensity). The experiment encompasses gradient- selection and sensitivity-enhancement. It is shown that transverse relaxation rates derived with this method are in good agreement with the ones measured by the classical Carr-Purcell-Meiboom-Gill (CPMG) sequences. An application of this method to the study of the carboxyl-terminal LIM domain of quail cysteine and glycine-rich protein qCRP2(LIM2) is presented

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

Heteronuclear multidimensional NMR and homology modelling studies of the C-terminal nucleotide-binding domain of the human mitochondrial ABC transporter ABCB6

Energy Technology Data Exchange (ETDEWEB)

Kurashima-Ito, Kaori [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Ikeya, Teppei [National Institute of Advanced Industrial Science and Technology (AIST), (Japan); Senbongi, Hiroshi [Mitochondrial Diseases Group, MRC Dunn Human NutritionUnit (United Kingdom); Tochio, Hidehito [International Graduate School of Arts and Sciences, Supramolecular Biology, Yokohama City University, Molecular Biophysics Laboratory (Japan); Mikawa, Tsutomu [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Shibata, Takehiko [RIKEN, Shibata Distinguished Senior Scientist Laboratory (Japan); Ito, Yutaka [RIKEN, Cellular and Molecular Biology Laboratory (Japan)], E-mail: ito-yutaka@center.tmu.ac.jp

2006-05-15

Human ATP-binding cassette, sub-family B, member 6 (ABCB6) is a mitochondrial ABC transporter, and presumably contributes to iron homeostasis. Aimed at understanding the structural basis for the conformational changes accompanying the substrate-transportation cycle, we have studied the C-terminal nucleotide-binding domain of ABCB6 (ABCB6-C) in both the nucleotide-free and ADP-bound states by heteronuclear multidimensional NMR and homology modelling. A non-linear sampling scheme was utilised for indirectly acquired {sup 13}C and {sup 15}N dimensions of all 3D triple-resonance NMR experiments, in order to overcome the instability and the low solubility of ABCB6-C. The backbone resonances for approximately 25% of non-proline residues, which are mostly distributed around the functionally important loops and in the Helical domain, were not observed for nucleotide-free form of ABCB6-C. From the pH, temperature and magnetic field strength dependencies of the resonance intensities, we concluded that this incompleteness in the assignments is mainly due to the exchange between multiple conformations at an intermediate rate on the NMR timescale. These localised conformational dynamics remained in ADP-bound ABCB6-C except for the loops responsible for adenine base and {alpha}/{beta}-phosphate binding. These results revealed that the localised dynamic cooperativity, which was recently proposed for a prokaryotic ABC MJ1267, also exists in a higher eukaryotic ABC, and is presumably shared by all members of the ABC family. Since the Helical domain is the putative interface to the transmembrane domain, this cooperativity may explain the coupled functions between domains in the substrate-transportation cycle.

Fragment based drug discovery: practical implementation based on ¹⁹F NMR spectroscopy.

Science.gov (United States)

Jordan, John B; Poppe, Leszek; Xia, Xiaoyang; Cheng, Alan C; Sun, Yax; Michelsen, Klaus; Eastwood, Heather; Schnier, Paul D; Nixey, Thomas; Zhong, Wenge

2012-01-26

Fragment based drug discovery (FBDD) is a widely used tool for discovering novel therapeutics. NMR is a powerful means for implementing FBDD, and several approaches have been proposed utilizing (1)H-(15)N heteronuclear single quantum coherence (HSQC) as well as one-dimensional (1)H and (19)F NMR to screen compound mixtures against a target of interest. While proton-based NMR methods of fragment screening (FBS) have been well documented and are widely used, the use of (19)F detection in FBS has been only recently introduced (Vulpetti et al. J. Am. Chem. Soc.2009, 131 (36), 12949-12959) with the aim of targeting "fluorophilic" sites in proteins. Here, we demonstrate a more general use of (19)F NMR-based fragment screening in several areas: as a key tool for rapid and sensitive detection of fragment hits, as a method for the rapid development of structure-activity relationship (SAR) on the hit-to-lead path using in-house libraries and/or commercially available compounds, and as a quick and efficient means of assessing target druggability.

Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

Science.gov (United States)

Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

2015-08-24

High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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)

Enhanced 29Si spin-lattice relaxation and observation of three-dimensional lattice connectivity in zeolites by two-dimensional 29Si MASS NMR

International Nuclear Information System (INIS)

Sivadinarayana, C.; Choudhary, V.R.; Ganapathy, S.

1994-01-01

It is shown that considerable sensitivity enhancement is achieved in the 29 Si magic angle sample spinning (MASS) NMR spectra of highly siliceous zeolites by pre treating the material with oxygen. The presence of adsorbed molecular oxygen in zeolite channels promotes an efficient 29 Si spin-lattice relaxation via a paramagnetic interaction between the lattice 29 Si T-site and the adsorbed oxygen on zeolite channels. This affords an efficient 2-D data collection and leads to increased sensitivity. The utility of this method is demonstrated in a two-dimensional COSY-45 NMR experiment of a high silica zeolite ZSM-5. (author). 20 refs., 3 figs., 1 tab

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.

Metabolite characterization in serum samples from normal healthy ...

African Journals Online (AJOL)

Metabolite characterization in serum samples from normal healthy human subjects by 1H and 13C NMR spectroscopy. D Misra, U Bajpai. Abstract. One and two dimensional NMR spectroscopy has been employed to characterize the various metabolites of serum control healthy samples. Two dimensional heteronuclear ...

Adiabatic Low-Pass J Filters for Artifact Suppression in Heteronuclear NMR

DEFF Research Database (Denmark)

Meier, Sebastian; Benie, Andrew J; Duus, Jens Øllgaard

2009-01-01

NMR artifact purging: Modern NMR experiments depend on efficient coherence transfer pathways for their sensitivity and on suppression of undesired pathways leading to artifacts for their spectral clarity. A novel robust adiabatic element suppresses hard-to-get-at artifacts....

Development of uniformly stable isotope labeling system in higher plants for hetero-nuclear NMR experiments in vitro and in vivo

International Nuclear Information System (INIS)

Kikuchi, J.

2005-01-01

Full text: Novel methods for measurement of living systems are making new breakthroughs in life science. In the era of the metabolome (analysis of all measurable metabolites), a MS-based approach is considered to be the major technology, whereas a NMR-based method is recognized as minor technology due to its low sensitivity. Therefore, my laboratory is currently focusing to develop novel methodologies for an NMR-based metabolomics. This will be achieved by uniform stable isotope labeling of higher plants allowing application of multi-dimensional NMR experiments used in protein structure determination. Using these novel methods, I will analyze the dynamic molecular networks inside tissues. Especially, use of stable isotope labeling methods has enormous advantage for discrimination of incorporated or de novo synthesized compounds. Furthermore, potentiality of in vivo-NMR metabolomics will be discussed in the conference. (author)

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

NARCIS (Netherlands)

Singh, S.; Folkers, G.E.; Bonvin, A.M.J.J.; Boelens, R.; Wechselberger, R.W.; Niztayev, A.; Kaptein, R.

2002-01-01

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix±hairpin±helix (HhH) motifs

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)

A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.

Science.gov (United States)

Lu, George J; Son, Woo Sung; Opella, Stanley J

2011-04-01

A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly ¹⁵N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly ¹⁵N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

Three-dimensional structure of a glycosylated cell surface antigen from D. discoideum: a primordial adhesion motif

International Nuclear Information System (INIS)

Mabbutt, B.C.; Swarbrick, J.; Cubeddu, L.; Hill, A.

1999-01-01

Full text: We have determined the solution structure of pre-spore specific antigen (PsA), a predominant cell surface glycoprotein from the slime mould Dictyostelium discoideum. The structure and function of this protein suggests that it serves as a molecular signal for multicellular organisation, and that it may also be an adhesion motif mediating direct cell-cell contact. PsA consists of a 90-residue N-terminal globular domain tethered to the cell membrane via a heavily O-glycosylated stalk and a GPI anchor. No homologous sequences have been identified for the N-terminal domain. At Macquarie University, the D. discoideum organism has been well developed as a eukaryotic expression host for glycosylated proteins. For NMR, we have engineered a soluble form of PsA (residues 1-122) containing the globular 'head' and the glycopeptide linker. 15 N- and 15 N/ 13 C-labelled PsA was generated in this organism via a protocol that is readily adaptable for the cost-effective production of milligram quantities of other isotopically labelled recombinant proteins. Using 3D heteronuclear NMR, we have solved the three-dimensional structure of the PsA glycoprotein. It defines an eight stranded β-sandwich of five-on-three topology in a unique arrangement. A long loop is constrained by a cis proline residue and a disulphide bond to form an opening across one end of the sandwich, exposing portions of the hydrophobic interior. We postulate that this distortion of the sandwich fold structures a binding site. Structural and dynamics information was also obtained concerning the intact glycopeptide linker of the protein, which comprises a repeating P-T-V-T motif. In our recombinant form, each Thr residue is modified by a single GlcNAc sugar. This simple structure yields interpretable NMR spectra, which show the glycosylated linker to be in extended conformation, and undergoing distinctly different mobility from the globular domain. These same sugar residues provide an ideal attachment

1H and 15N resonance assignments of oxidized flavodoxin from Anacystis nidulans with 3D NMR

International Nuclear Information System (INIS)

Clubb, R.T.; Thanabal, V.; Wagner, G.; Osborne, C.

1991-01-01

Proton and nitrogen-15 sequence-specific nuclear magnetic resonance assignments have been determined for recombinant oxidized flavodoxin from Anacystis nidulans. Assignments were obtained by using 15 N- 1 H heteronuclear three-dimensional (3D) NMR spectroscopy on a uniformly nitrogen-15 enriched sample of the protein, pH 6.6, at 30C. For 165 residues, the backbone and a large fraction of the side-chain proton resonances have been assigned. Medium- and long-range NOE's have been used to characterize the secondary structure. In solution, flavodoxin consists of a five-stranded parallel β sheet involving residues 3-9, 31-37, 49-56, 81-89, 114-117, and 141-144. Medium-range NOE's indicate that presence of several helices. Several 15 N and 1 H resonances of the flavin mononucleotide (FMN) prosthetic group have been assigned. The FMN-binding site has been investigated by using polypeptide-FMN NOE's

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

2D 1H -13C Heteronuclear Shift Correlation Of 2a - Hydroxy Aiantolactone From Pulicaria Undulata C.A. Mey

Directory of Open Access Journals (Sweden)

A. Rustaiyan

1992-07-01

Full Text Available We have reported recently the isolation and characterization of several sesquiterpene lactones from Pulicaria undulata (1."nThe lactones were isolated from an Et20 - Petrol (1:3 fraction by different chromatographic techniques including HPLC (RP 8, MeOH - H2O, 13:7."nIn this way three eudesmanolides 1 - 3, a guaianolide 4, a nor -guaianolide 5, as well as the pseudoguaianolide 6 and the xanthanolide 7 were isolated. One of the eudesmanolides (2a - hydroxy aiantolactone, 1, was present as the main component."nSuch lactones being known as biologically active substances, we have decided to describe for the first time a detailed interpretation of proton, 1H -NMR, 13C - NMR and 2D lH -13C - heteronuclear shift correlation spectra of 2a - hydroxy aiantolactone. The stereochemistry of C - 2 , C - 7 and C - 8 was determined by the NOESY experiments, H - 7 and H - 8 are in the a configuration and H - 2 is in the b configuration.

Computed tomography and three-dimensional imaging

International Nuclear Information System (INIS)

Harris, L.D.; Ritman, E.L.; Robb, R.A.

1987-01-01

Presented here is a brief introduction to two-, three-, and four-dimensional computed tomography. More detailed descriptions of the mathematics of reconstruction and of CT scanner operation are presented elsewhere. The complementary tomographic imaging methods of single-photon-emission tomography (SPECT) positron-emission tomography (PET), nuclear magnetic resonance (NMR) imaging, ulltrasound sector scanning, and ulltrasound computer-assisted tomography [UCAT] are only named here. Each imaging modality ''probes'' the body with a different energy form, yielding unique and useful information about tomographic sections through the body

Carbon-13 NMR spectroscopy of biological systems

CERN Document Server

Beckmann, Nicolau

1995-01-01

This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

Heteronuclear 2D (1H-13C) MAS NMR Resolves the Electronic Structure of Coordinated Histidines in Light-Harvesting Complex II: Assessment of Charge Transfer and Electronic Delocalization Effect

International Nuclear Information System (INIS)

Matysik, Joerg; Boer, Ido de; Gast, Peter; Gorkom, Hans J. van; Groot, Huub J.M. de

2004-01-01

In a recent MAS NMR study, two types of histidine residues in the light-harvesting complex II (LH2) of Rhodopseudomonas acidophila were resolved: Type 1 (neutral) and Type 2 (positively charged) (Alia et al. J. Am. Chem. Soc.). The isotropic 13 C shifts of histidines coordinating to B850 BChl a are similar to fully positively charged histidine, while the 15 N shift anisotropy shows a predominantly neutral character. In addition the possibility that the ring currents are quenched by overlap in the superstructure of the complete ring of 18 B850 molecules in the LH2 complex could not be excluded. In the present work, by using two-dimensional heteronuclear ( 1 H- 13 C) dipolar correlation spectroscopy with phase-modulated Lee-Goldburg homonuclear 1 H decoupling applied during the t 1 period, a clear and unambiguous assignment of the protons of histidine interacting with the magnesium of a BChl a molecule is obtained and a significant ring current effect from B850 on the coordinating histidine is resolved. Using the ring current shift on 1 H, we refine the 13 C chemical shift assignment of the coordinating histidine and clearly distinguish the electronic structure of coordinating histidines from that of fully positively charged histidine. The DFT calculations corroborate that the coordinating histidines carry ∼0.2 electronic equivalent of positive charge in LH2. In addition, the data indicate that the ground state electronic structures of individual BChl a/His complexes is largely independent of supermolecular π interactions in the assembly of 18 B850 ring in LH2

A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells

Energy Technology Data Exchange (ETDEWEB)

Hikone, Yuya [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Hirai, Go [RIKEN, Synthetic Organic Chemistry Laboratory (Japan); Mishima, Masaki [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Inomata, Kohsuke [RIKEN, Quantitative Biology Center (Japan); Ikeya, Teppei; Arai, Souichiro [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Shirakawa, Masahiro [Japan Agency for Medical Research and Development, AMED-CREST (Japan); Sodeoka, Mikiko [RIKEN, Synthetic Organic Chemistry Laboratory (Japan); Ito, Yutaka, E-mail: ito-yutaka@tmu.ac.jp [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan)

2016-10-15

Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N–H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells.

Science.gov (United States)

Hikone, Yuya; Hirai, Go; Mishima, Masaki; Inomata, Kohsuke; Ikeya, Teppei; Arai, Souichiro; Shirakawa, Masahiro; Sodeoka, Mikiko; Ito, Yutaka

2016-10-01

Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N-H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells

International Nuclear Information System (INIS)

Hikone, Yuya; Hirai, Go; Mishima, Masaki; Inomata, Kohsuke; Ikeya, Teppei; Arai, Souichiro; Shirakawa, Masahiro; Sodeoka, Mikiko; Ito, Yutaka

2016-01-01

Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N–H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

Introduction to the conformational investigation of peptides and proteins by using two-dimensional proton NMR experiments

International Nuclear Information System (INIS)

Neumann, J.M.; Macquaire, F.

1991-01-01

This report presents the elementary bases for an initiation to the conformational study of peptides and proteins by using two-dimensional proton NMR experiments. First, some general features of protein structures are summarized. A second chapter is devoted to the basic NMR experiments and to the spectral parameters which provide a structural information. This description is illustrated by NMR spectra of peptides. The third chapter concerns the most standard two-dimensional proton NMR experiments and their use for a conformational study of peptides and proteins. Lastly, an example of NMR structural investigation of a peptide is reported [fr

Heteronuclear Long-Range Correlation

DEFF Research Database (Denmark)

Sørensen, Ole W.

The lecture will cover heteronuclear long-range correlation techniques like HMBC, H2BC, and HAT HMBC with the emphasis on determining the number of covalent bonds between two spins being correlated. H2BC and HMBC spectra are quite complementary as a peak can be strong in one of the two spectra...

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

Application of heteronuclear couplings to conformational analysis of oligonucleotides

International Nuclear Information System (INIS)

Zhu, G.; Live, D.; Bax, A.

1994-01-01

The value of vicinal coupling constants extracted from NMR spectra in deducing torsion angles for conformational analysis is well recognized. Due to the abundance of protons, their couplings have been mostly widely used. In many instances, couplings between protons and other nuclei may be a valuable complement to proton-proton couplings or, in some instances, may be the only coupling available to characterize the torsion angle about a bond. Recently, heteronuclear couplings have been used to great benefit in studies of isotopically enriched proteins, and this general approach has been extended to peptides at natural abundance. The possibility of using this approach to study oligonucleotides is also attractive but has not as yet been widely exploited. With the development of strategies for labeling such molecules, particularly RNAs, this may become an important component in conformational analysis. For DNA, labeling is less accessible, but sufficient quantities of unlabeled material are readily available for measuring these couplings at natural abundance. We chose several DNA systems to explore the usefulness of heteronuclear couplings in addressing the sugar conformation and the glycosidic torsion angle. Intensities of cross peaks in long-range HMQC experiments can be related to the couplings. Crosspeaks involving H1' and C1' atoms have been emphasized because of the superior shift dispersion at these positions between sugar protons and carbon atoms. Results will be shown for the self-complementary Dickerson duplex dodecamer sequence d(CGCGAATTCGCG) and for d(GGTCGG), which dimerizes to form a G-tetrad structure incorporating both syn and anti base orientations. The couplings provide a clear discrimination between presence of C3'-endo and C2'-endo conformations of the sugars and syn and anti bases arrangements

Application of heteronuclear couplings to conformational analysis of oligonucleotides

Energy Technology Data Exchange (ETDEWEB)

Zhu, G. [Univ. of Maryland, College Park, MD (United States); Live, D. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Bax, A. [NIDDK National Institutes of Health, Bethesda, MD (United States)

1994-12-01

The value of vicinal coupling constants extracted from NMR spectra in deducing torsion angles for conformational analysis is well recognized. Due to the abundance of protons, their couplings have been mostly widely used. In many instances, couplings between protons and other nuclei may be a valuable complement to proton-proton couplings or, in some instances, may be the only coupling available to characterize the torsion angle about a bond. Recently, heteronuclear couplings have been used to great benefit in studies of isotopically enriched proteins, and this general approach has been extended to peptides at natural abundance. The possibility of using this approach to study oligonucleotides is also attractive but has not as yet been widely exploited. With the development of strategies for labeling such molecules, particularly RNAs, this may become an important component in conformational analysis. For DNA, labeling is less accessible, but sufficient quantities of unlabeled material are readily available for measuring these couplings at natural abundance. We chose several DNA systems to explore the usefulness of heteronuclear couplings in addressing the sugar conformation and the glycosidic torsion angle. Intensities of cross peaks in long-range HMQC experiments can be related to the couplings. Crosspeaks involving H1{prime} and C1{prime} atoms have been emphasized because of the superior shift dispersion at these positions between sugar protons and carbon atoms. Results will be shown for the self-complementary Dickerson duplex dodecamer sequence d(CGCGAATTCGCG) and for d(GGTCGG), which dimerizes to form a G-tetrad structure incorporating both syn and anti base orientations. The couplings provide a clear discrimination between presence of C3{prime}-endo and C2{prime}-endo conformations of the sugars and syn and anti bases arrangements.

APSY-NMR for protein backbone assignment in high-throughput structural biology

Energy Technology Data Exchange (ETDEWEB)

Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

2015-01-15

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

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

Structural study of pyrones by NMR

International Nuclear Information System (INIS)

Mandarino, D.G.

1985-01-01

Extracts of two species of Aniba, designed Aniba-SA (light petroleum extract) and Aniba-SB (benzene extract), afforded by chromatographic fraccionation some compounds. The isolated compounds were identified using spectrometric data and C 13 -NMR coupled and decompled spectra of pyrones were registered. Measurement of the heteronuclear residual coupling by irradiation proton frequency off-resonance was used for distinguish C-5, C-7 and C-8 carbons of the pyrones SB-1, SB-3, SB-4 and SB-5. (M.J.C.) [pt

Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Hou, Guangjin, E-mail: hou@udel.edu, E-mail: tpolenov@udel.edu; Lu, Xingyu, E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net; Vega, Alexander J., E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net; Polenova, Tatyana, E-mail: hou@udel.edu, E-mail: tpolenov@udel.edu [Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261 (United States)

2014-09-14

We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear {sup 1}H-X (X = {sup 13}C, {sup 15}N, {sup 31}P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the {sup 1}H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the {sup 1}H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from {sup 1}H chemical shift anisotropy, while keeping the {sup 1}H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [{sup 15}N]-N-acetyl-valine and [U-{sup 13}C,{sup 15}N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate {sup 1}H-{sup 15}N dipolar couplings in the context of 3D experiments is presented on U-{sup 13}C,{sup 15}N-enriched dynein light chain protein LC8.

Two-dimensional NMR studies of allyl palladium complexes of ...

Indian Academy of Sciences (India)

Administrator

h3-Allyl complexes are intermediates in organic synthetic reactions such as allylic alkylation and amination. There is growing interest in understanding the structures of chiral h3-allyl intermediates as this would help to unravel the mechanism of enantioselective C–C bond forming reactions. Two-dimensional NMR study is a.

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.

Assessment of protein solution versus crystal structure determination using spin- diffusion-suppressed NOE and heteronuclear relaxation data

International Nuclear Information System (INIS)

LeMaster, David M.

1997-01-01

A spin-diffusion-suppressed NOE buildup series has been measured for E. coli thioredoxin.The extensive 13C and 15N relaxation data previously reported for this protein allow for direct interpretation of dynamical contributions to the 1H-1H cross-relaxation rates for a large proportion of the NOE cross peaks. Estimates of the average accuracy for these derived NOE distances are bounded by 4% and 10%, based on a comparison to the corresponding X-ray distances. An independent fluctuation model is proposed for prediction of the dynamical corrections to 1H-1H cross-relaxation rates, based solely on experimental structural and heteronuclear relaxation data. This analysis is aided by the demonstration that heteronuclear order parameters greater than 0.6 depend only on the variance of the H-X bond orientation,independent of the motional model in either one- or two-dimensional diffusion (i.e., 1- S2 = 3/4 sin2 2 θσ). The combination of spin-diffusion-suppressed NOE data and analysis of dynamical corrections to 1H-1H cross-relaxation rates based on heteronuclear relaxation data has allowed for a detailed interpretation of various discrepancies between the reported solution and crystal structures

J-UNIO protocol used for NMR structure determination of the 206-residue protein NP-346487.1 from Streptococcus pneumoniae TIGR4

Energy Technology Data Exchange (ETDEWEB)

Jaudzems, Kristaps [Latvian Institute of Organic Synthesis (Latvia); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Geralt, Michael; Serrano, Pedro; Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

2015-01-15

The NMR structure of the 206-residue protein NP-346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77 % of the backbone assignments, which were interactively validated and extended to 97 %. With an input of the near-complete backbone assignments and three 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra, automated side chain assignment with UNIO-ATNOS/ASCAN resulted in 77 % of the expected assignments, which was extended interactively to about 90 %. Automated NOE assignment and structure calculation with UNIO-ATNOS/CANDID in combination with CYANA was used for the structure determination of this two-domain protein. The individual domains in the NMR structure coincide closely with the crystal structure, and the NMR studies further imply that the two domains undergo restricted hinge motions relative to each other in solution. NP-346487.1 is so far the largest polypeptide chain to which the J-UNIO structure determination protocol has successfully been applied.

Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

Science.gov (United States)

Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

2017-10-01

Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1 H, 13 C, and 15 N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.

Targeted natural product isolation guided by HPLC-SPE-NMR: Constituents of Hubertia species

DEFF Research Database (Denmark)

Sprogoe, K.; Staek, D.; Jager, A.K.

2007-01-01

-hydroxyphenyl)acetyl]quinic acid (3), was performed. Finally, targeted isolation of 1 was achieved by SPE fractionation and preparative HPLC, followed by evaluation of its antioxidant and antimicrobial activity. In contrast to chlorogenic acid and 3,5-di-O-caffeoylquinic acid, which act as antioxidants...... full or partial identification of all major extract constituents and demonstrated the presence of unusual quinic acid derivatives containing the (1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl residue that exhibit strongly coupled ABXY patterns, the parameters of which were obtained by spin simulations....... Using homo- and heteronuclear 2D NMR data acquired in the HPLC-SPE-NMR mode, complete structure determination of three new natural products, i.e., 3,5-di-O-caffeoyl-4-O-[(1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl]quini c acid (1), its 2-hydroxy derivative (2), and 3,5-di-O-caffeoyl-4-O-[(4...

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

NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: Application to the human prion protein hPrP(23-230)

International Nuclear Information System (INIS)

Liu Aizhuo; Riek, Roland; Wider, Gerhard; Schroetter, Christine von; Zahn, Ralph; Wuethrich, Kurt

2000-01-01

A combination of three heteronuclear three-dimensional NMR experiments tailored for sequential resonance assignments in uniformly 15 N, 13 C-labeled flexible polypeptide chains is described. The 3D (H)N(CO-TOCSY)NH, 3D (H)CA(CO-TOCSY)NH and 3D (H)CBCA(CO-TOCSY)NH schemes make use of the favorable 15 N chemical shift dispersion in unfolded polypeptides, exploit the slow transverse 15 N relaxation rates of unfolded polypeptides in high resolution constant-time [ 1 H, 15 N]-correlation experiments, and use carbonyl carbon homonuclear isotropic mixing to transfer magnetization sequentially along the amino acid sequence. Practical applications are demonstrated with the 100-residue flexible tail of the recombinant human prion protein, making use of spectral resolution up to 0.6 Hz in the 15 N dimension, simultaneous correlation with the two adjacent amino acid residues to overcome problems associated with spectral overlap, and the potential of the presently described experiments to establish nearest-neighbor correlations across proline residues in the amino acid sequence

NMR magnetization exchange dynamics for three spin-1/2 systems

International Nuclear Information System (INIS)

Demco, D.E.; Filip, X.; Filip, C.

1997-01-01

The magnetization exchange dynamics in one-dimensional NMR exchange experiments performed with static samples is analyzed for the relevant case of three spin systems. The magnetization decays recorded in the experiments performed with different chemical shift filters for the short mixing times are derived analytically. In this regime the decay rates depend on the dipolar coupling between the spins belonging to different functional groups. The predictions of the theoretical model are compared with the magnetization exchange data obtained for cross-linked poly(styrene-co-butadiene) samples. The residual dipolar coupling between the functional CH- and CH2-groups of butadiene are measured from the magnetization exchange experiments in the short mixing time regime. (authors)

Immobilization of (dd)heteronuclear hexacyanoferrates(II) in a gelatin matrix

International Nuclear Information System (INIS)

Mikhajlov, O.V.

2008-01-01

Data pertinent to potentiality of preparing salts of (dd)heteronuclear hexacyanoferrates(II) with(M 1 ) II and (M 2 ) II (M 1 , M 2 = Mn, Co, Ni, Cu, Zn, Cd) as a result of contact between M 1 2 [Fe(CN) 6 ] immobilized in a gelatin matrix and aqueous solutions of metal chlorides have been systematized and summarized. The decisive role of the gelatin matrix, performing the function of an organizing system in formation of (dd)heteronuclear hexacyanoferrates(II) of metals, has been pointed out [ru

Three dimensional illustrating - three-dimensional vision and deception of sensibility

Directory of Open Access Journals (Sweden)

Anita Gánóczy

2009-03-01

Full Text Available The wide-spread digital photography and computer use gave the opportunity for everyone to make three-dimensional pictures and to make them public. The new opportunities with three-dimensional techniques give chance for the birth of new artistic photographs. We present in detail the biological roots of three-dimensional visualization, the phenomena of movement parallax, which can be used efficiently in making three-dimensional graphics, the Zöllner- and Corridor-illusion. There are present in this paper the visual elements, which contribute to define a plane two-dimensional image in three-dimension: coherent lines, the covering, the measurement changes, the relative altitude state, the abatement of detail profusion, the shadings and the perspective effects of colors.

Two-site jumps in dimethyl sulfone studied by one- and two-dimensional 17O NMR spectroscopy

Science.gov (United States)

Beerwerth, J.; Storek, M.; Greim, D.; Lueg, J.; Siegel, R.; Cetinkaya, B.; Hiller, W.; Zimmermann, H.; Senker, J.; Böhmer, R.

2018-03-01

Polycrystalline dimethyl sulfone is studied using central-transition oxygen-17 exchange NMR. The quadrupolar and chemical shift tensors are determined by combining quantum chemical calculations with line shape analyses of rigid-lattice spectra measured for stationary and rotating samples at several external magnetic fields. Quantum chemical computations predict that the largest principal axes of the chemical shift anisotropy and electrical field gradient tensors enclose an angle of about 73°. This prediction is successfully tested by comparison with absorption spectra recorded at three different external magnetic fields. The experimental one-dimensional motionally narrowed spectra and the two-dimensional exchange spectrum are compatible with model calculations involving jumps of the molecules about their two-fold symmetry axis. This motion is additionally investigated by means of two-time stimulated-echo spectroscopy which allows for a determination of motional correlation functions over a wider temperature range than previously reported using carbon and deuteron NMR. On the basis of suitable second-order quadrupolar frequency distributions, sin-sin stimulated-echo amplitudes are calculated for a two-site model in the limit of vanishing evolution time and compared with experimental findings. The present study thus establishes oxygen-17 NMR as a powerful method that will be particularly useful for the study of solids and liquids devoid of nuclei governed by first-order anisotropies.

Collisional properties of weakly bound heteronuclear dimers

NARCIS (Netherlands)

Marcelis, B.; Kokkelmans, S.J.J.M.F.; Shlyapnikov, G.V.; Petrov, D.S.

2008-01-01

We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional stability due to an effective dimer-dimer repulsion originating

Mechanism of phosphoryl transfer and protein-protein interaction in the PTS system-an NMR study

Energy Technology Data Exchange (ETDEWEB)

Rajagopal, P.; Klevit, R.E. [Univ. of Washington, Seattle, WA (United States)

1994-12-01

HPr and Enzyme IIA{sup Glc} are two of the components of the bacterial PTS (phosphoenolpyruvate: sugar phosphotranferase system) and are involved in the phosphorylation and concomitant translocation of sugars across the membrane. These PTS protein complexes also regulate sugar transport. HPr, phosphorylated at a histidine N1 site by Enzyme I and phosphoenol pyruvate, transfers the phosphoryl group to a histidine N3 position in Enzyme IIA{sup Glc}. HPrs from Gram-positive bacteria undergo regulatory phosphorylation at Ser{sup 46}, whereby phosphorylation of the histidine residue is inhibited. Conversely, histidine phosphorylation inhibits phosphorylation at Ser{sup 46}. HPrs from Gram-negative bacteria possess a serine residue at position 46, but do not undergo regulatory phosphorylation. HPr forms an open-faced sandwich structure with a four-strand S-sheet and 2 to 3 helices lying on top of the sheet. The active-site histidine and Ser{sup 46} occur in conformationally flexible regions. P-His-HPr from the Gram-positive bacterium Bacillus subtilus has been investigated by both homonuclear and heteronuclear two-dimensional and three-dimensional NMR experiments using an in-situ enzymatic regeneration system to maintain a constant level of P-His-HPr. The results show that localized conformational changes occur in the vicinity of the active-site histidine and also near Ser{sup 46}. HPr-Enzyme IIA{sup Glc} complexes from both Bacillus subtilis and Gram-negative Escherichia coli were also studied by a variety of {sup 15}N-edited two-dimensional NMR experiments, which were performed on uniformly {sup 15}N-labeled HPr complexed to unlabeled Enzyme IIA{sup Glc}. The complex is in fast exchange with a molecular weight of about 27 kDa. The focus of our work is to assess the changes undergone by HPr (the smaller of the two components), and so all the experiments were performed with excess Enzyme IIA present in the system.

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

KAUST Repository

Elbaz, Ayman M.

2015-11-12

There is an increasing interest in the comprehensive study of heavy fuel oil (HFO) due to its growing use in furnaces, boilers, marines, and recently in gas turbines. In this work, the thermal combustion characteristics and chemical composition of HFO were investigated using a range of techniques. Thermogravimetric analysis (TGA) was conducted to study the nonisothermal HFO combustion behavior. Chemical characterization of HFO was accomplished using various standard methods in addition to direct 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) spectroscopy. By analyzing thermogravimetry and differential thermogravimetry (TG/DTG) results, three different reaction regions were identified in the combustion of HFO with air, specifically, low temperature oxidation region (LTO), fuel deposition (FD), and high temperature oxidation (HTO) region. At the high end of the LTO region, a mass transfer resistance (skin effect) was evident. Kinetic analysis in LTO and HTO regions was conducted using two different kinetic models to calculate the apparent activation energy. In both models, HTO activation energies are higher than those for LTO. The FT-ICR MS technique resolved thousands of aromatic and sulfur containing compounds in the HFO sample and provided compositional details for individual molecules of three major class species. The major classes of compounds included species with one sulfur atom (S1), with two sulfur atoms (S2), and purely hydrocarbons (HC). The DBE (double bond equivalent) abundance plots established for S1 and HC provided additional information on their distributions in the HFO sample. The 1H NMR and 13C NMR results revealed that nearly 59% of the 1H nuclei were distributed as paraffinic CH2 and 5% were in aromatic groups. Nearly 21% of 13C nuclei were

Synthesis and investigation of new heteronuclear [Zn-La] coordination compounds based on unsaturated lanthanum complex with N,N'-tetraethyl-N''-trichloacetylphosphortriamide

International Nuclear Information System (INIS)

Amyirkhanov, O.V.; Sliva, T.Yu.; Moroz, O.V.; Trush, Je.A.; Frits'kij, Yi.O.

2011-01-01

New heteronuclear [Zn-La] coordination compounds, perspective luminescent materials, with general formulas [Zn(Ve)La(X) 2 (Ac)] ({Zn-La;Ve;X}) and [Zn(Vp)La(X) 2 (Ac)] ({Zn-La;Vp;X}) have been synthesized HX=CCl 3 C(O)NHP(O)[N(C 2 H 5 ) 2 ] 2 - N,N'-tetraethyl-N''-trichloracetylphosphortriamide, H 2 Ve and H 2 Vp are products of the condensation of 1,2-diaminoethane and 1,3-diaminopropane with o-vanillin, respectively). The composition of [Zn-La] complexes has been determined, and the coordination mode of a phosphorylated ligand has been suggested by element analysis, IR- and 1 H, 31 P NMR-spectroscopy.

Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

Science.gov (United States)

Takegoshi, K.; Miyazawa, Norihiro; Sharma, Kshama; Madhu, P. K.

2015-04-01

We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order.

Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

International Nuclear Information System (INIS)

Takegoshi, K.; Miyazawa, Norihiro; Sharma, Kshama; Madhu, P. K.

2015-01-01

We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order

Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

Energy Technology Data Exchange (ETDEWEB)

Takegoshi, K., E-mail: takeyan@kuchem.kyoto-u.ac.jp; Miyazawa, Norihiro [Division of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto (Japan); Sharma, Kshama [TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500 075 (India); Madhu, P. K. [TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500 075 (India); Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

2015-04-07

We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order.

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.

Na/Ca Intermixing around Silicate and Phosphate Groups in Bioactive Phosphosilicate Glasses Revealed by Heteronuclear Solid-State NMR and Molecular Dynamics Simulations.

Science.gov (United States)

Mathew, Renny; Stevensson, Baltzar; Edén, Mattias

2015-04-30

We characterize the intermixing of network-modifying Na(+)/Ca(2+) ions around the silicate (QSi(n)) and phosphate (QP(n)) tetrahedra in a series of 16 Na2O–CaO–SiO2–P2O5 glasses, whose P content and silicate network connectivity were varied independently. The set includes both bioactive and bioinactive compositions and also encompasses two soda-lime-silicate members devoid of P, as well as two CaO–SiO2 glasses and one Na2O–SiO2–P2O5 glass. The various Si/P↔Na/Ca contacts were probed by molecular dynamics (MD) simulations together with heteronuclear magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) experimentation utilizing (23)Na{(31)P} and (23)Na{(29)Si} REDOR, as well as (31)P{ (23)Na} and (29)Si{(23)Na} REAPDOR. We introduce an approach for quantifying the extent of Na(+)/Ca(2+) ordering around a given QP(n) or QSi(n) group, encoded by the preference factor 0⩽ PM ⩽ 1 conveying the relative weights of a random cation intermixing (PM = 0) and complete preference/ordering (PM = 1) for one of the species M, which represents either Na(+) or Ca(2+). The MD-derived preference factors reveal phosphate and silicate species surrounded by Na(+)/Ca(2+) ions intermixed nearly randomly (PM ≲ 0.15), except for the QSi(4) and QSi(1) groups, which manifest more significant cation ordering with preference for Na+ and Ca2+, respectively. The overall weak preferences are essentially independent of the Si and P contents of the glass, whereas PM primarily correlates with the total amount of network modifiers: as the latter is increased, the Na/Ca distribution around the {QP(0), QSi(1), QSi(2)} groups with preference for Ca2(+ )tend to randomize (i.e., PCa decreases), while the PNa-values grow slightly for the {QP(1), QSi(3), QSi(4)} species already preferring coordination of Na. The set of experimental preference factors {PCa} for the orthophosphate (QP(0)) groups extracted from (31)P{(23)Na} REAPDOR NMR-derived M2(P–Na) dipolar second moments agrees

Increasing the sensitivity of NMR diffusion measurements by paramagnetic longitudinal relaxation enhancement, with application to ribosome–nascent chain complexes

International Nuclear Information System (INIS)

Chan, Sammy H. S.; Waudby, Christopher A.; Cassaignau, Anaïs M. E.; Cabrita, Lisa D.; Christodoulou, John

2015-01-01

The translational diffusion of macromolecules can be examined non-invasively by stimulated echo (STE) NMR experiments to accurately determine their molecular sizes. These measurements can be important probes of intermolecular interactions and protein folding and unfolding, and are crucial in monitoring the integrity of large macromolecular assemblies such as ribosome–nascent chain complexes (RNCs). However, NMR studies of these complexes can be severely constrained by their slow tumbling, low solubility (with maximum concentrations of up to 10 μM), and short lifetimes resulting in weak signal, and therefore continuing improvements in experimental sensitivity are essential. Here we explore the use of the paramagnetic longitudinal relaxation enhancement (PLRE) agent NiDO2A on the sensitivity of 15 N XSTE and SORDID heteronuclear STE experiments, which can be used to monitor the integrity of these unstable complexes. We exploit the dependence of the PLRE effect on the gyromagnetic ratio and electronic relaxation time to accelerate recovery of 1 H magnetization without adversely affecting storage on N z during diffusion delays or introducing significant transverse relaxation line broadening. By applying the longitudinal relaxation-optimized SORDID pulse sequence together with NiDO2A to 70S Escherichia coli ribosomes and RNCs, NMR diffusion sensitivity enhancements of up to 4.5-fold relative to XSTE are achieved, alongside ∼1.9-fold improvements in two-dimensional NMR sensitivity, without compromising the sample integrity. We anticipate these results will significantly advance the use of NMR to probe dynamic regions of ribosomes and other large, unstable macromolecular assemblies.Graphical Abstract

Viscoelastic polymer flows and elastic turbulence in three-dimensional porous structures.

Science.gov (United States)

Mitchell, Jonathan; Lyons, Kyle; Howe, Andrew M; Clarke, Andrew

2016-01-14

Viscoelastic polymer solutions flowing through reservoir rocks have been found to improve oil displacement efficiency when the aqueous-phase shear-rate exceeds a critical value. A possible mechanism for this enhanced recovery is elastic turbulence that causes breakup and mobilization of trapped oil ganglia. Here, we apply nuclear magnetic resonance (NMR) pulsed field gradient (PFG) diffusion measurements in a novel way to detect increased motion of disconnected oil ganglia. The data are acquired directly from a three-dimensional (3D) opaque porous structure (sandstone) when viscoelastic fluctuations are expected to be present in the continuous phase. The measured increase in motion of trapped ganglia provides unequivocal evidence of fluctuations in the flowing phase in a fully complex 3D system. This work provides direct evidence of elastic turbulence in a realistic reservoir rock - a measurement that cannot be readily achieved by conventional laboratory methods. We support the NMR data with optical microscopy studies of fluctuating ganglia in simple two-dimensional (2D) microfluidic networks, with consistent apparent rheological behaviour of the aqueous phase, to provide conclusive evidence of elastic turbulence in the 3D structure and hence validate the proposed flow-fluctuation mechanism for enhanced oil recovery.

Targeted natural product isolation guided by HPLC-SPE-NMR: constituents of Hubertia species.

Science.gov (United States)

Sprogøe, Kennett; Staerk, Dan; Jäger, Anna K; Adsersen, Anne; Hansen, Steen Honoré; Witt, Matthias; Landbo, Anne-Katrine R; Meyer, Anne S; Jaroszewski, Jerzy W

2007-09-01

The hyphenated technique, high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy (HPLC-SPE-NMR), has been applied for rapid identification of novel natural products in crude extracts of Hubertia ambavilla and Hubertia tomentosa. The technique allowed full or partial identification of all major extract constituents and demonstrated the presence of unusual quinic acid derivatives containing the (1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl residue that exhibit strongly coupled ABXY patterns, the parameters of which were obtained by spin simulations. Using homo- and heteronuclear 2D NMR data acquired in the HPLC-SPE-NMR mode, complete structure determination of three new natural products, i.e., 3,5-di-O-caffeoyl-4-O-[(1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl]quinic acid (1), its 2-hydroxy derivative (2), and 3,5-di-O-caffeoyl-4-O-[(4-hydroxyphenyl)acetyl]quinic acid (3), was performed. Finally, targeted isolation of 1 was achieved by SPE fractionation and preparative HPLC, followed by evaluation of its antioxidant and antimicrobial activity. In contrast to chlorogenic acid and 3,5-di-O-caffeoylquinic acid, which act as antioxidants, compound 1 proved at the same conditions to possess prooxidant activity in an assay evaluating the oxidation of human low-density lipoprotein induced by Cu(2+).

Selective {sup 2}H and {sup 13}C labeling in NMR analysis of solution protein structure and dynamics

Energy Technology Data Exchange (ETDEWEB)

LeMaster, D.M. [Northwestern Univ., Evanston, IL (United States)

1994-12-01

Preparation of samples bearing combined isotope enrichment patterns has played a central role in the recent advances in NMR analysis of proteins in solution. In particular, uniform {sup 13}C, {sup 15}N enrichment has made it possible to apply heteronuclear multidimensional correlation experiments for the mainchain assignments of proteins larger than 30 KDa. In contrast, selective labeling approaches can offer advantages in terms of the directedness of the information provided, such as chirality and residue type assignments, as well as through enhancements in resolution and sensitivity that result from editing the spectral complexity, the relaxation pathways and the scalar coupling networks. In addition, the combination of selective {sup 13}C and {sup 2}H enrichment can greatly facilitate the determination of heteronuclear relaxation behavior.

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.

Measurements of Grain Motion in a Dense, Three-Dimensional Granular Fluid

Science.gov (United States)

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

2002-03-01

We have used NMR to measure the short-time, three-dimensional displacement of grains in a system of mustard seeds vibrated vertically at 15g. The measurements are in the ballistic regime, giving direct access to the granular temperature profile. The data are compared to a recent hydrodynamic theory developed for high density granular flows. We find that the hydrodynamic theory works well for the dense, lower portion of the sample but breaks down near the free surface, where the mean free path becomes long.

Identification and quantification of flavonoids and ellagic acid derivatives in therapeutically important Drosera species by LC-DAD, LC-NMR, NMR, and LC-MS.

Science.gov (United States)

Zehl, Martin; Braunberger, Christina; Conrad, Jürgen; Crnogorac, Marija; Krasteva, Stanimira; Vogler, Bernhard; Beifuss, Uwe; Krenn, Liselotte

2011-06-01

Droserae herba is a drug commonly used for treatment of convulsive or whooping cough since the seventeenth century. Because of the contribution of flavonoids and ellagic acid derivatives to the therapeutic activity of Droserae herba, an LC-DAD method has been developed for quantification of these analytes in four Drosera species used in medicine (Drosera anglica, D. intermedia, D. madagascariensis, and D. rotundifolia). During elaboration of the method 13 compounds, including three substances not previously described for Drosera species, were detected and unambiguously identified by means of extensive LC-MS and LC-NMR experiments and by off-line heteronuclear 2D NMR after targeted isolation. The most prominent component of D. rotundifolia and D. anglica, 2″-O-galloylhyperoside, with myricetin-3-O-β-glucopyranoside and kaempferol-3-O-(2″-O-galloyl)-β-galactopyranoside, were identified for the very first time in this genus. The LC-DAD method for quantification was thoroughly validated, and enables, for the first time, separation and precise analysis of these analytes in Droserae herba. Simple sample preparation and use of a narrow-bore column guarantee low cost and simplicity of the suggested system, which is excellently suited to quality control of the drug or herbal medicinal products containing this drug.

Structural studies on leukaemia inhibitory factor

Energy Technology Data Exchange (ETDEWEB)

Norton, R.S.; Maurer, T.; Smith, D.K. [Biomolecular Research Institute, Parville (Australia); Nicola, N.A. [Institute of Medical Research, Melbourne (Australia)

1994-12-01

Leukaemia Inhibitory Factor (LIF) is a pleiotropic cytokine that acts on a wide range of target cells, including mega-karyocytes, osteoblasts, hepatocytes, adipocytes, neurons, embryonic stem cells, and primordial germ cells. Many of its activities are shared with other cytokines, particularly interleukin-6, oncostatin-M, ciliary neurotrophic factor, and granulocyte colony-stimulating factor (G-CSF). Although secreted in vivo as a glycoprotein, nonglycosylated recombinant protein expressed in E. coli is fully active and has been used in our nuclear magnetic resonance (NMR) studies of the three-dimensional structure and structure-function relationships of LIF. With 180 amino acids and a molecular mass of about 20 kDa, OF is too large for direct structure determination by two-dimensional and three-dimensional {sup 1}HNMR. It is necessary to label the protein with the stable isotopes {sup 15}N and {sup 13}C and employ heteronuclear three-dimensional NMR in order to resolve and interpret the spectral information required for three-dimensional structure determination. This work has been undertaken with both human LIF and a mouse-human chimaera that binds to the human LIF receptor with the same affinity as the human protein and yet expresses in E. coli at much higher levels. Sequence-specific resonance assignments and secondary structure elements for these proteins will be presented and progress towards determination of their three-dimensional structures described.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

Energy Technology Data Exchange (ETDEWEB)

Gopinath, T. [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States); Mote, Kaustubh R. [University of Minnesota, Department of Chemistry (United States); Veglia, Gianluigi, E-mail: vegli001@umn.edu [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States)

2015-05-15

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living {sup 15}N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through {sup 15}N–{sup 15}N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish {sup 15}N–{sup 15}N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

Science.gov (United States)

Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

2015-05-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

International Nuclear Information System (INIS)

Gopinath, T.; Mote, Kaustubh R.; Veglia, Gianluigi

2015-01-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living 15 N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through 15 N– 15 N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish 15 N– 15 N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments

The covariance of the differences between experimental and theoretical chemical shifts as an aid for assigning two-dimensional heteronuclear correlation solid-state NMR spectra

Czech Academy of Sciences Publication Activity Database

Czernek, Jiří; Brus, Jiří

2014-01-01

Roč. 608, 21 July (2014), s. 334-339 ISSN 0009-2614 R&D Projects: GA ČR(CZ) GA14-03636S Institutional support: RVO:61389013 Keywords : NMR * DFT * covariance Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.897, year: 2014

Solution structures of α-conotoxin G1 determined by two-dimensional NMR spectroscopy

International Nuclear Information System (INIS)

Pardi, A.; Galdes, A.; Florance, J.; Maniconte, D.

1989-01-01

Two-dimensional NMR data have been used to generate solution structures of α-conotoxin G1, a potent peptide antagonist of the acetylcholine receptor. Structural information was obtained in the form of proton-proton internuclear distance constraints, and initial structures were produced with a distance geometry algorithm. Energetically more favorable structures were generated by using the distance geometry structures as input for a constrained energy minimization program. The results of both of these calculations indicate that the overall backbone conformation of the molecule is well-defined by the NMR data whereas the side-chain conformations are generally less well-defined. The main structural features derived from the NMR data were the presence of tight turns centered on residues Pro 5 and Arg 9 . The solution structures are compared with previous proposed models of conotoxin G1, and the NMR data are interpreted in conjunction with chemical modification studies and structural properties of other antagonists of the acetylcholine receptor to gain insight into structure-activity relationships in these peptide toxins

Three-dimensional ICT reconstruction

International Nuclear Information System (INIS)

Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia

2005-01-01

The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context, qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)

Three-dimensional ICT reconstruction

International Nuclear Information System (INIS)

Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia

2004-01-01

The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by order, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)

Three-dimensional analysis of craniofacial bones using three-dimensional computer tomography

Energy Technology Data Exchange (ETDEWEB)

Ono, Ichiro; Ohura, Takehiko; Kimura, Chu (Hokkaido Univ., Sapporo (Japan). School of Medicine) (and others)

1989-08-01

Three-dimensional computer tomography (3DCT) was performed in patients with various diseases to visualize stereoscopically the deformity of the craniofacial bones. The data obtained were analyzed by the 3DCT analyzing system. A new coordinate system was established using the median sagittal plane of the face (a plane passing through sella, nasion and basion) on the three-dimensional image. Three-dimensional profilograms were prepared for detailed analysis of the deformation of craniofacial bones for cleft lip and palate, mandibular prognathia and hemifacial microsomia. For patients, asymmetry in the frontal view and twist-formed complicated deformities were observed, as well as deformity of profiles in the anteroposterior and up-and-down directions. A newly developed technique allows three-dimensional visualization of changes in craniofacial deformity. It would aid in determining surgical strategy, including crani-facial surgery and maxillo-facial surgery, and in evaluating surgical outcome. (N.K.).

Three-dimensional analysis of craniofacial bones using three-dimensional computer tomography

International Nuclear Information System (INIS)

Ono, Ichiro; Ohura, Takehiko; Kimura, Chu

1989-01-01

Three-dimensional computer tomography (3DCT) was performed in patients with various diseases to visualize stereoscopically the deformity of the craniofacial bones. The data obtained were analyzed by the 3DCT analyzing system. A new coordinate system was established using the median sagittal plane of the face (a plane passing through sella, nasion and basion) on the three-dimensional image. Three-dimensional profilograms were prepared for detailed analysis of the deformation of craniofacial bones for cleft lip and palate, mandibular prognathia and hemifacial microsomia. For patients, asymmetry in the frontal view and twist-formed complicated deformities were observed, as well as deformity of profiles in the anteroposterior and up-and-down directions. A newly developed technique allows three-dimensional visualization of changes in craniofacial deformity. It would aid in determining surgical strategy, including crani-facial surgery and maxillo-facial surgery, and in evaluating surgical outcome. (N.K.)

Pumping vortex into a Bose-Einstein condensate of heteronuclear molecules

International Nuclear Information System (INIS)

Xu, Z F; Wang, R Q; You, L

2009-01-01

Heteronuclear molecules have attracted wide attention due to their permanent electric dipole moments. Analogous to atoms with magnetic dipoles, the existence of nonzero electric dipoles significantly enhances the possibilities and mechanisms for the control and design of quantum degenerate molecule systems with electric (E) fields. This work proposes a vortex creation mechanism inside a condensate of heteronuclear molecules through the adiabatic flipping of the axial bias of an analogous E-field Ioffe-Pritchard trap (IPT), extending the original protocol of Isoshima et al (2000 Phys. Rev. A 61 063610) for an atomic spinor condensate inside a magnetic (B)-field IPT. We provide both analytic proof and numerical simulations to illustrate the high fidelity operation of this vortex pump protocol. We hope our work provides stimulating experimental possibilities for active investigations in quantum degenerate molecule systems.

Dante-Z sequence as selective impulsion in high field mono and multidimensional NMR. Application to the study of proteins, peptides and their interactions

International Nuclear Information System (INIS)

Roumestand, C.; Toma, F.

1992-01-01

DANTE-Z is a simple and efficient way for NMR spectral selection. We present here different applications of DANTE-Z in high-resolution NMR of peptides and proteins. We have been using proton selective excitation by DANTE-Z to perform 1D-correlated (homo- or heteronuclear) experiments corresponding to one line of either 2D or 3D experiments. Following the same scheme, we could also edit planes of 3D experiments by concatenating 1D-correlated experiments with conventional 2D experiments. In the heteronuclear case (i.e. 1 H, 31 P), we could also edit planes of a 4D experiment by the simultaneous selection of 1 H and the X nucleus. Owing to the favourable excitation profile of DANTE-Z, we used it successfully for topological excitations (spectral width from 150 Hz up to 1500 Hz) in 'semi-soft'-2D experiments and 'soft'-2D experiment. These applications are illustrated by the results obtained at 600 MHz on a protein and a phosphonamide peptide

Sine-squared shifted pulses for recoupling interactions in solid-state NMR

Science.gov (United States)

Jain, Mukul G.; Rajalakshmi, G.; Equbal, Asif; Mote, Kaustubh R.; Agarwal, Vipin; Madhu, P. K.

2017-06-01

Rotational-Echo DOuble-Resonance (REDOR) is a versatile experiment for measuring internuclear distance between two heteronuclear spins in solid-state NMR. At slow to intermediate magic-angle spinning (MAS) frequencies, the measurement of distances between strongly coupled spins is challenging due to rapid dephasing of magnetisation. This problem can be remedied by employing the pulse-shifted version of REDOR known as Shifted-REDOR (S-REDOR) that scales down the recoupled dipolar coupling. In this study, we propose a new variant of the REDOR sequence where the positions of the π pulses are determined by a sine-squared function. This new variant has scaling properties similar to S-REDOR. We use theory, numerical simulations, and experiments to compare the dipolar recoupling efficiencies and the experimental robustness of the three REDOR schemes. The proposed variant has advantages in terms of radiofrequency field requirements at fast MAS frequencies.

Three dimensional strained semiconductors

Science.gov (United States)

Voss, Lars; Conway, Adam; Nikolic, Rebecca J.; Leao, Cedric Rocha; Shao, Qinghui

2016-11-08

In one embodiment, an apparatus includes a three dimensional structure comprising a semiconductor material, and at least one thin film in contact with at least one exterior surface of the three dimensional structure for inducing a strain in the structure, the thin film being characterized as providing at least one of: an induced strain of at least 0.05%, and an induced strain in at least 5% of a volume of the three dimensional structure. In another embodiment, a method includes forming a three dimensional structure comprising a semiconductor material, and depositing at least one thin film on at least one surface of the three dimensional structure for inducing a strain in the structure, the thin film being characterized as providing at least one of: an induced strain of at least 0.05%, and an induced strain in at least 5% of a volume of the structure.

Structural Studies of Bcl-xL/ligand Complexes using {sup 19}F NMR

Energy Technology Data Exchange (ETDEWEB)

Yu Liping; Hajduk, Philip J.; Mack, Jamey; Olejniczak, Edward T. [GPRD, Abbott Laboratories, Pharmaceutical Discovery Division (United States)], E-mail: Edward.olejniczak@abbott.com

2006-04-15

Fluorine atoms are often incorporated into drug molecules as part of the lead optimization process in order to improve affinity or modify undesirable metabolic and pharmacokinetic profiles. From an NMR perspective, the abundance of fluorinated drug leads provides an exploitable niche for structural studies using {sup 19}F NMR in the drug discovery process. As {sup 19}F has no interfering background signal from biological sources, {sup 19}F NMR studies of fluorinated drugs bound to their protein receptors can yield easily interpretable and unambiguous structural constraints. {sup 19}F can also be selectively incorporated into proteins to obtain additional constraints for structural studies. Despite these advantages, {sup 19}F NMR has rarely been exploited for structural studies due to its broad lines in macromolecules and their ligand complexes, leading to weak signals in {sup 1}H/{sup 19}F heteronuclear NOE experiments. Here we demonstrate several different experimental strategies that use {sup 19}F NMR to obtain ligand-protein structural constraints for ligands bound to the anti-apoptotic protein Bcl-xL, a drug target for anti-cancer therapy. These examples indicate the applicability of these methods to typical structural problems encountered in the drug development process.

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.

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).

Three-dimensional, three-component wall-PIV

Science.gov (United States)

Berthe, André; Kondermann, Daniel; Christensen, Carolyn; Goubergrits, Leonid; Garbe, Christoph; Affeld, Klaus; Kertzscher, Ulrich

2010-06-01

This paper describes a new time-resolved three-dimensional, three-component (3D-3C) measurement technique called wall-PIV. It was developed to assess near wall flow fields and shear rates near non-planar surfaces. The method is based on light absorption according to Beer-Lambert’s law. The fluid containing a molecular dye and seeded with buoyant particles is illuminated by a monochromatic, diffuse light. Due to the dye, the depth of view is limited to the near wall layer. The three-dimensional particle positions can be reconstructed by the intensities of the particle’s projection on an image sensor. The flow estimation is performed by a new algorithm, based on learned particle trajectories. Possible sources of measurement errors related to the wall-PIV technique are analyzed. The accuracy analysis was based on single particle experiments and a three-dimensional artificial data set simulating a rotating sphere.

Rapid and novel discrimination and quantification of oleanolic and ursolic acids in complex plant extracts using two-dimensional nuclear magnetic resonance spectroscopy-Comparison with HPLC methods

International Nuclear Information System (INIS)

Kontogianni, Vassiliki G.; Exarchou, Vassiliki; Troganis, Anastassios; Gerothanassis, Ioannis P.

2009-01-01

A novel strategy for NMR analysis of mixtures of oleanolic and ursolic acids that occur in natural products is described. These important phytochemicals have similar structure and their discrimination and quantification is rather difficult. We report herein the combined use of proton-carbon heteronuclear single-quantum coherence ( 1 H- 13 C HSQC) and proton-carbon heteronuclear multiple-bond correlation ( 1 H- 13 C HMBC) NMR spectroscopy, in the identification and quantitation of oleanolic acid (OA) and ursolic acid (UA)in plant extracts of the Lamiaceae and Oleaceae family. The combination of 1 H- 13 C HSQC and 1 H- 13 C HMBC techniques allows the connection of the proton and carbon-13 spins across the molecular backbone resulting in the identification and, thus, discrimination of oleanolic and ursolic acid without resorting to physicochemical separation of the components. The quantitative results provided by 2D 1 H- 13 C HSQC NMR data were obtained within a short period of time (∼14 min) and are in excellent agreement with those obtained by HPLC, which support the efficiency of the suggested methodology

Two-Dimensional NMR Evidence for Cleavage of Lignin and Xylan Substituents in Wheat Straw Through Hydrothermal Pretreatment and Enzymatic Hydrolysis

Science.gov (United States)

Daniel J. Yelle; Prasad Kaparaju; Christopher G. Hunt; Kolby Hirth; Hoon Kim; John Ralph; Claus Felby

2012-01-01

Solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy of plant cell walls is a powerful tool for characterizing changes in cell wall chemistry during the hydrothermal pretreatment process of wheat straw for second-generation bioethanol production. One-bond 13C-1H NMR correlation spectroscopy, via...

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.)

Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins.

Science.gov (United States)

Traaseth, Nathaniel J; Chao, Fa-An; Masterson, Larry R; Mangia, Silvia; Garwood, Michael; Michaeli, Shalom; Seelig, Burckhard; Veglia, Gianluigi

2012-06-01

NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R(1ρ) and Carr-Purcell-Meiboom-Gill (CPMG) R(2) experiments are commonly used to characterize μs to ms dynamics, which play a critical role in enzyme folding and catalysis. In an effort to complement these approaches, we introduced the Heteronuclear Adiabatic Relaxation Dispersion (HARD) method, where dispersion in rotating frame relaxation rate constants (longitudinal R(1ρ) and transverse R(2ρ)) is created by modulating the shape and duration of adiabatic full passage (AFP) pulses. Previously, we showed the ability of the HARD method to detect chemical exchange dynamics in the fast exchange regime (k(ex)∼10(4)-10(5) s(-1)). In this article, we show the sensitivity of the HARD method to slower exchange processes by measuring R(1ρ) and R(2ρ) relaxation rates for two soluble proteins (ubiquitin and 10C RNA ligase). One advantage of the HARD method is its nominal dependence on the applied radio frequency field, which can be leveraged to modulate the dispersion in the relaxation rate constants. In addition, we also include product operator simulations to define the dynamic range of adiabatic R(1ρ) and R(2ρ) that is valid under all exchange regimes. We conclude from both experimental observations and simulations that this method is complementary to CPMG-based and rotating frame spin-lock R(1ρ) experiments to probe conformational exchange dynamics for biomolecules. Finally, this approach is germane to several NMR-active nuclei, where relaxation rates are frequency-offset independent. Copyright © 2012 Elsevier Inc. All rights reserved.

Solution NMR study of the yeast cytochrome c peroxidase: cytochrome c interaction

Energy Technology Data Exchange (ETDEWEB)

Volkov, Alexander N., E-mail: ovolkov@vub.ac.be; Nuland, Nico A. J. van [Vrije Universiteit Brussel, Jean Jeener NMR Centre, Structural Biology Brussels (Belgium)

2013-07-15

Here we present a solution NMR study of the complex between yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP), a paradigm for understanding the biological electron transfer. Performed for the first time, the CcP-observed heteronuclear NMR experiments were used to probe the Cc binding in solution. Combining the Cc- and CcP-detected experiments, the binding interface on both proteins was mapped out, confirming that the X-ray structure of the complex is maintained in solution. Using NMR titrations and chemical shift perturbation analysis, we show that the interaction is independent of the CcP spin-state and is only weakly affected by the Cc redox state. Based on these findings, we argue that the complex of the ferrous Cc and the cyanide-bound CcP is a good mimic of the catalytically-active Cc-CcP compound I species. Finally, no chemical shift perturbations due to the Cc binding at the low-affinity CcP site were observed at low ionic strength. We discuss possible reasons for the absence of the effects and outline future research directions.

Two-dimensional NMR investigations of the dynamic conformations of phospholipids and liquid crystals

Energy Technology Data Exchange (ETDEWEB)

Hong, Mei [Univ. of California, Berkeley, CA (United States). Applied Science and Technology

1996-05-01

Two-dimensional 13C, 1H, and 31P nuclear magnetic resonance (NMR) techniques are developed and used to study molecular structure and dynamics in liquid-crystalline systems, primarily phospholipids and nematic liquid crystals. NMR spectroscopy characterizes molecular conformation in terms of orientations and distances of molecular segments. In anisotropically mobile systems, this is achieved by measuring motionally-averaged nuclear dipolar couplings and chemical shift anisotropies. The short-range couplings yield useful bond order parameters, while the long-range interactions constrain the overall conformation. In this work, techniques for probing proton dipolar local fields are further developed to obtain highlyresolved dipolar couplings between protons and rare spins. By exploiting variable-angle sample spinning techniques, orientation-sensitive NMR spectra are resolved according to sitespecific isotropic chemical shifts. Moreover, the signs and magnitudes of various short-range dipolar couplings are obtained. They are used in novel theoretical analyses that provide information about segmental orientations and their distributions. Such information is obtained in a model-independent fashion or with physically reasonable assumptions. The structural investigation of phospholipids is focused on the dynam

Simultaneous acquisition of three NMR spectra in a single ...

Indian Academy of Sciences (India)

Simultaneous acquisition of three NMR spectra in a single experiment ... set, which is based on a combination of different fast data acquisition techniques such as G-matrix ..... The sign and intensity of the CHn resonance depends on the delay.

Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets

International Nuclear Information System (INIS)

Bellstedt, Peter; Seiboth, Thomas; Häfner, Sabine; Kutscha, Henriette; Ramachandran, Ramadurai; Görlach, Matthias

2013-01-01

NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though heteronuclear through-bond correlation methods are available for that purpose, challenging situations arise in cases where the protein in question only yields samples of limited concentration and/or stability. Here we present a strategy based upon specific individual unlabeling of all 20 standard amino acids to complement standard NMR experiments and to achieve unambiguous backbone assignments for the fast precipitating 23 kDa catalytic domain of human aprataxin of which only incomplete standard NMR data sets could be obtained. Together with the validation of this approach utilizing the protein GB1 as a model, a comprehensive insight into metabolic interconversion ('scrambling”) of NH and CO groups in a standard Escherichia coli expression host is provided

Three-dimensional effects in fracture mechanics

International Nuclear Information System (INIS)

Benitez, F.G.

1991-01-01

An overall view of the pioneering theories and works, which enlighten the three-dimensional nature of fracture mechanics during the last years is given. the main aim is not an exhaustive reviewing but the displaying of the last developments on this scientific field in a natural way. This work attempts to envisage the limits of disregarding the three-dimensional behaviour in theories, analyses and experiments. Moreover, it tries to draw attention on the scant fervour, although increasing, this three-dimensional nature of fracture has among the scientific community. Finally, a constructive discussion is presented on the use of two-dimensional solutions in the analysis of geometries which bear a three-dimensional configuration. the static two-dimensional solutions and its applications fields are reviewed. also, the static three-dimensional solutions, wherein a comparative analysis with elastoplastic and elastostatic solutions are presented. to end up, the dynamic three-dimensional solutions are compared to the asymptotic two-dimensional ones under the practical applications point of view. (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. PMID:18926747

Biological activities of a new compound isolated from the aerial parts ...

African Journals Online (AJOL)

A new compound trivially named vitexcarpan was isolated from the ethyl acetate fraction of Vitex agnus castus. The structure of compound was elucidated with the help of spectroscopic techniques: 13C NMR, 1H NMR, heteronuclear multiple bond correlation (HMBC), heteronuclear multiple quantum coherence (HMQC), ...

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

Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

Energy Technology Data Exchange (ETDEWEB)

Zhang, Zhiyong [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel); Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005 (China); Smith, Pieter E. S.; Frydman, Lucio, E-mail: lucio.frydman@weizmann.ac.il [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel)

2014-11-21

Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns.

Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

International Nuclear Information System (INIS)

Zhang, Zhiyong; Smith, Pieter E. S.; Frydman, Lucio

2014-01-01

Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns

Heteronuclear Micro-Helmholtz Coil Facilitates µm-Range Spatial and Sub-Hz Spectral Resolution NMR of nL-Volume Samples on Customisable Microfluidic Chips.

Directory of Open Access Journals (Sweden)

Nils Spengler

Full Text Available We present a completely revised generation of a modular micro-NMR detector, featuring an active sample volume of ∼ 100 nL, and an improvement of 87% in probe efficiency. The detector is capable of rapidly screening different samples using exchangeable, application-specific, MEMS-fabricated, microfluidic sample containers. In contrast to our previous design, the sample holder chips can be simply sealed with adhesive tape, with excellent adhesion due to the smooth surfaces surrounding the fluidic ports, and so withstand pressures of ∼2.5 bar, while simultaneously enabling high spectral resolution up to 0.62 Hz for H2O, due to its optimised geometry. We have additionally reworked the coil design and fabrication processes, replacing liquid photoresists by dry film stock, whose final thickness does not depend on accurate volume dispensing or precise levelling during curing. We further introduced mechanical alignment structures to avoid time-intensive optical alignment of the chip stacks during assembly, while we exchanged the laser-cut, PMMA spacers by diced glass spacers, which are not susceptible to melting during cutting. Doing so led to an overall simplification of the entire fabrication chain, while simultaneously increasing the yield, due to an improved uniformity of thickness of the individual layers, and in addition, due to more accurate vertical positioning of the wirebonded coils, now delimited by a post base plateau. We demonstrate the capability of the design by acquiring a 1H spectrum of ∼ 11 nmol sucrose dissolved in D2O, where we achieved a linewidth of 1.25 Hz for the TSP reference peak. Chemical shift imaging experiments were further recorded from voxel volumes of only ∼ 1.5 nL, which corresponded to amounts of just 1.5 nmol per voxel for a 1 M concentration. To extend the micro-detector to other nuclei of interest, we have implemented a trap circuit, enabling heteronuclear spectroscopy, demonstrated by two 1H/13C 2D HSQC

Three-dimensional neuroimaging

International Nuclear Information System (INIS)

Toga, A.W.

1990-01-01

This book reports on new neuroimaging technologies that are revolutionizing the study of the brain be enabling investigators to visualize its structure and entire pattern of functional activity in three dimensions. The book provides a theoretical and practical explanation of the new science of creating three-dimensional computer images of the brain. The coverage includes a review of the technology and methodology of neuroimaging, the instrumentation and procedures, issues of quantification, analytic protocols, and descriptions of neuroimaging systems. Examples are given to illustrate the use of three-dimensional enuroimaging to quantitate spatial measurements, perform analysis of autoradiographic and histological studies, and study the relationship between brain structure and function

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

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

REDOR NMR of stable-isotope-labeled protein binding sites

Energy Technology Data Exchange (ETDEWEB)

Schaefer, J. [Washington Univ., St. Louis, MO (United States)

1994-12-01

Rotational-echo, double resonance (REDOR) NMR, a new analytical spectroscopic technique for solids spinning at the magic angle, has been developed over the last 5 years. REDOR provides a direct measure of heteronuclear dipolar coupling between isolated pairs of labeled nuclei. In a solid with a {sup 13}C-{sup 15}N labeled pair, for example, the {sup 13}C rotational echoes that form each rotor period following a{sup 1}H-{sup 13}C cross-polarization transfer can be prevented from reaching full intensity by insertion of a {sup 15}N {pi} pulse each half rotor period. The REDOR difference (the difference between a {sup 13}C NMR spectrum obtained under these conditions and one obtained with no {sup 15}N {pi} pulses) has a strong dependence on the {sup 13}C-{sup 15}N dipolar coupling, and hence, the {sup 13}C-{sup 15}N internuclear distance. REDOR is described as double-resonance even though three radio frequencies (typically {sup 1}H, {sup 13}C, and {sup 15}N) are used because the protons are removed from the important evolution part of the experiment by resonant decoupling. The dephasing of magnetization in REDOR arises from a local dipolar {sup 13}C-{sup 15}N field gradient and involves no polarization transfer. REDOR has no dependence on {sup 13}C or {sup 15}N chemical-shift tensors and does not require resolution of a {sup 13}C-{sup 15}N coupling in the chemical-shift dimension.

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.

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.

Measurement and Characterization of Hydrogen-Deuterium Exchange Chemistry Using Relaxation Dispersion NMR Spectroscopy.

Science.gov (United States)

Khirich, Gennady; Holliday, Michael J; Lin, Jasper C; Nandy, Aditya

2018-03-01

One-dimensional heteronuclear relaxation dispersion NMR spectroscopy at 13 C natural abundance successfully characterized the dynamics of the hydrogen-deuterium exchange reaction occurring at the N ε position in l-arginine by monitoring C δ in varying amounts of D 2 O. A small equilibrium isotope effect was observed and quantified, corresponding to ΔG = -0.14 kcal mol -1 . A bimolecular rate constant of k D = 5.1 × 10 9 s -1 M -1 was determined from the pH*-dependence of k ex (where pH* is the direct electrode reading of pH in 10% D 2 O and k ex is the nuclear spin exchange rate constant), consistent with diffusion-controlled kinetics. The measurement of ΔG serves to bridge the millisecond time scale lifetimes of the detectable positively charged arginine species with the nanosecond time scale lifetime of the nonobservable low-populated neutral arginine intermediate species, thus allowing for characterization of the equilibrium lifetimes of the various arginine species in solution as a function of fractional solvent deuterium content. Despite the system being in fast exchange on the chemical shift time scale, the magnitude of the secondary isotope shift due to the exchange reaction at N ε was accurately measured to be 0.12 ppm directly from curve-fitting D 2 O-dependent dispersion data collected at a single static field strength. These results indicate that relaxation dispersion NMR spectroscopy is a robust and general method for studying base-catalyzed hydrogen-deuterium exchange chemistry at equilibrium.

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.

Pulsed zero field NMR of solids and liquid crystals

International Nuclear Information System (INIS)

Thayer, A.M.

1987-02-01

This work describes the development and applications to solids and liquid crystals of zero field nuclear magnetic resonance (NMR) experiments with pulsed dc magnetic fields. Zero field NMR experiments are one approach for obtaining high resolution spectra of amorphous and polycrystalline materials which normally (in high field) display broad featureless spectra. The behavior of the spin system can be coherently manipulated and probed in zero field with dc magnetic field pulses which are employed in a similar manner to radiofrequency pulses in high field NMR experiments. Nematic phases of liquid crystalline systems are studied in order to observe the effects of the removal of an applied magnetic field on sample alignment and molecular order parameters. In nematic phases with positive and negative magnetic susceptibility anisotropies, a comparison between the forms of the spin interactions in high and low fields is made. High resolution zero field NMR spectra of unaligned smectic samples are also obtained and reflect the symmetry of the liquid crystalline environment. These experiments are a sensitive measure of the motionally induced asymmetry in biaxial phases. Homonuclear and heteronuclear solute spin systems are compared in the nematic and smectic phases. Nonaxially symmetric dipolar couplings are reported for several systems. The effects of residual fields in the presence of a non-zero asymmetry parameter are discussed theoretically and presented experimentally. Computer programs for simulations of these and other experimental results are also reported. 179 refs., 75 figs

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

Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

KAUST Repository

Yagi, Hiromasa

2013-06-01

Site-specific attachment of paramagnetic lanthanide ions to a protein generates pseudocontact shifts (PCS) in the nuclear magnetic resonance (NMR) spectra of the protein that are easily measured as changes in chemical shifts. By labeling the protein with lanthanide tags at four different sites, PCSs are observed for most amide protons and accurate information is obtained about their coordinates in three-dimensional space. The approach is demonstrated with the chaperone ERp29, for which large differences have been reported between X-ray and NMR structures of the C-terminal domain, ERp29-C. The results unambiguously show that the structure of rat ERp29-C in solution is similar to the crystal structure of human ERp29-C. PCSs of backbone amides were the only structural restraints required. Because these can be measured for more dilute protein solutions than other NMR restraints, the approach greatly widens the range of proteins amenable to structural studies in solution. © 2013 Elsevier Ltd. All rights reserved.

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

Three dimensional canonical transformations

International Nuclear Information System (INIS)

Tegmen, A.

2010-01-01

A generic construction of canonical transformations is given in three-dimensional phase spaces on which Nambu bracket is imposed. First, the canonical transformations are defined as based on cannonade transformations. Second, it is shown that determination of the generating functions and the transformation itself for given generating function is possible by solving correspondent Pfaffian differential equations. Generating functions of type are introduced and all of them are listed. Infinitesimal canonical transformations are also discussed as the complementary subject. Finally, it is shown that decomposition of canonical transformations is also possible in three-dimensional phase spaces as in the usual two-dimensional ones.

Trace level detection of compounds related to the chemical weapons convention by 1H-detected 13C NMR spectroscopy executed with a sensitivity-enhanced, cryogenic probehead.

Science.gov (United States)

Cullinan, David B; Hondrogiannis, George; Henderson, Terry J

2008-04-15

Two-dimensional 1H-13C HSQC (heteronuclear single quantum correlation) and fast-HMQC (heteronuclear multiple quantum correlation) pulse sequences were implemented using a sensitivity-enhanced, cryogenic probehead for detecting compounds relevant to the Chemical Weapons Convention present in complex mixtures. The resulting methods demonstrated exceptional sensitivity for detecting the analytes at trace level concentrations. 1H-13C correlations of target analytes at chemical shift information could be derived quickly and simultaneously from the resulting spectra. The fast-HMQC pulse sequences generated magnitude mode spectra suitable for detailed analysis in approximately 4.5 h and can be used in experiments to efficiently screen a large number of samples. The HSQC pulse sequences, on the other hand, required roughly twice the data acquisition time to produce suitable spectra. These spectra, however, were phase-sensitive, contained considerably more resolution in both dimensions, and proved to be superior for detecting analyte 1H-13C correlations. Furthermore, a HSQC spectrum collected with a multiplicity-edited pulse sequence provided additional structural information valuable for identifying target analytes. The HSQC pulse sequences are ideal for collecting high-quality data sets with overnight acquisitions and logically follow the use of fast-HMQC pulse sequences to rapidly screen samples for potential target analytes. Use of the pulse sequences considerably improves the performance of NMR spectroscopy as a complimentary technique for the screening, identification, and validation of chemical warfare agents and other small-molecule analytes present in complex mixtures and environmental samples.

Three-dimensional microbubble streaming flows

Science.gov (United States)

Rallabandi, Bhargav; Marin, Alvaro; Rossi, Massimiliano; Kaehler, Christian; Hilgenfeldt, Sascha

2014-11-01

Streaming due to acoustically excited bubbles has been used successfully for applications such as size-sorting, trapping and focusing of particles, as well as fluid mixing. Many of these applications involve the precise control of particle trajectories, typically achieved using cylindrical bubbles, which establish planar flows. Using astigmatic particle tracking velocimetry (APTV), we show that, while this two-dimensional picture is a useful description of the flow over short times, a systematic three-dimensional flow structure is evident over long time scales. We demonstrate that this long-time three-dimensional fluid motion can be understood through asymptotic theory, superimposing secondary axial flows (induced by boundary conditions at the device walls) onto the two-dimensional description. This leads to a general framework that describes three-dimensional flows in confined microstreaming systems, guiding the design of applications that profit from minimizing or maximizing these effects.

Two-dimensional NMR spectroscopy strongly enhances soil organic matter composition analysis

Science.gov (United States)

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

2016-04-01

Soil organic matter (SOM) is the largest terrestrial carbon pool and strongly affects soil properties. With climate change, understanding SOM processes and turnover and how they could be affected by increasing temperatures becomes critical. This is particularly key for organic soils as they represent a huge carbon pool in very sensitive ecosystems, like boreal ecosystems and peatlands. Nevertheless, characterization of SOM molecular composition, which is essential to elucidate soil carbon processes, is not easily achieved, and further advancements in that area are greatly needed. Solid-state one-dimensional (1D) 13C nuclear magnetic resonance (NMR) spectroscopy is often used to characterize its molecular composition, but only provides data on a few major functional groups, which regroup many different molecular fragments. For instance, 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. Here we show that two-dimensional (2D) liquid-state 1H-13C NMR spectra provided much richer data on the composition of boreal plant litter and organic surface soil. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra and displayed signals from hundreds of identifiable molecular groups. For example, in the aromatics region, signals from individual lignin units could be recognized. It was hence possible to follow the fate of specific structural moieties in soils. We observed differences between litter and soil samples, and were able to relate them to the decomposition of identifiable moieties. Sample preparation and data acquisition were both simple and fast. Further, using multivariate data analysis, we aimed at linking the detailed chemical fingerprints of SOM to turnover rates in a soil incubation experiment. With the multivariate models, we were able to identify specific molecular

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.

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...

Simulations of NMR pulse sequences during equilibrium and non-equilibrium chemical exchange

International Nuclear Information System (INIS)

Helgstrand, Magnus; Haerd, Torleif; Allard, Peter

2000-01-01

The McConnell equations combine the differential equations for a simple two-state chemical exchange process with the Bloch differential equations for a classical description of the behavior of nuclear spins in a magnetic field. This equation system provides a useful starting point for the analysis of slow, intermediate and fast chemical exchange studied using a variety of NMR experiments. The McConnell equations are in the mathematical form of an inhomogeneous system of first-order differential equations. Here we rewrite the McConnell equations in a homogeneous form in order to facilitate fast and simple numerical calculation of the solution to the equation system. The McConnell equations can only treat equilibrium chemical exchange. We therefore also present a homogeneous equation system that can handle both equilibrium and non-equilibrium chemical processes correctly, as long as the kinetics is of first-order. Finally, the same method of rewriting the inhomogeneous form of the McConnell equations into a homogeneous form is applied to a quantum mechanical treatment of a spin system in chemical exchange. In order to illustrate the homogeneous McConnell equations, we have simulated pulse sequences useful for measuring exchange rates in slow, intermediate and fast chemical exchange processes. A stopped-flow NMR experiment was simulated using the equations for non-equilibrium chemical exchange. The quantum mechanical treatment was tested by the simulation of a sensitivity enhanced 15 N-HSQC with pulsed field gradients during slow chemical exchange and by the simulation of the transfer efficiency of a two-dimensional heteronuclear cross-polarization based experiment as a function of both chemical shift difference and exchange rate constants

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.

Hydrogen and deuterium NMR of solids by magic-angle spinning

International Nuclear Information System (INIS)

Eckman, R.R.

1982-10-01

The nuclear magnetic resonance of solids has long been characterized by very large specral broadening which arises from internuclear dipole-dipole coupling or the nuclear electric quadrupole interaction. These couplings can obscure the smaller chemical shift interaction and make that information unavailable. Two important and difficult cases are that of hydrogen and deuterium. The development of cross polarization, heteronuclear radiofrequency decoupling, and coherent averaging of nuclear spin interactions has provided measurement of chemical shift tensors in solids. Recently, double quantum NMR and double quantum decoupling have led to measurement of deuterium and proton chemical shift tensors, respectively. A general problem of these experiments is the overlapping of the tensor powder pattern spectra of magnetically distinct sites which cannot be resolved. In this work, high resolution NMR of hydrogen and deuterium in solids is demonstrated. For both nuclei, the resonances are narrowed to obtain liquid-like isotropic spectra by high frequency rotation of the sample about an axis inclined at the magic angle, β/sub m/ = Arccos (3/sup -1/2/), with respect to the direction of the external magnetic field. For deuterium, the powder spectra were narrowed by over three orders of magnitude by magic angle rotation with precise control of β. A second approach was the observation of deuterium double quantum transitions under magic angle rotation. For hydrogen, magic angle rotation alone could be applied to obtain the isotropic spectrum when H/sub D/ was small. This often occurs naturally when the nuclei are semi-dilute or involved in internal motion. In the general case of large H/sub D/, isotropic spectra were obtained by dilution of 1 H with 2 H combined with magic angle rotation. The resolution obtained represents the practical limit for proton NMR of solids

Trifasciatosides A-J, Steroidal Saponins from Sansevieria trifasciata.

Science.gov (United States)

Teponno, Rémy Bertrand; Tanaka, Chiaki; Jie, Bai; Tapondjou, Léon Azefack; Miyamoto, Tomofumi

2016-01-01

Four previously unreported steroidal saponins, trifasciatosides A-D (1-4), three pairs of previously undescribed steroidal saponins, trifasciatosides E-J (5a, b-7a, b) including acetylated ones, together with twelve known compounds were isolated from the n-butanol soluble fraction of the methanol extract of Sansevieria trifasciata. Their structures were elucidated on the basis of detailed spectroscopic analysis, including (1)H-NMR, (13)C-NMR, (1)H-(1)H correlated spectroscopy (COSY), heteronuclear single quantum coherence (HSQC), heteronuclear multiple bond connectivity (HMBC), total correlated spectroscopy (TOCSY), nuclear Overhauser enhancement and exchange spectroscopy (NOESY), electrospray ionization-time of flight (ESI-TOF)-MS and chemical methods. Compounds 2, 4, and 7a, b exhibited moderate antiproliferative activity against HeLa cells.

Hyphenation of solid-phase extraction with liquid chromatography and nuclear magnetic resonance: application of HPLC-DAD-SPE-NMR to identification of constituents of Kanahia laniflora.

Science.gov (United States)

Clarkson, Cailean; Staerk, Dan; Hansen, Steen Honoré; Jaroszewski, Jerzy W

2005-06-01

The introduction of on-line solid-phase extraction (SPE) in HPLC-NMR has dramatically enhanced the sensitivity of this technique by concentration of the analytes in a small-volume NMR flow cell and by increasing the amount of the analyte by multiple peak trapping. In this study, the potential of HPLC-DAD-SPE-NMR hyphenation was demonstrated by structure determination of complex constituents of flower, leaf, root, and stem extracts of an African medicinal plant Kanahia laniflora. The technique was shown to allow acquisition of high-quality homo- and heteronuclear 2D NMR data following analytical-scale HPLC separation of extract constituents. Four flavonol glycosides [kaempferol 3-O-(6-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside; kaempferol 3-O-(2,6-di-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside; quercetin 3-O-(2,6-di-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside (rutin); and isorhamnetin, 3-O-(6-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside] and three 5alpha-cardenolides [coroglaucigenin 3-O-6-deoxy-beta-d-allopyranoside; coroglaucigenin 3-O-(4-O-beta-d-glucopyranosyl)-6-deoxy-beta-d-glucopyranoside; 3'-O-acetyl-3'-epiafroside] were identified, with complete assignments of 1H and 13C resonances based on HSQC and HMBC spectra whenever required. Confirmation of the structures was provided by HPLC-MS data. The HPLC-DAD-SPE-NMR technique therefore speeds up the dereplication of complex mixtures of natural origin significantly, by characterization of individual extract components prior to preparative isolation work.

Long-range dispersion interactions. I. Formalism for two heteronuclear atoms

International Nuclear Information System (INIS)

Zhang, J.-Y.; Mitroy, J.

2007-01-01

A general procedure for systematically evaluating the long-range dispersion interaction between two heteronuclear atoms in arbitrary states is outlined. The C 6 dispersion parameter can always be written in terms of sum rules involving oscillator strengths only and formulas for a number of symmetry cases are given. The dispersion coefficients for excited alkali-metal atoms interacting with the ground-state H and He are tabulated

Adiabatic fast passage application in solid state NMR study of cross relaxation and molecular dynamics in heteronuclear systems.

Science.gov (United States)

Baranowski, M; Woźniak-Braszak, A; Jurga, K

2016-01-01

The paper presents the benefits of using fast adiabatic passage for the study of molecular dynamics in the solid state heteronuclear systems in the laboratory frame. A homemade pulse spectrometer operating at the frequency of 30.2MHz and 28.411MHz for protons and fluorines, respectively, has been enhanced with microcontroller direct digital synthesizer DDS controller [1-4]. This work briefly describes how to construct a low-cost and easy-to-assemble adiabatic extension set for homemade and commercial spectrometers based on recently very popular Arduino shields. The described set was designed for fast adiabatic generation. Timing and synchronization problems are discussed. The cross-relaxation experiments with different initial states of the two spin systems have been performed. Contrary to our previous work [5] where the steady-state NOE experiments were conducted now proton spins (1)H are polarized in the magnetic field B0 while fluorine spins (19)F are perturbed by selective saturation for a short time and then the system is allowed to evolve for a period in the absence of a saturating field. The adiabatic passage application leads to a reversal of magnetization of fluorine spins and increases the amplitude of the signal. Copyright © 2015 Elsevier Inc. All rights reserved.

Three-dimensional magnetospheric equilibrium with isotropic pressure

International Nuclear Information System (INIS)

Cheng, C.Z.

1995-05-01

In the absence of the toroidal flux, two coupled quasi two-dimensional elliptic equilibrium equations have been derived to describe self-consistent three-dimensional static magnetospheric equilibria with isotropic pressure in an optimal (Ψ,α,χ) flux coordinate system, where Ψ is the magnetic flux function, χ is a generalized poloidal angle, α is the toroidal angle, α = φ - δ(Ψ,φ,χ) is the toroidal angle, δ(Ψ,φ,χ) is periodic in φ, and the magnetic field is represented as rvec B = ∇Ψ x ∇α. A three-dimensional magnetospheric equilibrium code, the MAG-3D code, has been developed by employing an iterative metric method. The main difference between the three-dimensional and the two-dimensional axisymmetric solutions is that the field-aligned current and the toroidal magnetic field are finite for the three-dimensional case, but vanish for the two-dimensional axisymmetric case. With the same boundary flux surface shape, the two-dimensional axisymmetric results are similar to the three-dimensional magnetosphere at each local time cross section

Three dimensional visualization of medical images

International Nuclear Information System (INIS)

Suto, Yasuzo

1992-01-01

Three dimensional visualization is a stereoscopic technique that allows the diagnosis and treatment of complicated anatomy site of the bone and organ. In this article, the current status and technical application of three dimensional visualization are introduced with special reference to X-ray CT and MRI. The surface display technique is the most common for three dimensional visualization, consisting of geometric model, voxel element, and stereographic composition techniques. Recent attention has been paid to display method of the content of the subject called as volume rendering, whereby information on the living body is provided accurately. The application of three dimensional visualization is described in terms of diagnostic imaging and surgical simulation. (N.K.)

(Weakly) three-dimensional caseology

International Nuclear Information System (INIS)

Pomraning, G.C.

1996-01-01

The singular eigenfunction technique of Case for solving one-dimensional planar symmetry linear transport problems is extended to a restricted class of three-dimensional problems. This class involves planar geometry, but with forcing terms (either boundary conditions or internal sources) which are weakly dependent upon the transverse spatial variables. Our analysis involves a singular perturbation about the classic planar analysis, and leads to the usual Case discrete and continuum modes, but modulated by weakly dependent three-dimensional spatial functions. These functions satisfy parabolic differential equations, with a different diffusion coefficient for each mode. Representative one-speed time-independent transport problems are solved in terms of these generalised Case eigenfunctions. Our treatment is very heuristic, but may provide an impetus for more rigorous analysis. (author)

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)

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

Production of three-dimensional structures of PHB using selective laser sintering

International Nuclear Information System (INIS)

Pereira, Tatiana F.; Costa, Marysilvia F.; Thire, Rossana M.S.M.; Oliveira, Marcelo F.; Maia, Izaque A.; Silva, Jorge V.L.

2011-01-01

Selective Laser Sintering (SLS) is a technology of layer-by-layer fabrication of three-dimensional physical models directly from their computational design. The poly(3-hydroxybutyrate) (PHB) is a microbial, biodegradable and semicrystalline polyester. The objective of this work was to produce PHB parts, evaluating the reuse of material in the production of the new parts. Images of SEM of part surface showed the formation of neck that indicates sintering between PHB particles during processing. Analysis of NMR and DSC of the reused polymer showed no changes in the chemical structure and thermal properties of PHB. The parts produced from virgin and reused PHB showed no significant difference in their thermal properties. This could suggest that the reuse of raw material did not influence the process reproducibility. (author)

Natural abundance 15N NMR assignments delineate structural differences between intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

Science.gov (United States)

Krishnamoorthi, R; Nemmers, S; Tobias, B

1992-06-15

15N NMR assignments were made to the backbone amide nitrogen atoms at natural isotopic abundance of intact and reactive-site (Arg5-Ile6) hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III and CMTI-III*, respectively) by means of 2D proton-detected heteronuclear single bond chemical shift correlation (HSBC) spectroscopy, utilizing the previously made sequence-specific 1H NMR assignments (Krishnamoorthi et al. (1992) Biochemistry 31, 898-904). Comparison of the 15N chemical shifts of the two forms of the inhibitor molecule revealed significant changes not only for residues located near the reactive-site region, but also for those distantly located. Residues Cys3, Arg5, Leu7, Met8, Cys10, Cys16, Glu19, His25, Tyr27, Cys28 and Gly29 showed significant chemical shift changes ranging from 0.3 to 6.1 ppm, thus indicating structural perturbations that were transmitted throughout the molecule. These findings confirm the earlier conclusions based on 1H NMR investigations.

Determination of relative configurations and conformations of oxindole alkaloids from Uncaria guianensis by NMR; Determinacao por RMN das configuracoes relativas e conformacoes de alcaloides oxindolicos isolados de Uncaria guianensis

Energy Technology Data Exchange (ETDEWEB)

Carbonezi, Carlos Alberto; Hamerski, Lidilhone; Flausino Junior, Otavio Aparecido; Furlan, Maysa; Bolzani, Vanderlan da Silva [UNESP, Araraquara, SP (Brazil). Inst. de Quimica]. E-mail: bolzaniv@iq.unesp.br; Young, Maria Claudia Marx [Instituto de Botanica, Sao Paulo, SP (Brazil). Secao de Fisiologia e Bioquimica de Plantas

2004-12-01

Phytochemical studies with leaves of Uncaria guianensis resulted in the isolation of the oxindole alkaloids isomitraphylline (1), 3-isoajmalicine (2) mitraphylline (3), and isomitraphylinic acid (4). Structural assignments of these alkaloids, including relative configurations and conformations, were performed through spectral data and physical properties. 1D and 2D homonuclear and heteronuclear NMR spectroscopy was a valuable tool for the establishment of the relative stereochemistry of those compounds. (author)

Two-dimensional NMR spectroscopy of 13C methanol at less than 5 μT

Science.gov (United States)

Shim, Jeong Hyun; Lee, Seong-Joo; Hwang, Seong-min; Yu, Kwon-Kyu; Kim, Kiwoong

2014-09-01

Two-dimensional (2D) spectroscopy is one of the most significant applications of nuclear magnetic resonance (NMR). Here, we demonstrate that the 2D NMR can be performed even at a low magnetic field of less than 5 μT, which is ten times less than the Earth’s magnetic field. The pulses used in the experiment were composed of circularly polarized fields for coherent as well as wideband excitations. Since the excitation band covers the entire spectral range, the simplest two-pulse sequence delivered the full 2D spectrum. At 5 μT, methanol with 13C enriched up to 99% belongs to a strongly coupled regime, and thus its 2D spectrum exhibits complicated spectral correlations, which can be exploited as a fingerprint in chemical analysis. In addition, we show that, with compressive sensing, the acquisition of the 2D spectrum can be accelerated to take only 45% of the overall duration.

Three-dimensional particle image velocimetry measurement technique

International Nuclear Information System (INIS)

Hassan, Y.A.; Seeley, C.H.; Henderson, J.A.; Schmidl, W.D.

2004-01-01

The experimental flow visualization tool, Particle Image Velocimetry (PIV), is being used to determine the velocity field in two-dimensional fluid flows. In the past few years, the technique has been improved to allow the capture of flow fields in three dimensions. This paper describes changes which were made to two existing two-dimensional tracking algorithms to enable them to track three-dimensional PIV data. Results of the tests performed on these three-dimensional routines with synthetic data are presented. Experimental data was also used to test the tracking algorithms. The test setup which was used to acquire the three-dimensional experimental data is described, along with the results from both of the tracking routines which were used to analyze the experimental data. (author)

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)

Avoiding bias effects in NMR experiments for heteronuclear dipole-dipole coupling determinations: principles and application to organic semiconductor materials.

Science.gov (United States)

Kurz, Ricardo; Cobo, Marcio Fernando; de Azevedo, Eduardo Ribeiro; Sommer, Michael; Wicklein, André; Thelakkat, Mukundan; Hempel, Günter; Saalwächter, Kay

2013-09-16

Carbon-proton dipole-dipole couplings between bonded atoms represent a popular probe of molecular dynamics in soft materials or biomolecules. Their site-resolved determination, for example, by using the popular DIPSHIFT experiment, can be challenged by spectral overlap with nonbonded carbon atoms. The problem can be solved by using very short cross-polarization (CP) contact times, however, the measured modulation curves then deviate strongly from the theoretically predicted shape, which is caused by the dependence of the CP efficiency on the orientation of the CH vector, leading to an anisotropic magnetization distribution even for isotropic samples. Herein, we present a detailed demonstration and explanation of this problem, as well as providing a solution. We combine DIPSHIFT experiments with the rotor-directed exchange of orientations (RODEO) method, and modifications of it, to redistribute the magnetization and obtain undistorted modulation curves. Our strategy is general in that it can also be applied to other types of experiments for heteronuclear dipole-dipole coupling determinations that rely on dipolar polarization transfer. It is demonstrated with perylene-bisimide-based organic semiconductor materials, as an example, in which measurements of dynamic order parameters reveal correlations of the molecular dynamics with the phase structure and functional properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Elastocapillary fabrication of three-dimensional microstructures

NARCIS (Netherlands)

van Honschoten, J.W.; Berenschot, Johan W.; Ondarcuhu, T.; Sanders, Remco G.P.; Sundaram, J.; Elwenspoek, Michael Curt; Tas, Niels Roelof

2010-01-01

We describe the fabrication of three-dimensional microstructures by means of capillary forces. Using an origami-like technique, planar silicon nitride structures of various geometries are folded to produce three-dimensional objects of 50–100 m. Capillarity is a particularly effective mechanism since

Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing

OpenAIRE

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. Recalculat...

Three dimensional nuclear magnetic resonance spectroscopic imaging of sodium ions using stochastic excitation and oscillating gradients

International Nuclear Information System (INIS)

Frederick, B.deB.

1994-12-01

Nuclear magnetic resonance (NMR) spectroscopic imaging of 23 Na holds promise as a non-invasive method of mapping Na + distributions, and for differentiating pools of Na + ions in biological tissues. However, due to NMR relaxation properties of 23 Na in vivo, a large fraction of Na + is not visible with conventional NMR imaging methods. An alternate imaging method, based on stochastic excitation and oscillating gradients, has been developed which is well adapted to measuring nuclei with short T 2 . Contemporary NMR imaging techniques have dead times of up to several hundred microseconds between excitation and sampling, comparable to the shortest in vivo 23 Na T 2 values, causing significant signal loss. An imaging strategy based on stochastic excitation has been developed which greatly reduces experiment dead time by reducing peak radiofrequency (RF) excitation power and using a novel RF circuit to speed probe recovery. Continuously oscillating gradients are used to eliminate transient eddy currents. Stochastic 1 H and 23 Na spectroscopic imaging experiments have been performed on a small animal system with dead times as low as 25μs, permitting spectroscopic imaging with 100% visibility in vivo. As an additional benefit, the encoding time for a 32x32x32 spectroscopic image is under 30 seconds. The development and analysis of stochastic NMR imaging has been hampered by limitations of the existing phase demodulation reconstruction technique. Three dimensional imaging was impractical due to reconstruction time, and design and analysis of proposed experiments was limited by the mathematical intractability of the reconstruction method. A new reconstruction method for stochastic NMR based on Fourier interpolation has been formulated combining the advantage of a several hundredfold reduction in reconstruction time with a straightforward mathematical form

Understanding API-polymer proximities in amorphous stabilized composite drug products using fluorine-carbon 2D HETCOR solid-state NMR.

Science.gov (United States)

Abraham, Anuji; Crull, George

2014-10-06

A simple and robust method for obtaining fluorine-carbon proximities was established using a (19)F-(13)C heteronuclear correlation (HETCOR) two-dimensional (2D) solid-state nuclear magnetic resonance (ssNMR) experiment under magic-angle spinning (MAS). The method was applied to study a crystalline active pharmaceutical ingredient (API), avagacestat, containing two types of fluorine atoms and its API-polymer composite drug product. These results provide insight into the molecular structure, aid with assigning the carbon resonances, and probe API-polymer proximities in amorphous spray dried dispersions (SDD). This method has an advantage over the commonly used (1)H-(13)C HETCOR because of the large chemical shift dispersion in the fluorine dimension. In the present study, fluorine-carbon distances up to 8 Å were probed, giving insight into the API structure, crystal packing, and assignments. Most importantly, the study demonstrates a method for probing an intimate molecular level contact between an amorphous API and a polymer in an SDD, giving insights into molecular association and understanding of the role of the polymer in API stability (such as recrystallization, degradation, etc.) in such novel composite drug products.

Performance of new 400-MHz HTS power-driven magnet NMR technology on typical pharmaceutical API, cinacalcet HCl.

Science.gov (United States)

Silva Elipe, Maria Victoria; Donovan, Neil; Krull, Robert; Pooke, Donald; Colson, Kimberly L

2018-04-17

After years towards higher field strength magnets, nuclear magnetic resonance (NMR) technology in commercial instruments in the past decade has expanded at low and high magnetic fields to take advantage of new opportunities. At lower field strengths, permanent magnets are well established, whereas for midrange and high field, developments utilize superconducting magnets cooled with cryogenic liquids. Recently, the desire to locate NMR spectrometers in nontypical NMR laboratories has created interest in the development of cryogen-free magnets. These magnets require no cryogenic maintenance, eliminating routine filling and large cryogen dewars in the facility. Risks of spontaneous quenches and safety concerns when working with cryogenic liquids are eliminated. The highest field commercially available cryogen-free NMR magnet previously reported was at 4.7 T in 2013. Here we tested a prototype cryogen-free 9.4-T power-driven high-temperature-superconducting (HTS) magnet mated to commercial NMR spectrometer electronics. We chose cinacalcet HCl, a typical active pharmaceutical ingredient, to evaluate its performance towards structure elucidation. Satisfactory standard 1D and 2D homonuclear and heteronuclear NMR results were obtained and compared with those from a standard 9.4-T cryogenically cooled superconducting NMR instrument. The results were similar between both systems with minor differences. Further comparison with different shims and probes in the HTS magnet system confirmed that the magnet homogeneity profile could be matched with commercially available NMR equipment for optimal results. We conclude that HTS magnet technology works well providing results comparable with those of standard instruments, leading us to investigate additional applications for this magnet technology outside a traditional NMR facility. Copyright © 2018 John Wiley & Sons, Ltd.

Isolation and identification of flavonoids, including flavone rotamers, from the herbal drug 'Crataegi folium cum flore' (hawthorn).

Science.gov (United States)

Rayyan, S; Fossen, T; Solheim Nateland, H; Andersen, O M

2005-01-01

Twelve flavonoids, including seven flavones, four flavonols and one flavanone, were isolated from methanolic extract of the herbal drug 'Crataegi folium cum flore' (hawthorn leaves and flowers) by a combination of CC (over Amberlite XAD-7 and Sephadex LH-20) and preparative HPLC. Their structures, including that of the novel flavonol 8-methoxykaempferol 3-O-(6"-malonyl-beta-glucopyranoside), were elucidated by homo- and heteronuclear NMR and electrospray/MS. The 1H- and 13C-NMR of all compounds, including rotameric pairs of five flavone C-glycosides, were assigned. The presence and relative proportion of each rotamer was shown by various NMR experiments, including two-dimensional nuclear Overhauser and exchange spectroscopy, to depend on solvent, linkage position and structure of the C-glycosyl substituent.

Three-dimensional printing and pediatric liver disease.

Science.gov (United States)

Alkhouri, Naim; Zein, Nizar N

2016-10-01

Enthusiastic physicians and medical researchers are investigating the role of three-dimensional printing in medicine. The purpose of the current review is to provide a concise summary of the role of three-dimensional printing technology as it relates to the field of pediatric hepatology and liver transplantation. Our group and others have recently demonstrated the feasibility of printing three-dimensional livers with identical anatomical and geometrical landmarks to the native liver to facilitate presurgical planning of complex liver surgeries. Medical educators are exploring the use of three-dimensional printed organs in anatomy classes and surgical residencies. Moreover, mini-livers are being developed by regenerative medicine scientist as a way to test new drugs and, eventually, whole livers will be grown in the laboratory to replace organs with end-stage disease solving the organ shortage problem. From presurgical planning to medical education to ultimately the bioprinting of whole organs for transplantation, three-dimensional printing will change medicine as we know in the next few years.

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

Visual Interpretation with Three-Dimensional Annotations (VITA): Three-Dimensional Image Interpretation Tool for Radiological Reporting

OpenAIRE

Roy, Sharmili; Brown, Michael S.; Shih, George L.

2013-01-01

This paper introduces a software framework called Visual Interpretation with Three-Dimensional Annotations (VITA) that is able to automatically generate three-dimensional (3D) visual summaries based on radiological annotations made during routine exam reporting. VITA summaries are in the form of rotating 3D volumes where radiological annotations are highlighted to place important clinical observations into a 3D context. The rendered volume is produced as a Digital Imaging and Communications i...

Three-dimensional reconstruction of functional brain images

International Nuclear Information System (INIS)

Inoue, Masato; Shoji, Kazuhiko; Kojima, Hisayoshi; Hirano, Shigeru; Naito, Yasushi; Honjo, Iwao

1999-01-01

We consider PET (positron emission tomography) measurement with SPM (Statistical Parametric Mapping) analysis to be one of the most useful methods to identify activated areas of the brain involved in language processing. SPM is an effective analytical method that detects markedly activated areas over the whole brain. However, with the conventional presentations of these functional brain images, such as horizontal slices, three directional projection, or brain surface coloring, makes understanding and interpreting the positional relationships among various brain areas difficult. Therefore, we developed three-dimensionally reconstructed images from these functional brain images to improve the interpretation. The subjects were 12 normal volunteers. The following three types of images were constructed: routine images by SPM, three-dimensional static images, and three-dimensional dynamic images, after PET images were analyzed by SPM during daily dialog listening. The creation of images of both the three-dimensional static and dynamic types employed the volume rendering method by VTK (The Visualization Toolkit). Since the functional brain images did not include original brain images, we synthesized SPM and MRI brain images by self-made C++ programs. The three-dimensional dynamic images were made by sequencing static images with available software. Images of both the three-dimensional static and dynamic types were processed by a personal computer system. Our newly created images showed clearer positional relationships among activated brain areas compared to the conventional method. To date, functional brain images have been employed in fields such as neurology or neurosurgery, however, these images may be useful even in the field of otorhinolaryngology, to assess hearing and speech. Exact three-dimensional images based on functional brain images are important for exact and intuitive interpretation, and may lead to new developments in brain science. Currently, the surface

Three-dimensional reconstruction of functional brain images

Energy Technology Data Exchange (ETDEWEB)

Inoue, Masato; Shoji, Kazuhiko; Kojima, Hisayoshi; Hirano, Shigeru; Naito, Yasushi; Honjo, Iwao [Kyoto Univ. (Japan)

1999-08-01

We consider PET (positron emission tomography) measurement with SPM (Statistical Parametric Mapping) analysis to be one of the most useful methods to identify activated areas of the brain involved in language processing. SPM is an effective analytical method that detects markedly activated areas over the whole brain. However, with the conventional presentations of these functional brain images, such as horizontal slices, three directional projection, or brain surface coloring, makes understanding and interpreting the positional relationships among various brain areas difficult. Therefore, we developed three-dimensionally reconstructed images from these functional brain images to improve the interpretation. The subjects were 12 normal volunteers. The following three types of images were constructed: routine images by SPM, three-dimensional static images, and three-dimensional dynamic images, after PET images were analyzed by SPM during daily dialog listening. The creation of images of both the three-dimensional static and dynamic types employed the volume rendering method by VTK (The Visualization Toolkit). Since the functional brain images did not include original brain images, we synthesized SPM and MRI brain images by self-made C++ programs. The three-dimensional dynamic images were made by sequencing static images with available software. Images of both the three-dimensional static and dynamic types were processed by a personal computer system. Our newly created images showed clearer positional relationships among activated brain areas compared to the conventional method. To date, functional brain images have been employed in fields such as neurology or neurosurgery, however, these images may be useful even in the field of otorhinolaryngology, to assess hearing and speech. Exact three-dimensional images based on functional brain images are important for exact and intuitive interpretation, and may lead to new developments in brain science. Currently, the surface

Application of Simulated Three Dimensional CT Image in Orthognathic Surgery

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyun Don; Park, Chang Seo [Dept. of Dental Radiology, College of Dentistry, Yensei University, Seoul (Korea, Republic of); Yoo, Sun Kook; Lee, Kyoung Sang [Dept. of Medical Engineering, College of Medicine, Yensei University, Seoul (Korea, Republic of)

1998-08-15

In orthodontics and orthognathic surgery, cephalogram has been routine practice in diagnosis and treatment evaluation of craniofacial deformity. But its inherent distortion of actual length and angles during projecting three dimensional object to two dimensional plane might cause errors in quantitative analysis of shape and size. Therefore, it is desirable that three dimensional object is diagnosed and evaluated three dimensionally and three dimensional CT image is best for three dimensional analysis. Development of clinic necessitates evaluation of result of treatment and comparison before and after surgery. It is desirable that patient that was diagnosed and planned by three dimensional computed tomography before surgery is evaluated by three dimensional computed tomography after surgery, too. But Because there is no standardized normal values in three dimension now and three dimensional Computed Tomography needs expensive equipment and because of its expenses and amount of exposure to radiation, limitations still remain to be solved in its application to routine practice. If postoperative three dimensional image is constructed by pre and postoperative lateral and postero-anterior cephalograms and preoperative three dimensional computed tomogram, pre and postoperative image will be compared and evaluated three dimensionally without three dimensional computed tomography after surgery and that will contribute to standardize normal values in three dimension. This study introduced new method that computer-simulated three dimensional image was constructed by preoperative three dimensional computed tomogram and pre and postoperative lateral and postero-anterior cephalograms, and for validation of new method, in four cases of dry skull that position of mandible was displaced and four patients of orthognathic surgery, computer-simulated three dimensional image and actual postoperative three dimensional image were compared. The results were as follows. 1. In four cases of

Application of Simulated Three Dimensional CT Image in Orthognathic Surgery

International Nuclear Information System (INIS)

Kim, Hyun Don; Park, Chang Seo; Yoo, Sun Kook; Lee, Kyoung Sang

1998-01-01

In orthodontics and orthognathic surgery, cephalogram has been routine practice in diagnosis and treatment evaluation of craniofacial deformity. But its inherent distortion of actual length and angles during projecting three dimensional object to two dimensional plane might cause errors in quantitative analysis of shape and size. Therefore, it is desirable that three dimensional object is diagnosed and evaluated three dimensionally and three dimensional CT image is best for three dimensional analysis. Development of clinic necessitates evaluation of result of treatment and comparison before and after surgery. It is desirable that patient that was diagnosed and planned by three dimensional computed tomography before surgery is evaluated by three dimensional computed tomography after surgery, too. But Because there is no standardized normal values in three dimension now and three dimensional Computed Tomography needs expensive equipment and because of its expenses and amount of exposure to radiation, limitations still remain to be solved in its application to routine practice. If postoperative three dimensional image is constructed by pre and postoperative lateral and postero-anterior cephalograms and preoperative three dimensional computed tomogram, pre and postoperative image will be compared and evaluated three dimensionally without three dimensional computed tomography after surgery and that will contribute to standardize normal values in three dimension. This study introduced new method that computer-simulated three dimensional image was constructed by preoperative three dimensional computed tomogram and pre and postoperative lateral and postero-anterior cephalograms, and for validation of new method, in four cases of dry skull that position of mandible was displaced and four patients of orthognathic surgery, computer-simulated three dimensional image and actual postoperative three dimensional image were compared. The results were as follows. 1. In four cases of

NMR of water in biological systems. I.-theoretical considerations

International Nuclear Information System (INIS)

Villa, M.; Borghi, L.; De Ambrosis, A.; Aldrovandi, S.

1983-01-01

A simple relationship has been thought to exist between the dynamics of water in heterogeneous (liquid-solid) systems and NMR response. This relationship is usually expressed by the Bloembergen-Purcell-Puond (BPP) equations for relaxation and the phase model. However, a requirement for the use of the BPP theory is that motions take place in an isotropic, infinite and three-dimensional space. It is shown that the mere presence of solid surfaces causes the appearance of solid-like features in the NMR response of the liquid even if its dynamics is directly affected by the surfaces. Some of these ''topological'' or ''indirect'' surface effects are of the same kind as the low-dimensionality effects. Their order of magnitude is estimated for simple geometries and by treating the liquid motion in a hydrodynamic approximation. Comparison with the experiment is carried on in a companion paper

An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates

International Nuclear Information System (INIS)

Gal, Maayan; Kern, Thomas; Schanda, Paul; Frydman, Lucio; Brutscher, Bernhard

2009-01-01

Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1 H- 15 N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds

Three-dimensional low-energy topological invariants

International Nuclear Information System (INIS)

Bakalarska, M.; Broda, B.

2000-01-01

A description of the one-loop approximation formula for the partition function of a three-dimensional abelian version of the Donaldson-Witten theory is proposed. The one-loop expression is shown to contain such topological invariants of a three-dimensional manifold M like the Reidemeister-Ray-Singer torsion τ R and Betti numbers. (orig.)

HN-NCA heteronuclear TOCSY-NH experiment for {sup 1}H{sup N} and {sup 15}N sequential correlations in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins

Energy Technology Data Exchange (ETDEWEB)

Wiedemann, Christoph; Goradia, Nishit; Häfner, Sabine [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Görlach, Matthias; Ohlenschläger, Oliver; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany)

2015-10-15

A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue ‘i’ with that of residues ‘i−1’ and ‘i+1’ in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of {sup 1}J{sub CαN} and {sup 2}J{sub CαN} couplings to transfer the {sup 15}N{sub x} magnetisation from amino acid residue ‘i’ to adjacent residues via the application of a band-selective {sup 15}N–{sup 13}C{sup α} heteronuclear cross-polarisation sequence of ∼100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described.

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

[Bone drilling simulation by three-dimensional imaging].

Science.gov (United States)

Suto, Y; Furuhata, K; Kojima, T; Kurokawa, T; Kobayashi, M

1989-06-01

The three-dimensional display technique has a wide range of medical applications. Pre-operative planning is one typical application: in orthopedic surgery, three-dimensional image processing has been used very successfully. We have employed this technique in pre-operative planning for orthopedic surgery, and have developed a simulation system for bone-drilling. Positive results were obtained by pre-operative rehearsal; when a region of interest is indicated by means of a mouse on the three-dimensional image displayed on the CRT, the corresponding region appears on the slice image which is displayed simultaneously. Consequently, the status of the bone-drilling is constantly monitored. In developing this system, we have placed emphasis on the quality of the reconstructed three-dimensional images, on fast processing, and on the easy operation of the surgical planning simulation.

Three-Dimensional Printing Surgical Applications.

Science.gov (United States)

AlAli, Ahmad B; Griffin, Michelle F; Butler, Peter E

2015-01-01

Three-dimensional printing, a technology used for decades in the industrial field, gains a lot of attention in the medical field for its potential benefits. With advancement of desktop printers, this technology is accessible and a lot of research is going on in the medical field. To evaluate its application in surgical field, which may include but not limited to surgical planning, surgical education, implants, and prosthesis, which are the focus of this review. Research was conducted by searching PubMed, Web of science, and other reliable sources. We included original articles and excluded articles based on animals, those more than 10 years old, and those not in English. These articles were evaluated, and relevant studies were included in this review. Three-dimensional printing shows a potential benefit in surgical application. Printed implants were used in patient in a few cases and show successful results; however, longer follow-up and more trials are needed. Surgical and medical education is believed to be more efficient with this technology than the current practice. Printed surgical instrument and surgical planning are also believed to improve with three-dimensional printing. Three-dimensional printing can be a very powerful tool in the near future, which can aid the medical field that is facing a lot of challenges and obstacles. However, despite the reported results, further research on larger samples and analytical measurements should be conducted to ensure this technology's impact on the practice.

The Three-dimensional Digital Factory for Shipbuilding Technology Research

Directory of Open Access Journals (Sweden)

Xu Wei

2016-01-01

Full Text Available The three-dimensional digital factory technology research is the hotspot in shipbuilding recently. The three-dimensional digital factory technology not only focus on design the components of the product, but also discuss on the simulation and analyses of the production process.Based on the three-dimensional model, the basic data layer, application control layer and the presentation layer of hierarchical structure are established in the three-dimensional digital factory of shipbuilding in this paper. And the key technologies of three-dimensional digital factory of shipbuilding are analysed. Finally, a case study is applied and the results show that the three-dimensional digital factory will play an important role in the future.

Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR

Science.gov (United States)

Teramura, Hiroshi; Sasaki, Kengo; Oshima, Tomoko; Aikawa, Shimpei; Matsuda, Fumio; Okamoto, Mami; Shirai, Tomokazu; Kawaguchi, Hideo; Ogino, Chiaki; Yamasaki, Masanori; Kikuchi, Jun; Kondo, Akihiko

2015-01-01

A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45–0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = –0.95 to –0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate. PMID:26083431

Towards three-dimensional optical metamaterials

Science.gov (United States)

Tanaka, Takuo; Ishikawa, Atsushi

2017-12-01

Metamaterials have opened up the possibility of unprecedented and fascinating concepts and applications in optics and photonics. Examples include negative refraction, perfect lenses, cloaking, perfect absorbers, and so on. Since these metamaterials are man-made materials composed of sub-wavelength structures, their development strongly depends on the advancement of micro- and nano-fabrication technologies. In particular, the realization of three-dimensional metamaterials is one of the big challenges in this research field. In this review, we describe recent progress in the fabrication technologies for three-dimensional metamaterials, as well as proposed applications.

Three-dimensional imaging modalities in endodontics

Science.gov (United States)

Mao, Teresa

2014-01-01

Recent research in endodontics has highlighted the need for three-dimensional imaging in the clinical arena as well as in research. Three-dimensional imaging using computed tomography (CT) has been used in endodontics over the past decade. Three types of CT scans have been studied in endodontics, namely cone-beam CT, spiral CT, and peripheral quantitative CT. Contemporary endodontics places an emphasis on the use of cone-beam CT for an accurate diagnosis of parameters that cannot be visualized on a two-dimensional image. This review discusses the role of CT in endodontics, pertaining to its importance in the diagnosis of root canal anatomy, detection of peri-radicular lesions, diagnosis of trauma and resorption, presurgical assessment, and evaluation of the treatment outcome. PMID:25279337

Three-dimensional imaging modalities in endodontics

Energy Technology Data Exchange (ETDEWEB)

Mao, Teresa; Neelakantan, Prasanna [Dept. of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospitals, Saveetha University, Chennai (India)

2014-09-15

Recent research in endodontics has highlighted the need for three-dimensional imaging in the clinical arena as well as in research. Three-dimensional imaging using computed tomography (CT) has been used in endodontics over the past decade. Three types of CT scans have been studied in endodontics, namely cone-beam CT, spiral CT, and peripheral quantitative CT. Contemporary endodontics places an emphasis on the use of cone-beam CT for an accurate diagnosis of parameters that cannot be visualized on a two-dimensional image. This review discusses the role of CT in endodontics, pertaining to its importance in the diagnosis of root canal anatomy, detection of peri-radicular lesions, diagnosis of trauma and resorption, presurgical assessment, and evaluation of the treatment outcome.

Three-dimensional imaging modalities in endodontics

International Nuclear Information System (INIS)

Mao, Teresa; Neelakantan, Prasanna

2014-01-01

Recent research in endodontics has highlighted the need for three-dimensional imaging in the clinical arena as well as in research. Three-dimensional imaging using computed tomography (CT) has been used in endodontics over the past decade. Three types of CT scans have been studied in endodontics, namely cone-beam CT, spiral CT, and peripheral quantitative CT. Contemporary endodontics places an emphasis on the use of cone-beam CT for an accurate diagnosis of parameters that cannot be visualized on a two-dimensional image. This review discusses the role of CT in endodontics, pertaining to its importance in the diagnosis of root canal anatomy, detection of peri-radicular lesions, diagnosis of trauma and resorption, presurgical assessment, and evaluation of the treatment outcome

A three-dimensional field solutions of Halbach

International Nuclear Information System (INIS)

Chen Jizhong; Xiao Jijun; Zhang Yiming; Xu Chunyan

2008-01-01

A three-dimensional field solutions are presented for Halback cylinder magnet. Based on Ampere equivalent current methods, the permanent magnets are taken as distributing of current density. For getting the three-dimensional field solution of ideal polarized permanent magnets, the solution method entails the use of the vector potential and involves the closed-form integration of the free-space Green's function. The programmed field solution are ideal for performing rapid parametric studies of the dipole Halback cylinder magnets made from rare earth materials. The field solutions are verified by both an analytical two-dimensional algorithm and three-dimensional finite element software. A rapid method is presented for extensive analyzing and optimizing Halbach cylinder magnet. (authors)

Three-dimensional structure of the human immunodeficiency virus type 1 matrix protein.

Science.gov (United States)

Massiah, M A; Starich, M R; Paschall, C; Summers, M F; Christensen, A M; Sundquist, W I

1994-11-25

The HIV-1 matrix protein forms an icosahedral shell associated with the inner membrane of the mature virus. Genetic analyses have indicated that the protein performs important functions throughout the viral life-cycle, including anchoring the transmembrane envelope protein on the surface of the virus, assisting in viral penetration, transporting the proviral integration complex across the nuclear envelope, and localizing the assembling virion to the cell membrane. We now report the three-dimensional structure of recombinant HIV-1 matrix protein, determined at high resolution by nuclear magnetic resonance (NMR) methods. The HIV-1 matrix protein is the first retroviral matrix protein to be characterized structurally and only the fourth HIV-1 protein of known structure. NMR signal assignments required recently developed triple-resonance (1H, 13C, 15N) NMR methodologies because signals for 91% of 132 assigned H alpha protons and 74% of the 129 assignable backbone amide protons resonate within chemical shift ranges of 0.8 p.p.m. and 1 p.p.m., respectively. A total of 636 nuclear Overhauser effect-derived distance restraints were employed for distance geometry-based structure calculations, affording an average of 13.0 NMR-derived distance restraints per residue for the experimentally constrained amino acids. An ensemble of 25 refined distance geometry structures with penalties (sum of the squares of the distance violations) of 0.32 A2 or less and individual distance violations under 0.06 A was generated; best-fit superposition of ordered backbone heavy atoms relative to mean atom positions afforded root-mean-square deviations of 0.50 (+/- 0.08) A. The folded HIV-1 matrix protein structure is composed of five alpha-helices, a short 3(10) helical stretch, and a three-strand mixed beta-sheet. Helices I to III and the 3(10) helix pack about a central helix (IV) to form a compact globular domain that is capped by the beta-sheet. The C-terminal helix (helix V) projects away

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

Three Dimensional Dirac Semimetals

Science.gov (United States)

Zaheer, Saad

2014-03-01

Dirac points on the Fermi surface of two dimensional graphene are responsible for its unique electronic behavior. One can ask whether any three dimensional materials support similar pseudorelativistic physics in their bulk electronic spectra. This possibility has been investigated theoretically and is now supported by two successful experimental demonstrations reported during the last year. In this talk, I will summarize the various ways in which Dirac semimetals can be realized in three dimensions with primary focus on a specific theory developed on the basis of representations of crystal spacegroups. A three dimensional Dirac (Weyl) semimetal can appear in the presence (absence) of inversion symmetry by tuning parameters to the phase boundary separating a bulk insulating and a topological insulating phase. More generally, we find that specific rules governing crystal symmetry representations of electrons with spin lead to robust Dirac points at high symmetry points in the Brillouin zone. Combining these rules with microscopic considerations identifies six candidate Dirac semimetals. Another method towards engineering Dirac semimetals involves combining crystal symmetry and band inversion. Several candidate materials have been proposed utilizing this mechanism and one of the candidates has been successfully demonstrated as a Dirac semimetal in two independent experiments. Work carried out in collaboration with: Julia A. Steinberg, Steve M. Young, J.C.Y. Teo, C.L. Kane, E.J. Mele and Andrew M. Rappe.

Three-dimensional instability of standing waves

Science.gov (United States)

Zhu, Qiang; Liu, Yuming; Yue, Dick K. P.

2003-12-01

We investigate the three-dimensional instability of finite-amplitude standing surface waves under the influence of gravity. The analysis employs the transition matrix (TM) approach and uses a new high-order spectral element (HOSE) method for computation of the nonlinear wave dynamics. HOSE is an extension of the original high-order spectral method (HOS) wherein nonlinear wave wave and wave body interactions are retained up to high order in wave steepness. Instead of global basis functions in HOS, however, HOSE employs spectral elements to allow for complex free-surface geometries and surface-piercing bodies. Exponential convergence of HOS with respect to the total number of spectral modes (for a fixed number of elements) and interaction order is retained in HOSE. In this study, we use TM-HOSE to obtain the stability of general three-dimensional perturbations (on a two-dimensional surface) on two classes of standing waves: plane standing waves in a rectangular tank; and radial/azimuthal standing waves in a circular basin. For plane standing waves, we confirm the known result of two-dimensional side-bandlike instability. In addition, we find a novel three-dimensional instability for base flow of any amplitude. The dominant component of the unstable disturbance is an oblique (standing) wave oriented at an arbitrary angle whose frequency is close to the (nonlinear) frequency of the original standing wave. This finding is confirmed by direct long-time simulations using HOSE which show that the nonlinear evolution leads to classical Fermi Pasta Ulam recurrence. For the circular basin, we find that, beyond a threshold wave steepness, a standing wave (of nonlinear frequency Omega) is unstable to three-dimensional perturbations. The unstable perturbation contains two dominant (standing-wave) components, the sum of whose frequencies is close to 2Omega. From the cases we consider, the critical wave steepness is found to generally decrease/increase with increasing radial

31P-edited diffusion-ordered 1H NMR spectroscopy for the spectral isolation and identification of organophosphorus compounds related to chemical weapons agents and their degradation products.

Science.gov (United States)

Mayer, Brian P; Valdez, Carlos A; Hok, Saphon; Chinn, Sarah C; Hart, Bradley R

2012-12-04

Organophosphorus compounds represent a large class of molecules that include pesticides, flame-retardants, biologically relevant molecules, and chemical weapons agents (CWAs). The detection and identification of organophosphorus molecules, particularly in the cases of pesticides and CWAs, are paramount to the verification of international treaties by various organizations. To that end, novel analytical methodologies that can provide additional support to traditional analyses are important for unambiguous identification of these compounds. We have developed an NMR method that selectively edits for organophosphorus compounds via (31)P-(1)H heteronuclear single quantum correlation (HSQC) and provides an additional chromatographic-like separation based on self-diffusivities of the individual species via (1)H diffusion-ordered spectroscopy (DOSY): (1)H-(31)P HSQC-DOSY. The technique is first validated using the CWA VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) by traditional two-dimensional DOSY spectra. We then extend this technique to a complex mixture of VX degradation products and identify all the main phosphorus-containing byproducts generated after exposure to a zinc-cyclen organometallic homogeneous catalyst.

Cylindrical Three-Dimensional Porous Anodic Alumina Networks

Directory of Open Access Journals (Sweden)

Pedro M. Resende

2016-11-01

Full Text Available The synthesis of a conformal three-dimensional nanostructure based on porous anodic alumina with transversal nanopores on wires is herein presented. The resulting three-dimensional network exhibits the same nanostructure as that obtained on planar geometries, but with a macroscopic cylindrical geometry. The morphological analysis of the nanostructure revealed the effects of the initial defects on the aluminum surface and the mechanical strains on the integrity of the three-dimensional network. The results evidence the feasibility of obtaining 3D porous anodic alumina on non-planar aluminum substrates.

Multiparallel Three-Dimensional Optical Microscopy

Science.gov (United States)

Nguyen, Lam K.; Price, Jeffrey H.; Kellner, Albert L.; Bravo-Zanoquera, Miguel

2010-01-01

Multiparallel three-dimensional optical microscopy is a method of forming an approximate three-dimensional image of a microscope sample as a collection of images from different depths through the sample. The imaging apparatus includes a single microscope plus an assembly of beam splitters and mirrors that divide the output of the microscope into multiple channels. An imaging array of photodetectors in each channel is located at a different distance along the optical path from the microscope, corresponding to a focal plane at a different depth within the sample. The optical path leading to each photodetector array also includes lenses to compensate for the variation of magnification with distance so that the images ultimately formed on all the photodetector arrays are of the same magnification. The use of optical components common to multiple channels in a simple geometry makes it possible to obtain high light-transmission efficiency with an optically and mechanically simple assembly. In addition, because images can be read out simultaneously from all the photodetector arrays, the apparatus can support three-dimensional imaging at a high scanning rate.

Backlund transformations and three-dimensional lattice equations

NARCIS (Netherlands)

Nijhoff, F.W.; Capel, H.W.; Wiersma, G.L.; Quispel, G.R.W.

1984-01-01

A (nonlocal) linear integral equation is studied, which allows for Bäcklund transformations in the measure. The compatibility of three of these transformations leads to an integrable nonlinear three-dimensional lattice equation. In appropriate continuum limits the two-dimensional Toda-lattice

Arching in three-dimensional clogging

Science.gov (United States)

Török, János; Lévay, Sára; Szabó, Balázs; Somfai, Ellák; Wegner, Sandra; Stannarius, Ralf; Börzsönyi, Tamás

2017-06-01

Arching in dry granular material is a long established concept, however it remains still an open question how three-dimensional orifices clog. We investigate by means of numerical simulations and experimental data how the outflow creates a blocked configuration of particles. We define the concave surface of the clogged dome by two independent methods (geometric and density based). The average shape of the cupola for spheres is almost a hemisphere but individual samples have large holes in the structure indicating a blocked state composed of two-dimensional force chains rather than three-dimensional objects. The force chain structure justifies this assumption. For long particles the clogged configurations display large variations, and in certain cases the empty region reaches a height of 5 hole diameters. These structures involve vertical walls consisting of horizontally placed stable stacking of particles.

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

Three-dimensional structure of interleukin 8 in solution

International Nuclear Information System (INIS)

Clore, G.M.; Appella, E.; Gronenborn, A.M.; Yamada, Masaki; Matsushima, Kouji

1990-01-01

The solution structure of the interleukin 8 (IL-8) dimer has been solved by nuclear magnetic resonance (NMR) spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. The structure determination is based on a total of 1,880 experimental distance restraints (of which 82 are intersubunit) and 362 torsion angle restraints (comprising φ, ψ, and χ 1 torsion angles). A total of 30 simulated annealing structures were calculated, and the atomic rms distribution about the mean coordinate positions (excluding residues 1-5 of each subunit) is 0.41 ± 0.08 angstrom for the backbone atoms and 0.90 ± 0.08 angstrom for all atoms. The three-dimensional solution structure of the IL-8 dimer reveals a structural motif in which two symmetry-related antiparallel α-helices, approximately 24 angstrom long and separated by about 14 angstrom, lie on top of six-stranded antiparallel β-sheet platform derived from two three-stranded Greek keys, one from each monomer unit. The general architecture is similar to that of the α1/α2 domains of the human class I histocompatibility antigen HLA-A2. It is suggested that the two α-helices form the binding site for the cellular receptor and that the specificity of IL-8, as well as that of a number of related proteins involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response, is achieved by the distinct distribution of charged and polar residues at the surface of the helices

Three-dimensional structure of interleukin 8 in solution.

Science.gov (United States)

Clore, G M; Appella, E; Yamada, M; Matsushima, K; Gronenborn, A M

1990-02-20

The solution structure of the interleukin 8 (IL-8) dimer has been solved by nuclear magnetic resonance (NMR) spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. The structure determination is based on a total of 1880 experimental distance restraints (of which 82 are intersubunit) and 362 torsion angle restraints (comprising phi, psi, and chi 1 torsion angles). A total of 30 simulated annealing structures were calculated, and the atomic rms distribution about the mean coordinate positions (excluding residues 1-5 of each subunit) is 0.41 +/- 0.08 A for the backbone atoms and 0.90 +/- 0.08 A for all atoms. The three-dimensional solution structure of the IL-8 dimer reveals a structural motif in which two symmetry-related antiparallel alpha-helices, approximately 24 A long and separated by about 14 A, lie on top of a six-stranded antiparallel beta-sheet platform derived from two three-stranded Greek keys, one from each monomer unit. The general architecture is similar to that of the alpha 1/alpha 2 domains of the human class I histocompatibility antigen HLA-A2. It is suggested that the two alpha-helices form the binding site for the cellular receptor and that the specificity of IL-8, as well as that of a number of related proteins involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response, is achieved by the distinct distribution of charged and polar residues at the surface of the helices.

Three-dimensional reconstruction of the biliary tract using spiral computed tomography. Three-dimensional cholangiography

International Nuclear Information System (INIS)

Gon, Masanori; Ogura, Norihiro; Uetsuji, Shouji; Ueyama, Yasuo

1995-01-01

In this study, 310 patients with benign biliary diseases, 20 with gallbladder cancer, and 8 with biliary tract carcinoma underwent spiral CT (SCT) scanning at cholangiography. Depiction rate of the shape of the conjunction site of the gallbladder and biliary tract was 27.5% by conventional intravenous cholangiography (DIC), 92.5% by ERC, and 90.0% by DIC-SCT. Abnormal cystic duct course was admitted in 14.1%. Multiplanar reconstruction by DIC-SCT enabled identification of the common bile duct and intrahepatic bile duct stone. Three-dimensional reconstruction of DIC-SCT was effective in evaluating obstruction of the anastomosis or passing condition of after hepatico-jejunostomy. Two-dimensional SCT images through PTCD tube enabled degree of hepatic invasion in bile duct cancer, and three-dimensional images were useful in grasping the morphology of the bile duct branches near the obstruction site. DIC-SCT is therefore considered a useful procedure as non-invasive examination of bile duct lesions. (S.Y.)

NMR studies of the fate of adenine nucleotides in glucose-starved erythrocytes

International Nuclear Information System (INIS)

Bubb, W.A.; Mulquiney, P.J.; Kuchel, P.W.; Rohwer, J.; De Atauri, P.

2002-01-01

Full text: As a consequence of many refinements during the past 30 years, we now have a detailed understanding of the glycolytic pathway in human erythrocytes. By comparison, and notwithstanding their central importance to four key steps in erythrocyte glycolysis, our knowledge of the catabolism of adenine nucleotides remains relatively limited. In particular, the mechanism for the degradation of AMP, whose concentration rises under conditions of oxidative stress or glucose deprivation, remains poorly understood, AMP degradation may proceed via two possible pathways which converge in the production of inosine. Analysis of the key intermediates for the respective pathways, adenosine and AMP, as well as determination of end products is not straightforward. High-resolution NMR spectroscopy affords a potentially simple analytical solution to this problem but is complicated by spectral overlap and the sensitivity of key resonances to variations in pH and the concentrations of cations such as Mg 2+ . We describe a multinuclear NMR approach towards characterising the intermediates and end-products of adenine nucleotide metabolism in glucose-starved human erythrocytes. Assignments based on homo- and heteronuclear correlation experiments for both 13 C and 31 P are presented

Quantum atom-heteronuclear molecule dark state: Role of population imbalance

International Nuclear Information System (INIS)

Jing Hui; Cui Shuai

2010-01-01

Recently, the finite-number effect of initial atoms in coherent atom-molecule conversion was investigated by Zhao et al. [Phys. Rev. Lett. 101, 010401 (2008)]. Here, by extending to the atom-heteronuclear molecule dark state, we find that the initial populations imbalance of the atoms plays a significant role in quantum conversion rate and adiabatic fidelity. In particular, even for the finite total number of imbalanced two-species atoms, the mean-field conversion rate, contrary to the general belief, still can be remarkably close to the exact quantum results.

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.

Experiments and strategies for the assignment of fully13 C/15N-labelled polypeptides by solid state NMR

International Nuclear Information System (INIS)

Straus, Suzana K.; Bremi, Tobias; Ernst, Richard R.

1998-01-01

High-resolution heteronuclear NMR correlation experiments and strategies are proposed for the assignment of fully 13 C/ 15 N-labelled polypeptides in the solid state. By the combination of intra-residue and inter-residue 13 C- 15 N correlation experiments with 13 C- 13 C spin-diffusion studies, it becomes feasible to partially assign backbone and side-chain resonances in solid proteins. The performance of sequences using 15 N instead of 13 C detection is evaluated regarding sensitivity and resolution for a labelled dipeptide (L-Val-L-Phe). The techniques are used for a partial assignment of the 15 N and 13 C resonances in human ubiquitin

1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

International Nuclear Information System (INIS)

Cort, John R.; Cho, Herman M.

2009-01-01

Proton and 13C NMR chemical shift assignments and 1H-1H scalar couplings for the two diastereomers of the vitamin K epoxide reductase (VKOR) inhibitor brodifacoum have been determined from acetone solutions containing both diastereomers. Data were obtained from homo- and heteronuclear correlation spectra acquired at 1H frequencies of 750 and 900 MHz over a 268-303 K temperature range. Conformations inferred from scalar coupling and 1-D NOE measurements exhibit large differences between the diastereomers. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

Three-dimensional appearance of the lips muscles with three-dimensional isotropic MRI: in vivo study

Energy Technology Data Exchange (ETDEWEB)

Olszewski, Raphael; Reychler, H. [Universite Catholique de Louvain, Department of Oral and Maxillofacial Surgery, Cliniques Universitaires Saint Luc, Brussels (Belgium); Liu, Y.; Xu, T.M. [Peking University School and Hospital of Stomatology, Department of Orthodontics, Beijing (China); Duprez, T. [Universite Catholique de Louvain, Department of Radiology, Cliniques Universitaires Saint Luc, Brussels (Belgium)

2009-06-15

Our knowledge of facial muscles is based primarily on atlases and cadaveric studies. This study describes a non-invasive in vivo method (3D MRI) for segmenting and reconstructing facial muscles in a three-dimensional fashion. Three-dimensional (3D), T1-weighted, 3 Tesla, isotropic MRI was applied to a subject. One observer performed semi-automatic segmentation using the Editor module from the 3D Slicer software (Harvard Medical School, Boston, MA, USA), version 3.2. We were able to successfully outline and three-dimensionally reconstruct the following facial muscles: pars labialis orbicularis oris, m. levatro labii superioris alaeque nasi, m. levator labii superioris, m. zygomaticus major and minor, m. depressor anguli oris, m. depressor labii inferioris, m. mentalis, m. buccinator, and m. orbicularis oculi. 3D reconstruction of the lip muscles should be taken into consideration in order to improve the accuracy and individualization of existing 3D facial soft tissue models. More studies are needed to further develop efficient methods for segmentation in this field. (orig.)

Three-dimensional appearance of the lips muscles with three-dimensional isotropic MRI: in vivo study.

Science.gov (United States)

Olszewski, Raphael; Liu, Y; Duprez, T; Xu, T M; Reychler, H

2009-06-01

Our knowledge of facial muscles is based primarily on atlases and cadaveric studies. This study describes a non-invasive in vivo method (3D MRI) for segmenting and reconstructing facial muscles in a three-dimensional fashion. Three-dimensional (3D), T1-weighted, 3 Tesla, isotropic MRI was applied to a subject. One observer performed semi-automatic segmentation using the Editor module from the 3D Slicer software (Harvard Medical School, Boston, MA, USA), version 3.2. We were able to successfully outline and three-dimensionally reconstruct the following facial muscles: pars labialis orbicularis oris, m. levatro labii superioris alaeque nasi, m. levator labii superioris, m. zygomaticus major and minor, m. depressor anguli oris, m. depressor labii inferioris, m. mentalis, m. buccinator, and m. orbicularis oculi. 3D reconstruction of the lip muscles should be taken into consideration in order to improve the accuracy and individualization of existing 3D facial soft tissue models. More studies are needed to further develop efficient methods for segmentation in this field.

Three-Dimensional Messages for Interstellar Communication

Science.gov (United States)

Vakoch, Douglas A.

One of the challenges facing independently evolved civilizations separated by interstellar distances is to communicate information unique to one civilization. One commonly proposed solution is to begin with two-dimensional pictorial representations of mathematical concepts and physical objects, in the hope that this will provide a foundation for overcoming linguistic barriers. However, significant aspects of such representations are highly conventional, and may not be readily intelligible to a civilization with different conventions. The process of teaching conventions of representation may be facilitated by the use of three-dimensional representations redundantly encoded in multiple formats (e.g., as both vectors and as rasters). After having illustrated specific conventions for representing mathematical objects in a three-dimensional space, this method can be used to describe a physical environment shared by transmitter and receiver: a three-dimensional space defined by the transmitter--receiver axis, and containing stars within that space. This method can be extended to show three-dimensional representations varying over time. Having clarified conventions for representing objects potentially familiar to both sender and receiver, novel objects can subsequently be depicted. This is illustrated through sequences showing interactions between human beings, which provide information about human behavior and personality. Extensions of this method may allow the communication of such culture-specific features as aesthetic judgments and religious beliefs. Limitations of this approach will be noted, with specific reference to ETI who are not primarily visual.

Three-dimensional topological insulators and bosonization

Energy Technology Data Exchange (ETDEWEB)

Cappelli, Andrea [INFN, Sezione di Firenze,Via G. Sansone 1, 50019 Sesto Fiorentino - Firenze (Italy); Randellini, Enrico [INFN, Sezione di Firenze,Via G. Sansone 1, 50019 Sesto Fiorentino - Firenze (Italy); Dipartimento di Fisica e Astronomia, Università di Firenze,Via G. Sansone 1, 50019 Sesto Fiorentino - Firenze (Italy); Sisti, Jacopo [Scuola Internazionale Superiore di Studi Avanzati (SISSA),Via Bonomea 265, 34136 Trieste (Italy)

2017-05-25

Massless excitations at the surface of three-dimensional time-reversal invariant topological insulators possess both fermionic and bosonic descriptions, originating from band theory and hydrodynamic BF theory, respectively. We analyze the corresponding field theories of the Dirac fermion and compactified boson and compute their partition functions on the three-dimensional torus geometry. We then find some non-dynamic exact properties of bosonization in (2+1) dimensions, regarding fermion parity and spin sectors. Using these results, we extend the Fu-Kane-Mele stability argument to fractional topological insulators in three dimensions.

Biomimetic nanocomposites of carboxymethyl cellulose-hydroxyapatite: novel three dimensional load bearing bone grafts.

Science.gov (United States)

Garai, Subhadra; Sinha, Arvind

2014-03-01

An innovative biomimetic synthesis of novel three dimensional micro/macro porous carboxymethyl cellulose (CMC)-hydroxyapatite (HA) nanocomposites having four systematically different compositions has been established for its possible application as a load bearing synthetic bone graft. Our process, being in situ, involves a simple and cost effective route akin to a matrix mediated biomineralization process. Developed synthesis route not only controls the size of HA particles in the range of 15-50 nm, embedded in CMC matrix, but also assists in the formation of a mechanically strong three dimensional nanocomposite structures due to physical cross linking of HA impregnated CMC matrix. The process does not involve any toxic cross linker and works at near ambient conditions. The nanocomposites are systematically structurally and mechanically characterized using various techniques like scanning electron microscopy (SEM), atomic force microscopy (AFM), transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform IR (FTIR), solid state (13)C nuclear magnetic resonance ((13)C NMR), thermo-gravimetric analysis (TGA) and Universal mechanical test. It reveals that the ionic/polar or electrostatic interactions are the main driving force for formation of load bearing three dimensional nanocomposites via a process similar to matrix mediated biomineralization. Compressive strength and compressive modulus of nanocomposites, being in the range of 1.74-12 MPa and 157-330 MPa, respectively, meet the desired range of compressive strength for the synthetic grafts used in cancellous bone. An increase in the compressive strength with increase in the porosity has been an interesting observation in the present study. In vitro cytotoxicity of the synthesized nanocomposites has been evaluated using bone marrow mesenchymal stem cells (BMSC) isolated from Wistar rat. Copyright © 2013 Elsevier B.V. All rights reserved.

High-resolution three-dimensional mapping of semiconductor dopant potentials

DEFF Research Database (Denmark)

Twitchett, AC; Yates, TJV; Newcomb, SB

2007-01-01

Semiconductor device structures are becoming increasingly three-dimensional at the nanometer scale. A key issue that must be addressed to enable future device development is the three-dimensional mapping of dopant distributions, ideally under "working conditions". Here we demonstrate how a combin......Semiconductor device structures are becoming increasingly three-dimensional at the nanometer scale. A key issue that must be addressed to enable future device development is the three-dimensional mapping of dopant distributions, ideally under "working conditions". Here we demonstrate how...... a combination of electron holography and electron tomography can be used to determine quantitatively the three-dimensional electrostatic potential in an electrically biased semiconductor device with nanometer spatial resolution....

Equilibrium: three-dimensional configurations

International Nuclear Information System (INIS)

Anon.

1987-01-01

This chapter considers toroidal MHD configurations that are inherently three-dimensional. The motivation for investigation such complicated equilibria is that they possess the potential for providing toroidal confinement without the need of a net toroidal current. This leads to a number of advantages with respect to fusion power generation. First, the attractive feature of steady-state operation becomes more feasible since such configurations no longer require a toroidal current transformer. Second, with zero net current, one potentially dangerous class of MHD instabilities, the current-driven kink modes, is eliminated. Finally, three-dimensional configurations possess nondegenerate flux surfaces even in the absence of plasma pressure and plasma current. Although there is an enormous range of possible three-dimensional equilibria, the configurations of interest are accurately described as axisymmetric tori with superimposed helical fields; furthermore, they possess no net toroidal current. Instead, two different and less obvious restoring forces are developed: the helical sideband force and the toroidal dipole current force. Each is discussed in detail in Chapter 7. A detailed discussion of the parallel current constraint, including its physical significance, is given in section 7.2. A general analysis of helical sideband equilibria, along with a detailed description of the Elmo bumpy torus, is presented in sections 7.3 and 7.4. A general description of toroidal dipole-current equilibria, including a detailed discussion of stellarators, heliotrons, and torsatrons, is given in sections 7.5 and 7.6

Volume scanning three-dimensional display with an inclined two-dimensional display and a mirror scanner

Science.gov (United States)

Miyazaki, Daisuke; Kawanishi, Tsuyoshi; Nishimura, Yasuhiro; Matsushita, Kenji

2001-11-01

A new three-dimensional display system based on a volume-scanning method is demonstrated. To form a three-dimensional real image, an inclined two-dimensional image is rapidly moved with a mirror scanner while the cross-section patterns of a three-dimensional object are displayed sequentially. A vector-scan CRT display unit is used to obtain a high-resolution image. An optical scanning system is constructed with concave mirrors and a galvanometer mirror. It is confirmed that three-dimensional images, formed by the experimental system, satisfy all the criteria for human stereoscopic vision.

Three-dimensional bio-printing.

Science.gov (United States)

Gu, Qi; Hao, Jie; Lu, YangJie; Wang, Liu; Wallace, Gordon G; Zhou, Qi

2015-05-01

Three-dimensional (3D) printing technology has been widely used in various manufacturing operations including automotive, defence and space industries. 3D printing has the advantages of personalization, flexibility and high resolution, and is therefore becoming increasingly visible in the high-tech fields. Three-dimensional bio-printing technology also holds promise for future use in medical applications. At present 3D bio-printing is mainly used for simulating and reconstructing some hard tissues or for preparing drug-delivery systems in the medical area. The fabrication of 3D structures with living cells and bioactive moieties spatially distributed throughout will be realisable. Fabrication of complex tissues and organs is still at the exploratory stage. This review summarize the development of 3D bio-printing and its potential in medical applications, as well as discussing the current challenges faced by 3D bio-printing.

Acid-base properties of complexes with three-dimensional polyligands. Complexes with three-dimensional polyphosphoric acids

International Nuclear Information System (INIS)

Kopylova, V.D.; Bojko, Eh.T.; Saldadze, K.M.

1985-01-01

By the method of potentiometric titration acid-base properties of uranyl (2) complexes with three-dimensional polyphosphoric acids, KRF-8p, KF-1, KF-7 prepared by phosphorylation of copolymer of styrene and divinylbenzene or saponification of the copolymers of di-2,2'-chloroethyl ester of vinylphosphonic acid with divinyl benzene are studied. It is shown that in case of formation in the phase of three-dimensional polyphosphoric acids of UO 2 2+ complexes with the growth of bond covalence of metal ion-phosphonic group the acidjty of the second hydroxyl of the phosphonic group increases

Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz

International Nuclear Information System (INIS)

Bundle, D.R.; Cherwonogrodzky, J.W.; Perry, M.B.

1987-01-01

The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-α-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz 1 H and 125-MHz 13 C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent β-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-lined 4,6-dideoxy-4-formamido-α-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-α-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants

Three dimensional periodic foundations for base seismic isolation

International Nuclear Information System (INIS)

Yan, Y; Mo, Y L; Cheng, Z; Shi, Z; Menq, F; Tang, Y

2015-01-01

Based on the concept of phononic crystals, periodic foundations made of periodic materials are investigated in this paper. The periodic foundations can provide low frequency band gaps, which cover the main frequency ranges of seismic waves. Therefore, the periodic foundations are able to protect the upper structures during earthquake events. In this paper, the basic theory of three dimensional periodic foundations is studied and the finite element method was used to conduct the sensitivity study. A simplified three-dimensional periodic foundation with a superstructure was tested in the field and the feasibility of three dimensional periodic foundations was proved. The test results showed that the response of the upper structure with the three dimensional periodic foundation was reduced under excitation waves with the main frequency falling in the attenuation zones. The finite element analysis results are consistent with the experimental data, indicating that three dimensional periodic foundations are a feasible way of reducing seismic vibrations. (paper)

Simulation on three dimensional bubble formation using MARS

International Nuclear Information System (INIS)

Kunugi, Tomoaki

1997-01-01

This paper describes a numerical simulation on three-dimensional bubble formation by means of the MARS (Multi-interfaces Advection and Reconstruction Solver) developed by the author. The comparison between two-dimensional and three-dimensional simulation on an agglomeration of two bubbles is discussed. Moreover, some simulation results regarding a phase change phenomena such as a boiling and condensation in a two dimensional enclosure with heated and cooled walls are presented. (author)

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 spectroscopy

International Nuclear Information System (INIS)

Bax, A.; Lerner, L.

1986-01-01

Great spectral simplification can be obtained by spreading the conventional one-dimensional nuclear magnetic resonance (NMR) spectrum in two independent frequency dimensions. This so-called two-dimensional NMR spectroscopy removes spectral overlap, facilitates spectral assignment, and provides a wealth of additional information. For example, conformational information related to interproton distances is available from resonance intensities in certain types of two-dimensional experiments. Another method generates 1 H NMR spectra of a preselected fragment of the molecule, suppressing resonances from other regions and greatly simplifying spectral appearance. Two-dimensional NMR spectroscopy can also be applied to the study of 13 C and 15 N, not only providing valuable connectivity information but also improving sensitivity of 13 C and 15 N detection by up to two orders of magnitude. 45 references, 10 figures

Three-dimensional tori and Arnold tongues

Energy Technology Data Exchange (ETDEWEB)

Sekikawa, Munehisa, E-mail: sekikawa@cc.utsunomiya-u.ac.jp [Department of Mechanical and Intelligent Engineering, Utsunomiya University, Utsunomiya-shi 321-8585 (Japan); Inaba, Naohiko [Organization for the Strategic Coordination of Research and Intellectual Property, Meiji University, Kawasaki-shi 214-8571 (Japan); Kamiyama, Kyohei [Department of Electronics and Bioinformatics, Meiji University, Kawasaki-shi 214-8571 (Japan); Aihara, Kazuyuki [Institute of Industrial Science, the University of Tokyo, Meguro-ku 153-8505 (Japan)

2014-03-15

This study analyzes an Arnold resonance web, which includes complicated quasi-periodic bifurcations, by conducting a Lyapunov analysis for a coupled delayed logistic map. The map can exhibit a two-dimensional invariant torus (IT), which corresponds to a three-dimensional torus in vector fields. Numerous one-dimensional invariant closed curves (ICCs), which correspond to two-dimensional tori in vector fields, exist in a very complicated but reasonable manner inside an IT-generating region. Periodic solutions emerge at the intersections of two different thin ICC-generating regions, which we call ICC-Arnold tongues, because all three independent-frequency components of the IT become rational at the intersections. Additionally, we observe a significant bifurcation structure where conventional Arnold tongues transit to ICC-Arnold tongues through a Neimark-Sacker bifurcation in the neighborhood of a quasi-periodic Hopf bifurcation (or a quasi-periodic Neimark-Sacker bifurcation) boundary.

The direct measurement of the heteronuclear chemical shifts relative to tetramethylsilane

International Nuclear Information System (INIS)

Moritz, A.G.

1988-12-01

The measurement of heteronuclear chemical shifts using absolute frequencies of the heteronucleus and the 1 H resonance of tetramethylsilane has been examined. This method avoids the problems associated with external standards and gives results which can be obtained quickly and with high precision. The method has a number of advantages in the accurate measurement of chemical shifts, as for example 31 P in chemical warfare agents and related chemicals and allows multinuclear data to be obtained without dynamic range or potential interference problems. 15 refs., 4 tabs

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.

Three-dimensional CT of the pediatric spine

International Nuclear Information System (INIS)

Starshak, R.J.; Crawford, C.R.; Waisman, R.C.; Sty, J.R.

1987-01-01

CT of the spine has been shown to be useful in evaluating congenital, neoplastic, inflammatory, and traumatic lesions. Any portion of the neural arch may be involved by these disease processes. However, the complex nature of the spinal column can make evaluation of these abnormalities difficult on axial CT. This is especially true if the spine is distorted by scoliosis, kyphosis, or lordosis. The principal advantage of three-dimensional CT is its ability to display the surface relationships of complicated objects. The complexity of the spinal axis makes it ideal for study with three-dimensional CT. This presentation illustrates the advantages and drawbacks of three-dimensional CT in spinal abnormalities in children

Three-dimensional deformation of orthodontic brackets

Science.gov (United States)

Melenka, Garrett W; Nobes, David S; Major, Paul W

2013-01-01

Braces are used by orthodontists to correct the misalignment of teeth in the mouth. Archwire rotation is a particular procedure used to correct tooth inclination. Wire rotation can result in deformation to the orthodontic brackets, and an orthodontic torque simulator has been designed to examine this wire–bracket interaction. An optical technique has been employed to measure the deformation due to size and geometric constraints of the orthodontic brackets. Images of orthodontic brackets are collected using a stereo microscope and two charge-coupled device cameras, and deformation of orthodontic brackets is measured using a three-dimensional digital image correlation technique. The three-dimensional deformation of orthodontic brackets will be evaluated. The repeatability of the three-dimensional digital image correlation measurement method was evaluated by performing 30 archwire rotation tests using the same bracket and archwire. Finally, five Damon 3MX and five In-Ovation R self-ligating brackets will be compared using this technique to demonstrate the effect of archwire rotation on bracket design. PMID:23762201

Three-dimensional deformation of orthodontic brackets.

Science.gov (United States)

Melenka, Garrett W; Nobes, David S; Major, Paul W; Carey, Jason P

2013-01-01

Braces are used by orthodontists to correct the misalignment of teeth in the mouth. Archwire rotation is a particular procedure used to correct tooth inclination. Wire rotation can result in deformation to the orthodontic brackets, and an orthodontic torque simulator has been designed to examine this wire-bracket interaction. An optical technique has been employed to measure the deformation due to size and geometric constraints of the orthodontic brackets. Images of orthodontic brackets are collected using a stereo microscope and two charge-coupled device cameras, and deformation of orthodontic brackets is measured using a three-dimensional digital image correlation technique. The three-dimensional deformation of orthodontic brackets will be evaluated. The repeatability of the three-dimensional digital image correlation measurement method was evaluated by performing 30 archwire rotation tests using the same bracket and archwire. Finally, five Damon 3MX and five In-Ovation R self-ligating brackets will be compared using this technique to demonstrate the effect of archwire rotation on bracket design.

Three-dimensional plasma equilibrium near a separatrix

International Nuclear Information System (INIS)

Reiman, A.H.; Pomphrey, N.; Boozer, A.H.

1988-08-01

The limiting behavior of a general three-dimensional MHD equilibrium near a separatrix is calculated explicitly. No expansions in β or assumptions about island widths are made. Implications of the results for the numerical calculation of such equilibria, are discussed, as well as for issues concerning the existence of three-dimensional MHD equilibria. 16 refs., 2 figs

Advancing three-dimensional MEMS by complimentary laser micro manufacturing

Science.gov (United States)

Palmer, Jeremy A.; Williams, John D.; Lemp, Tom; Lehecka, Tom M.; Medina, Francisco; Wicker, Ryan B.

2006-01-01

This paper describes improvements that enable engineers to create three-dimensional MEMS in a variety of materials. It also provides a means for selectively adding three-dimensional, high aspect ratio features to pre-existing PMMA micro molds for subsequent LIGA processing. This complimentary method involves in situ construction of three-dimensional micro molds in a stand-alone configuration or directly adjacent to features formed by x-ray lithography. Three-dimensional micro molds are created by micro stereolithography (MSL), an additive rapid prototyping technology. Alternatively, three-dimensional features may be added by direct femtosecond laser micro machining. Parameters for optimal femtosecond laser micro machining of PMMA at 800 nanometers are presented. The technical discussion also includes strategies for enhancements in the context of material selection and post-process surface finish. This approach may lead to practical, cost-effective 3-D MEMS with the surface finish and throughput advantages of x-ray lithography. Accurate three-dimensional metal microstructures are demonstrated. Challenges remain in process planning for micro stereolithography and development of buried features following femtosecond laser micro machining.

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....

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...

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.

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

Computational study of three-dimensional wake structure

International Nuclear Information System (INIS)

Himeno, R.; Shirayama, S.; Kamo, K.; Kuwahara, K.

1986-01-01

Three-dimensional wake structure is studied by numerically solving the incompressible Navier-Stokes equations. Results are visualized by a three-dimensional color graphic system. It was found that a pair of vortex tubes separated from a body plays the most important role in the wake. Near the body vortex tubes are rather stable, however, they gradually become unsteady as they flow down

Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

International Nuclear Information System (INIS)

Hanrahan, Michael P.; Fought, Ellie L.; Windus, Theresa L.; Wheeler, Lance M.; Anderson, Nicholas C.

2017-01-01

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1 H– 29 Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1 H– 29 Si HETCOR and dipolar 2D 1 H– 1 H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Instead the 2D NMR spectra illustrate that there is large distribution of 1 H and 29 Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1 H– 29 Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29 Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH 3 ), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1 H and 29 Si chemical shifts. Furthermore, the approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.

Camphor: a good model for illustrating NMR techniques; Canfora: um bom modelo para ilustrar tecnicas de RMN

Energy Technology Data Exchange (ETDEWEB)

Yoneda, Julliane Diniz; Leal, Katia Zaccur [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Dept. de Fisico-Quimica]. E-mail: kzl@rmn.uff.br; Seidl, Peter Rudolf [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Escola de Quimica. Dept. de Processos Organicos; Azeredo, Rodrigo Bagueira de V. [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Inst. de Quimica. Dept. de Quimica Organica; Kleinpeter, Erich [Universitaet Potsdam (Germany). Chemisches Institut

2007-07-01

The use of Nuclear Magnetic Resonance spectroscopy to establish the three-dimensional structures of molecules is an important component of modern Chemistry courses. The combination of techniques that can be used for this purpose is conveniently illustrated by their application to the camphor molecule. This paper presents applications of several techniques used in NMR spectral interpretation in an increasing order of complexity. The result of individual experiments is illustrated in order to familiarize the user with the way connectivity through bonds and through space is established from 1D/2D-NMR spectra and molecular stereochemistry is determined from different NMR experiments. (author)

Standalone visualization tool for three-dimensional DRAGON geometrical models

International Nuclear Information System (INIS)

Lukomski, A.; McIntee, B.; Moule, D.; Nichita, E.

2008-01-01

DRAGON is a neutron transport and depletion code able to solve one-, two- and three-dimensional problems. To date DRAGON provides two visualization modules, able to represent respectively two- and three-dimensional geometries. The two-dimensional visualization module generates a postscript file, while the three dimensional visualization module generates a MATLAB M-file with instructions for drawing the tracks in the DRAGON TRACKING data structure, which implicitly provide a representation of the geometry. The current work introduces a new, standalone, tool based on the open-source Visualization Toolkit (VTK) software package which allows the visualization of three-dimensional geometrical models by reading the DRAGON GEOMETRY data structure and generating an axonometric image which can be manipulated interactively by the user. (author)

SNAP - a three dimensional neutron diffusion code

International Nuclear Information System (INIS)

McCallien, C.W.J.

1993-02-01

This report describes a one- two- three-dimensional multi-group diffusion code, SNAP, which is primarily intended for neutron diffusion calculations but can also carry out gamma calculations if the diffusion approximation is accurate enough. It is suitable for fast and thermal reactor core calculations and for shield calculations. SNAP can solve the multi-group neutron diffusion equations using finite difference methods. The one-dimensional slab, cylindrical and spherical geometries and the two-dimensional case are all treated as simple special cases of three-dimensional geometries. Numerous reflective and periodic symmetry options are available and may be used to reduce the number of mesh points necessary to represent the system. Extrapolation lengths can be specified at internal and external boundaries. (Author)

Three-dimensional fluorescence lifetime tomography

International Nuclear Information System (INIS)

Godavarty, Anuradha; Sevick-Muraca, Eva M.; Eppstein, Margaret J.

2005-01-01

Near-infrared fluorescence tomography using molecularly targeted lifetime-sensitive, fluorescent contrast agents have applications for early-stage cancer diagnostics. Yet, although the measurement of fluorescent lifetime imaging microscopy (FLIM) is extensively used in microscopy and spectroscopy applications, demonstration of fluorescence lifetime tomography for medical imaging is limited to two-dimensional studies. Herein, the feasibility of three-dimensional fluorescence-lifetime tomography on clinically relevant phantom volumes is established, using (i) a gain-modulated intensified charge coupled device (CCD) and modulated laser diode imaging system, (ii) two fluorescent contrast agents, e.g., Indocyanine green and 3-3'-Diethylthiatricarbocyanine iodide differing in their fluorescence lifetime by 0.62 ns, and (iii) a two stage approximate extended Kalman filter reconstruction algorithm. Fluorescence measurements of phase and amplitude were acquired on the phantom surface under different target to background fluorescence absorption (70:1, 100:1) and fluorescence lifetime (1:1, 2.1:1) contrasts at target depths of 1.4-2 cm. The Bayesian tomography algorithm was employed to obtain three-dimensional images of lifetime and absorption owing to the fluorophores

Structure and Dynamic Properties of Membrane Proteins using NMR

DEFF Research Database (Denmark)

Rösner, Heike; Kragelund, Birthe

2012-01-01

conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....

PASA - A Program for Automated Protein NMR Backbone Signal Assignment by Pattern-Filtering Approach

International Nuclear Information System (INIS)

Xu Yizhuang; Wang Xiaoxia; Yang Jun; Vaynberg, Julia; Qin Jun

2006-01-01

We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13 C α and/or 13 C β chemical shift matching. The pattern filter employs one or multiple constraints such as 13 C α /C β chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics

Development of three dimensional solid modeler

International Nuclear Information System (INIS)

Zahoor, R.M.A.

1999-01-01

The work presented in this thesis is aimed at developing a three dimensional solid modeler employing computer graphics techniques using C-Language. Primitives have been generated, by combination of plane surfaces, for various basic geometrical shapes including cylinder, cube and cone. Back face removal technique for hidden surface removal has also been incorporated. Various transformation techniques such as scaling, translation, and rotation have been included for the object animation. Three dimensional solid modeler has been created by the union of two primitives to demonstrate the capabilities of the developed program. (author)

Polycrystalline diamond detectors with three-dimensional electrodes

Energy Technology Data Exchange (ETDEWEB)

Lagomarsino, S., E-mail: lagomarsino@fi.infn.it [University of Florence, Department of Physics, Via Sansone 1, 50019 Sesto Fiorentino (Italy); INFN Firenze, Via B. Rossi 1, 50019 Sesto Fiorentino (Italy); Bellini, M. [INO-CNR Firenze, Largo E. Fermi 6, 50125 Firenze (Italy); Brianzi, M. [INFN Firenze, Via B. Rossi 1, 50019 Sesto Fiorentino (Italy); Carzino, R. [Smart Materials-Nanophysics, Istituto Italiano di Tecnologia, Genova, Via Morego 30, 16163 Genova (Italy); Cindro, V. [Joseph Stefan Institute, Jamova Cesta 39, 1000 Ljubljana (Slovenia); Corsi, C. [University of Florence, Department of Physics, Via Sansone 1, 50019 Sesto Fiorentino (Italy); LENS Firenze, Via N. Carrara 1, 50019 Sesto Fiorentino (Italy); Morozzi, A.; Passeri, D. [INFN Perugia, Perugia (Italy); Università degli Studi di Perugia, Dipartimento di Ingegneria, via G. Duranti 93, 06125 Perugia (Italy); Sciortino, S. [University of Florence, Department of Physics, Via Sansone 1, 50019 Sesto Fiorentino (Italy); INFN Firenze, Via B. Rossi 1, 50019 Sesto Fiorentino (Italy); Servoli, L. [INFN Perugia, Perugia (Italy)

2015-10-01

The three-dimensional concept in diamond detectors has been applied, so far, to high quality single-crystal material, in order to test this technology in the best available conditions. However, its application to polycrystalline chemical vapor deposited diamond could be desirable for two reasons: first, the short inter-electrode distance of three-dimensional detectors should improve the intrinsically lower collection efficiency of polycrystalline diamond, and second, at high levels of radiation damage the performances of the poly-crystal material are not expected to be much lower than those of the single crystal one. We report on the fabrication and test of three-dimensional polycrystalline diamond detectors with several inter-electrode distances, and we demonstrate that their collection efficiency is equal or higher than that obtained with conventional planar detectors fabricated with the same material. - Highlights: • Pulsed laser fabrication of polycristalline diamond detectors with 3D electrodes. • Measurement of the charge collection efficiency (CCE) under beta irradiation. • Comparation between the CCE of 3D and conventional planar diamond sensors. • A rationale for the behavior of three-dimensional and planar sensors is given.

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.

Three dimensional diffusion calculations of nuclear reactors

International Nuclear Information System (INIS)

Caspo, N.

1981-07-01

This work deals with the three dimensional calculation of nuclear reactors using the code TRITON. The purposes of the work were to perform three-dimensional computations of the core of the Soreq nuclear reactor and of the power reactor ZION and to validate the TRITON code. Possible applications of the TRITON code in Soreq reactor calculations and in power reactor research are suggested. (H.K.)

Study of three-dimensional image display by systemic CT

International Nuclear Information System (INIS)

Fujioka, Tadao; Ebihara, Yoshiyuki; Unei, Hiroshi; Hayashi, Masao; Shinohe, Tooru; Wada, Yuji; Sakai, Takatsugu; Kashima, Kenji; Fujita, Yoshihiro

1989-01-01

A head phantom for CT was scanned at 2 mm intervals from the cervix to the vertex in an attempt to obtain a three-dimensional image display of bones and facial epidermis from an ordinary axial image. Clinically, three-dimensional images were formed at eye sockets and hip joints. With the three-dimensional image using the head phantom, the entire head could be displayed at any angle. Clinically, images were obtained that could not be attained by ordinary CT scanning, such as broken bones in eye sockets and stereoscopic structure at the bottom of a cranium. The three-dimensional image display is considered to be useful in clinical diagnosis. (author)

Continuum modeling of three-dimensional truss-like space structures

Science.gov (United States)

Nayfeh, A. H.; Hefzy, M. S.

1978-01-01

A mathematical and computational analysis capability has been developed for calculating the effective mechanical properties of three-dimensional periodic truss-like structures. Two models are studied in detail. The first, called the octetruss model, is a three-dimensional extension of a two-dimensional model, and the second is a cubic model. Symmetry considerations are employed as a first step to show that the specific octetruss model has four independent constants and that the cubic model has two. The actual values of these constants are determined by averaging the contributions of each rod element to the overall structure stiffness. The individual rod member contribution to the overall stiffness is obtained by a three-dimensional coordinate transformation. The analysis shows that the effective three-dimensional elastic properties of both models are relatively close to each other.

Structural characterization of chemical warfare agent degradation products in decontamination solutions with proton band-selective (1)H-(31)P NMR spectroscopy.

Science.gov (United States)

Koskela, Harri; Hakala, Ullastiina; Vanninen, Paula

2010-06-15

Decontamination solutions, which are usually composed of strong alkaline chemicals, are used for efficient detoxification of chemical warfare agents (CWAs). The analysis of CWA degradation products directly in decontamination solutions is challenging due to the nature of the matrix. Furthermore, occasionally an unforeseen degradation pathway can result in degradation products which could be eluded to in standard analyses. Here, we present the results of the application of proton band-selective (1)H-(31)P NMR spectroscopy, i.e., band-selective 1D (1)H-(31)P heteronuclear single quantum coherence (HSQC) and band-selective 2D (1)H-(31)P HSQC-total correlation spectroscopy (TOCSY), for ester side chain characterization of organophosphorus nerve agent degradation products in decontamination solutions. The viability of the approach is demonstrated with a test mixture of typical degradation products of nerve agents sarin, soman, and VX. The proton band-selective (1)H-(31)P NMR spectroscopy is also applied in characterization of unusual degradation products of VX in GDS 2000 solution.

Three-dimensional simulations of resistance spot welding

DEFF Research Database (Denmark)

Nielsen, Chris Valentin; Zhang, Wenqi; Perret, William

2014-01-01

This paper draws from the fundamentals of electro-thermo-mechanical coupling to the main aspects of finite element implementation and three-dimensional modelling of resistance welding. A new simulation environment is proposed in order to perform three-dimensional simulations and optimization...... of resistance welding together with the simulations of conventional and special-purpose quasi-static mechanical tests. Three-dimensional simulations of resistance welding consider the electrical, thermal, mechanical and metallurgical characteristics of the material as well as the operating conditions...... of the welding machines. Simulations of the mechanical tests take into account material softening due to the accumulation of ductile damage and cover conventional tests, such as tensile–shear tests, cross-tension test and peel tests, as well as the possibility of special-purpose tests designed by the users...

Depth-enhanced three-dimensional-two-dimensional convertible display based on modified integral imaging.

Science.gov (United States)

Park, Jae-Hyeung; Kim, Hak-Rin; Kim, Yunhee; Kim, Joohwan; Hong, Jisoo; Lee, Sin-Doo; Lee, Byoungho

2004-12-01

A depth-enhanced three-dimensional-two-dimensional convertible display that uses a polymer-dispersed liquid crystal based on the principle of integral imaging is proposed. In the proposed method, a lens array is located behind a transmission-type display panel to form an array of point-light sources, and a polymer-dispersed liquid crystal is electrically controlled to pass or to scatter light coming from these point-light sources. Therefore, three-dimensional-two-dimensional conversion is accomplished electrically without any mechanical movement. Moreover, the nonimaging structure of the proposed method increases the expressible depth range considerably. We explain the method of operation and present experimental results.

An algorithm for three-dimensional imaging in the positron camera

International Nuclear Information System (INIS)

Chen Kun; Ma Mei; Xu Rongfen; Shen Miaohe

1986-01-01

A mathematical algorithm of back-projection filtered for image reconstructions using two-dimensional signals detected from parallel multiwire proportional chambers is described. The approaches of pseudo three-dimensional and full three-dimensional image reconstructions are introduced, and the available point response functions are defined as well. The designing parameters and computation procedure of the full three-dimensional method is presented

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

Evaluation of three-dimensional virtual perception of garments

Science.gov (United States)

Aydoğdu, G.; Yeşilpinar, S.; Erdem, D.

2017-10-01

In recent years, three-dimensional design, dressing and simulation programs came into prominence in the textile industry. By these programs, the need to produce clothing samples for every design in design process has been eliminated. Clothing fit, design, pattern, fabric and accessory details and fabric drape features can be evaluated easily. Also, body size of virtual mannequin can be adjusted so more realistic simulations can be created. Moreover, three-dimensional virtual garment images created by these programs can be used while presenting the product to end-user instead of two-dimensional photograph images. In this study, a survey was carried out to investigate the visual perception of consumers. The survey was conducted for three different garment types, separately. Questions about gender, profession etc. was asked to the participants and expected them to compare real samples and artworks or three-dimensional virtual images of garments. When survey results were analyzed statistically, it is seen that demographic situation of participants does not affect visual perception and three-dimensional virtual garment images reflect the real sample characteristics better than artworks for each garment type. Also, it is reported that there is no perception difference depending on garment type between t-shirt, sweatshirt and tracksuit bottom.

Rapid collection and identification of a novel component from Clausena lansium Skeels leaves by means of three-dimensional preparative gas chromatography and nuclear magnetic resonance/infrared/mass spectrometric analysis

Energy Technology Data Exchange (ETDEWEB)

Sciarrone, Danilo [Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, University of Messina, Viale Annunziata, 98168, Messina (Italy); Chromaleont s.r.l. A start-up of the University of Messina, c/o University of Messina, Viale Annunziata, 98168 Messina (Italy); Pantò, Sebastiano [Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, University of Messina, Viale Annunziata, 98168, Messina (Italy); Rotondo, Archimede [Dipartimento di Scienze Chimiche, Università di Messina, Via D’Alcontres 31, 98166 Messina (Italy); Tedone, Laura; Tranchida, Peter Quinto [Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, University of Messina, Viale Annunziata, 98168, Messina (Italy); Dugo, Paola [Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, University of Messina, Viale Annunziata, 98168, Messina (Italy); Centro Integrato di Ricerca (C.I.R.), Università Campus Bio-Medico, Via Álvaro del Portillo, 21 - 00128 Roma (Italy); Mondello, Luigi, E-mail: lmondello@unime.it [Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, University of Messina, Viale Annunziata, 98168, Messina (Italy); Centro Integrato di Ricerca (C.I.R.), Università Campus Bio-Medico, Via Álvaro del Portillo, 21 - 00128 Roma (Italy)

2013-06-27

Graphical abstract: -- Highlights: •A recently-developed three-dimensional prep-GC system has been applied to wampee essential oil. •The prep GC system enables the rapid collection of pure compounds from complex samples. •An isolated unknown solute was identified through NMR, IR and MS data. •The structure of an oxygenated sesquiterpene is here reported for the first time. -- Abstract: The present research reports the use of a three-dimensional preparative gas chromatography (prep GC) system, equipped with three Deans-switch devices and 5%diphenyl/wax/mid-polarity ionic liquid stationary phases, for the isolation of volatile components from a complex natural source, namely wampee essential oil (derived from Clausena lansium Skeels leaves). Collection was performed by using a simple and effective lab-constructed trapping device. Initially, an unknown (and abundant) wampee oil constituent was erroneously identified as α-sinensal, through an MS database search (a low similarity match was attained), performed after a GC-quadMS experiment., The unknown compound was then the isolated by using the novel prep GC system, in a highly pure form (at the mg level), and was correctly identified by using nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FTIR) and mass spectrometry (MS). Both FTIR and MS data were used to confirm the NMR information. The name given to the molecule was (2E,6E)-2-methyl-6-(4-methylcyclohex-3-enylidene)hept-2-enal. The results herein described will demonstrate the need for a high-resolution GC step, prior to analyte collection, in the prep GC analysis of complex samples.

Rapid collection and identification of a novel component from Clausena lansium Skeels leaves by means of three-dimensional preparative gas chromatography and nuclear magnetic resonance/infrared/mass spectrometric analysis

International Nuclear Information System (INIS)

Sciarrone, Danilo; Pantò, Sebastiano; Rotondo, Archimede; Tedone, Laura; Tranchida, Peter Quinto; Dugo, Paola; Mondello, Luigi

2013-01-01

Graphical abstract: -- Highlights: •A recently-developed three-dimensional prep-GC system has been applied to wampee essential oil. •The prep GC system enables the rapid collection of pure compounds from complex samples. •An isolated unknown solute was identified through NMR, IR and MS data. •The structure of an oxygenated sesquiterpene is here reported for the first time. -- Abstract: The present research reports the use of a three-dimensional preparative gas chromatography (prep GC) system, equipped with three Deans-switch devices and 5%diphenyl/wax/mid-polarity ionic liquid stationary phases, for the isolation of volatile components from a complex natural source, namely wampee essential oil (derived from Clausena lansium Skeels leaves). Collection was performed by using a simple and effective lab-constructed trapping device. Initially, an unknown (and abundant) wampee oil constituent was erroneously identified as α-sinensal, through an MS database search (a low similarity match was attained), performed after a GC-quadMS experiment., The unknown compound was then the isolated by using the novel prep GC system, in a highly pure form (at the mg level), and was correctly identified by using nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FTIR) and mass spectrometry (MS). Both FTIR and MS data were used to confirm the NMR information. The name given to the molecule was (2E,6E)-2-methyl-6-(4-methylcyclohex-3-enylidene)hept-2-enal. The results herein described will demonstrate the need for a high-resolution GC step, prior to analyte collection, in the prep GC analysis of complex samples

Three-dimensional reconstruction and visualization system for medical images

International Nuclear Information System (INIS)

Preston, D.F.; Batnitzky, S.; Kyo Rak Lee; Cook, P.N.; Cook, L.T.; Dwyer, S.J.

1982-01-01

A three-dimensional reconstruction and visualization system could be of significant advantage in medical application such as neurosurgery and radiation treatment planning. The reconstructed anatomic structures from CT head scans could be used in a head stereotactic system to help plan the surgical procedure and the radiation treatment for a brain lesion. Also, the use of three-dimensional reconstruction algorithm provides for quantitative measures such as volume and surface area estimation of the anatomic features. This aspect of the three-dimensional reconstruction system may be used to monitor the progress or staging of a disease and the effects of patient treatment. Two cases are presented to illustrate the three-dimensional surface reconstruction and visualization system

Three-dimensional labeling program for elucidation of the geometric properties of biological particles in three-dimensional space.

Science.gov (United States)

Nomura, A; Yamazaki, Y; Tsuji, T; Kawasaki, Y; Tanaka, S

1996-09-15

For all biological particles such as cells or cellular organelles, there are three-dimensional coordinates representing the centroid or center of gravity. These coordinates and other numerical parameters such as volume, fluorescence intensity, surface area, and shape are referred to in this paper as geometric properties, which may provide critical information for the clarification of in situ mechanisms of molecular and cellular functions in living organisms. We have established a method for the elucidation of these properties, designated the three-dimensional labeling program (3DLP). Algorithms of 3DLP are so simple that this method can be carried out through the use of software combinations in image analysis on a personal computer. To evaluate 3DLP, it was applied to a 32-cell-stage sea urchin embryo, double stained with FITC for cellular protein of blastomeres and propidium iodide for nuclear DNA. A stack of optical serial section images was obtained by confocal laser scanning microscopy. The method was found effective for determining geometric properties and should prove applicable to the study of many different kinds of biological particles in three-dimensional space.

Analysis and validation of carbohydrate three-dimensional structures

International Nuclear Information System (INIS)

Lütteke, Thomas

2009-01-01

The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described. Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures

Progress of radiotherapy by three-dimensional treatment planning

International Nuclear Information System (INIS)

Imada, Hajime; Nomoto, Satoshi; Takahashi, Hiroyuki; Nakata, Hajime

1998-01-01

The recent progress of three-dimensional radiation treatment planning was reviewed. And clinical cases such as lung cancer and breast cancer are introduced. In the University of Occupational and Development Health, the treatment system FOCUS which is made up of CT simulator and linac was used mainly. Three-dimensional treatment planning was carried for about 90% of 330 patients who underwent radiotherapy for one year. The target becomes to be accurate and dose distribution with all CT slices in radiation field can be confirmed by using three-dimensional radiation treatment planning apparatus. High dose irradiation localized to tumor part is possible. Relations between total dose and volume of normal tissue and/or tumor can be estimated numerically and easily by DVH. A prediction of indication and affection became possible by this procedure. In conclusion, generalization of three-dimensional radiation treatment planning will bring progress of more effective radiotherapy with less adverse reaction. (K.H.). 21 refs

Three Dimensional Polarimetric Neutron Tomography of Magnetic Fields

DEFF Research Database (Denmark)

Sales, Morten; Strobl, Markus; Shinohara, Takenao

2018-01-01

Through the use of Time-of-Flight Three Dimensional Polarimetric Neutron Tomography (ToF 3DPNT) we have for the first time successfully demonstrated a technique capable of measuring and reconstructing three dimensional magnetic field strengths and directions unobtrusively and non-destructively wi......Through the use of Time-of-Flight Three Dimensional Polarimetric Neutron Tomography (ToF 3DPNT) we have for the first time successfully demonstrated a technique capable of measuring and reconstructing three dimensional magnetic field strengths and directions unobtrusively and non...... and reconstructed, thereby providing the proof-of-principle of a technique able to reveal hitherto unobtainable information on the magnetic fields in the bulk of materials and devices, due to a high degree of penetration into many materials, including metals, and the sensitivity of neutron polarisation to magnetic...... fields. The technique puts the potential of the ToF time structure of pulsed neutron sources to full use in order to optimise the recorded information quality and reduce measurement time....

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

Application of three-dimensional CT reconstruction cranioplasty

International Nuclear Information System (INIS)

Yan Shuli; Yun Yongxing; Wan Kunming; Qiu Jian

2011-01-01

Objective: To study the application of three-dimensional CT reconstruction in cranioplasty. Methods: 46 patients with skull defect were divided into two group. One group underwent CT examination and three-dimensional reconstruction, and then the Titanium nets production company manufactured corresponding titanium meshes were shaped those data before the operation. The other group received traditional operation in which titanium meshes were shaped during operation. The average time of operation were compared. Results: The average time of operation of the first group is 86.6±13.6 mins, and that of the second group is 115±15.0 mins. The difference of average operation time between the two groups was statistically significant. Conclusion: Three-dimensional CT reconstruction techniques contribute to shorten the average operation time, reduce the intensity of neurosurgeon's work and the patien's risk. (authors)

Computational methods for three-dimensional microscopy reconstruction

CERN Document Server

Frank, Joachim

2014-01-01

Approaches to the recovery of three-dimensional information on a biological object, which are often formulated or implemented initially in an intuitive way, are concisely described here based on physical models of the object and the image-formation process. Both three-dimensional electron microscopy and X-ray tomography can be captured in the same mathematical framework, leading to closely-related computational approaches, but the methodologies differ in detail and hence pose different challenges. The editors of this volume, Gabor T. Herman and Joachim Frank, are experts in the respective methodologies and present research at the forefront of biological imaging and structural biology.   Computational Methods for Three-Dimensional Microscopy Reconstruction will serve as a useful resource for scholars interested in the development of computational methods for structural biology and cell biology, particularly in the area of 3D imaging and modeling.

Three-dimensional tokamak equilibria and stellarators with two-dimensional magnetic symmetry

International Nuclear Information System (INIS)

Garabedian, P.R.

1997-01-01

Three-dimensional computer codes have been developed to simulate equilibrium, stability and transport in tokamaks and stellarators. Bifurcated solutions of the tokamak problem suggest that three-dimensional effects may be more important than has generally been thought. Extensive calculations have led to the discovery of a stellarator configuration with just two field periods and with aspect ratio 3.2 that has a magnetic field spectrum B mn with toroidal symmetry. Numerical studies of equilibrium, stability and transport for this new device, called the Modular Helias-like Heliac 2 (MHH2), will be presented. (author)

Zero in on Key Open Problems in Automated NMR Protein Structure Determination

KAUST Repository

Abbas, Ahmed

2015-11-12

Nuclear magnetic resonance (NMR) is one of the main approaches for protein struc- ture determination. The biggest advantage of this approach is that it can determine the three-dimensional structure of the protein in the solution phase. Thus, the natural dynamics of the protein can be studied. However, NMR protein structure determina- tion is an expertise intensive and time-consuming process. If the structure determi- nation process can be accelerated or even automated by computational methods, that will significantly advance the structural biology field. Our goal in this dissertation is to propose highly efficient and error tolerant methods that can work well on real and noisy data sets of NMR. Our first contribution in this dissertation is the development of a novel peak pick- ing method (WaVPeak). First, WaVPeak denoises the NMR spectra using wavelet smoothing. A brute force method is then used to identify all the candidate peaks. Af- ter that, the volume of each candidate peak is estimated. Finally, the peaks are sorted according to their volumes. WaVPeak is tested on the same benchmark data set that was used to test the state-of-the-art method, PICKY. WaVPeak shows significantly better performance than PICKY in terms of recall and precision. Our second contribution is to propose an automatic method to select peaks pro- duced by peak picking methods. This automatic method is used to overcome the limitations of fixed number-based methods. Our method is based on the Benjamini- Hochberg (B-H) algorithm. The method is used with both WaVPeak and PICKY to automatically select the number of peaks to return from out of hundreds of candidate peaks. The volume (in WaVPeak) and the intensity (in PICKY) are converted into p-values. Peaks that have p-values below some certain threshold are selected. Ex- perimental results show that the new method is better than the fixed number-based method in terms of recall. To improve precision, we tried to eliminate false peaks using

Evaluation of diagnostic quality in musculoskeletal three-dimensional CT scans

International Nuclear Information System (INIS)

Vannier, M.W.; Hildebolt, C.F.; Gilula, L.A.; Sutherland, C.J.; Offutt, C.J.; Drebin, R.; Mantle, M.; Giordono, T.A.

1988-01-01

A major application of three-dimensional computed tomography (CT) is in the imaging of the skeleton. Three-dimensional CT has an important role in determining the presence and extent of congenital and acquired orthopedic abnormalities. The objective of this study was to compare the diagnostic sensitivity and specificity of three-dimensional CT, planar CT, and plain radiography in the detection and characterization of orthopedic abnormalities. Three-dimensional CT scan reconstructions were obtained by two methods, surface reconstruction and volumetric techniques. Seventy patients were imaged with CT, three-dimensional CT, and plain radiography. The consensus opinion of experts with access to all images plus clinical history, surgical findings, and follow-up findings were taken as truth. Expert radiologists read these cases in a blinded fashion. The results were compared using receiver operating characteristic (ROC) analysis. The diagnostic value of each three-dimensional reconstruction method and the parameters used to perform the reconstructions were evaluated

Three-dimensional echocardiography of normal and pathologic mitral valve: a comparison with two-dimensional transesophageal echocardiography

NARCIS (Netherlands)

Salustri, A.; Becker, A. E.; van Herwerden, L.; Vletter, W. B.; ten Cate, F. J.; Roelandt, J. R.

1996-01-01

This study was done to ascertain whether three-dimensional echocardiography can facilitate the diagnosis of mitral valve abnormalities. The value of the additional information provided by three-dimensional echocardiography compared with two-dimensional multiplane transesophageal echocardiography for

Study of the nonlinear three-dimensional Debye screening in plasmas

International Nuclear Information System (INIS)

Lin Chang; Zhao Jinbao; Zhang Xiulian

2000-01-01

The nonlinear three-dimensional Debye screening in plasmas is investigated. New analytical solutions for the three-dimensional Poisson equation have been obtained for the nonlinear Debye potential for the first time. We derive exact analytical expression for the special case of the nonlinear three-dimensional Debye screening in plasmas. (orig.)

Heat engine in the three-dimensional spacetime

Energy Technology Data Exchange (ETDEWEB)

Mo, Jie-Xiong [Institute of Theoretical Physics, Lingnan Normal University,Zhanjiang, 524048, Guangdong (China); Department of Physics, Lingnan Normal University,Zhanjiang, 524048, Guangdong (China); Liang, Feng [Department of Physics, Lingnan Normal University,Zhanjiang, 524048, Guangdong (China); Li, Gu-Qiang [Institute of Theoretical Physics, Lingnan Normal University,Zhanjiang, 524048, Guangdong (China); Department of Physics, Lingnan Normal University,Zhanjiang, 524048, Guangdong (China)

2017-03-02

We define a kind of heat engine via three-dimensional charged BTZ black holes. This case is quite subtle and needs to be more careful. The heat flow along the isochores does not equal to zero since the specific heat C{sub V}≠0 and this point completely differs from the cases discussed before whose isochores and adiabats are identical. So one cannot simply apply the paradigm in the former literatures. However, if one introduces a new thermodynamic parameter associated with the renormalization length scale, the above problem can be solved. We obtain the analytical efficiency expression of the three-dimensional charged BTZ black hole heat engine for two different schemes. Moreover, we double check with the exact formula. Our result presents the first specific example for the sound correctness of the exact efficiency formula. We argue that the three-dimensional charged BTZ black hole can be viewed as a toy model for further investigation of holographic heat engine. Furthermore, we compare our result with that of the Carnot cycle and extend the former result to three-dimensional spacetime. In this sense, the result in this paper would be complementary to those obtained in four-dimensional spacetime or ever higher. Last but not the least, the heat engine efficiency discussed in this paper may serve as a criterion to discriminate the two thermodynamic approaches introduced in ref. https://www.doi.org/10.1103/PhysRevD.92.124069 and our result seems to support the approach which introduces a new thermodynamic parameter R=r{sub 0}.

Subjective figure reversal in two- and three-dimensional perceptual space.

Science.gov (United States)

Radilová, J; Radil-Weiss, T

1984-08-01

A permanently illuminated pattern of Mach's truncated pyramid can be perceived according to the experimental instruction given, either as a three-dimensional reversible figure with spontaneously changing convex and concave interpretation (in one experiment), or as a two-dimensional reversible figure-ground pattern (in another experiment). The reversal rate was about twice as slow, without the subjects being aware of it, if it was perceived as a three-dimensional figure compared to the situation when it was perceived as two-dimensional. It may be hypothetized that in the three-dimensional case, the process of perception requires more sequential steps than in the two-dimensional one.

Three-Dimensional Reconstruction of Sandpile Interiors

Science.gov (United States)

Seidler, G. T.

2001-03-01

The granular bed, or sandpile, has become one of the condensed matter physicist's favorite systems. In addition to conceptual appeal, the simplest sandpile of monodisperse hard spheres is a valuable model system for understanding powders, liquids, and metallic glasses. Any fundamental approach to the transport and mechanical properties of three-dimensional mesoscale disordered materials must follow from a thorough understanding of their structure. However, in the overwhelming majority of cases, structure measurements have been limited to the mean filling fraction and the structural autocorrelation function. This is particularly unfortunate in the ongoing sandpile renaissance, where some of the most interesting questions concern structure and the relationship between structure and dynamics. I will discuss the combination of synchrotron x-ray microtomography and computer vision algorithms to perform three-dimensional virtual reconstructions of real sandpiles. This technique is rapid and noninvasive, and is applicable to samples large enough to separate bulk and boundary properties. The resulting complete knowledge of structure can be used to calculate otherwise inaccessible correlation functions. I will present results for several measures of the bond-orientational order in three-dimensional sandpiles, including fabric tensors and nematic order parameters.

A plastic surgery application in evolution: three-dimensional printing.

Science.gov (United States)

Gerstle, Theodore L; Ibrahim, Ahmed M S; Kim, Peter S; Lee, Bernard T; Lin, Samuel J

2014-02-01

Three-dimensional printing represents an evolving technology still in its infancy. Currently, individuals and small business entities have the ability to manufacture physical objects from digital renderings, computer-aided design, and open source files. Design modifications and improvements in extrusion methods have made this technology much more affordable. This article explores the potential uses of three-dimensional printing in plastic surgery. A review was performed detailing the known uses of three-dimensional printing in medicine. The potential applications of three-dimensional printing in plastic surgery are discussed. Various applications for three-dimensional printing technology have emerged in medicine, including printing organs, printing body parts, bio-printing, and computer-aided tissue engineering. In plastic surgery, these tools offer various prospective applications for surgical planning, resident education, and the development of custom prosthetics. Numerous applications exist in medicine, including the printing of devices, implants, tissue replacements, and even whole organs. Plastic surgeons may likely find this technology indispensable in surgical planning, education, and prosthetic device design and development in the near future.

Three-dimensional (3D) analysis of the temporomandibular joint

DEFF Research Database (Denmark)

Kitai, N.; Kreiborg, S.; Murakami, S.

Symposium Orthodontics 2001: Where are We Now? Where are We Going?, three-dimensional analysis, temporomandibular joint......Symposium Orthodontics 2001: Where are We Now? Where are We Going?, three-dimensional analysis, temporomandibular joint...

Study on three dimensional seismic isolation system

International Nuclear Information System (INIS)

Morishita, Masaki; Kitamura, Seiji

2003-01-01

Japan Nuclear Cycle Development Institute (JNC) and Japan Atomic Power Company (JAPC) launched joint research programs on structural design and three-dimensional seismic isolation technologies, as part of the supporting R and D activities for the feasibility studies on commercialized fast breeder reactor cycle systems. A research project by JAPC under the auspices of the Ministry of Economy, Trade, and Industry (METI) with technical support by JNC is included in this joint study. This report contains the results of the research on the three-dimensional seismic isolation technologies, and the results of this year's study are summarized in the following five aspects. (1) Study on Earthquake Condition for Developing 3-dimensional Base Isolation System. The case study S2 is one of the maximum ground motions, of which the records were investigated up to this time. But a few observed near the fault exceed the case study S2 in the long period domain, depending on the fault length and conditions. Generally it is appropriate that the response spectra ratio (vertical/horizontal) is 0.6. (2) Performance Requirement for 3-dimensional Base Isolation System and Devices. Although the integrity map of main equipment/piping dominate the design criteria for the 3-dimensional base isolation system, the combined integrity map is the same as those of FY 2000, which are under fv=1Hz and over hv=20%. (3) Developing Targets and Schedule for 3-dimensional Isolation Technology. The target items for 3-dimensional base isolation system were rearranged into a table, and developing items to be examined concerning the device were also adjusted. A development plan until FY 2009 was made from the viewpoint of realization and establishment of a design guideline on 3-dimensional base isolation system. (4) Study on 3-dimensional Entire Building Base Isolation System. Three ideas among six ideas that had been proposed in FY2001, i.e., '3-dimensional base isolation system incorporating hydraulic

Three-dimensional imaging utilizing energy discrimination

International Nuclear Information System (INIS)

Gunter, D.L.; Hoffman, K.R.; Beck, R.N.

1990-01-01

An algorithm is proposed for three-dimensional image reconstruction in nuclear medicine which uses scattered radiation rather than multiple projected images to determine the source depth within the body. Images taken from numerous energy windows are combined to construct the source distribution in the body. The gamma-ray camera is not moved during the imaging process. Experiments with both Tc-99m and Ga-67 demonstrate that two channels of depth information can be extracted from the low energy images produced by scattered radiation. By combining this technique with standard SPECT reconstruction using multiple projections the authors anticipate much improved spatial resolution in the overall three-dimensional reconstruction

Three dimensional analysis of laterally loaded piles

International Nuclear Information System (INIS)

Yilmaz, C.

1987-01-01

In this study static analysis of laterally loaded pile is studied by the three models. The first model is the beam on discrete elastic springs. This model is analyzed using a flexibility method. The second model is the beam on a two-parameter elastic foundation. This model is analyzed using the linear finite element method. The third model is the finite element model, using the three-dimensional iso-parametric parabolic brick element. Three-dimensional pile group analysis is also performed using elastic constants of single pile obtained by any one of the above analyses. The main objective is to develop computer programs for each model related to single piles and to group analysis. Then, the deflections, rotations, moments, shears, stresses and strains of the single pile are obtained at any arbitrary point. Comparison is made between each model and with other studies such as Poulos 1971, Desai and Appel 1976. In addition, to provide a benchmark of three-dimensional finite element analysis, the Boussinesq problem is analyzed. (orig.)

Three-dimensional attached viscous flow basic principles and theoretical foundations

CERN Document Server

Hirschel, Ernst Heinrich; Kordulla, Wilhelm

2014-01-01

Viscous flow is usually treated in the frame of boundary-layer theory and as a two-dimensional flow. At best, books on boundary layers provide the describing equations for three-dimensional boundary layers, and solutions only for certain special cases.   This book presents the basic principles and theoretical foundations of three-dimensional attached viscous flows as they apply to aircraft of all kinds. Though the primary flight speed range is that of civil air transport vehicles, flows past other flying vehicles up to hypersonic speeds are also considered. Emphasis is put on general three-dimensional attached viscous flows and not on three-dimensional boundary layers, as this wider scope is necessary in view of the theoretical and practical problems that have to be overcome in practice.   The specific topics covered include weak, strong, and global interaction; the locality principle; properties of three-dimensional viscous flows; thermal surface effects; characteristic properties; wall compatibility con...

Static and dynamic properties of three-dimensional dot-type magnonic crystals

International Nuclear Information System (INIS)

Maksymov, Artur; Spinu, Leonard

2016-01-01

The static and dynamic magnetization of three-dimensional magnonic metamaterials has been investigated. By numerical means it was analyzed the impact of space dimensionality on the properties of magnonic crystal with unit cell consisting of four dots. It is find out the possibility of multi-vortex core formation which is related to the increasing of the crystal height by three-dimensional periodicity of single crystal layer. Additionally is provided the analysis of ferromagnetic resonance phenomenon for two-dimensional and three-dimensional structures. For the unsaturated magnetization of three-dimensional crystal the several pronounced resonance frequencies were detected.

Static and dynamic properties of three-dimensional dot-type magnonic crystals

Energy Technology Data Exchange (ETDEWEB)

Maksymov, Artur, E-mail: maxyartur@gmail.com [Advanced Materials Research Institute, University of New Orleans, LA 70148 (United States); Department of General Physics, Chernivtsi National University, Chernivtsi 58012 (Ukraine); Spinu, Leonard [Advanced Materials Research Institute, University of New Orleans, LA 70148 (United States); Department of Physics, University of New Orleans, New Orleans, LA 70148 (United States)

2016-04-01

The static and dynamic magnetization of three-dimensional magnonic metamaterials has been investigated. By numerical means it was analyzed the impact of space dimensionality on the properties of magnonic crystal with unit cell consisting of four dots. It is find out the possibility of multi-vortex core formation which is related to the increasing of the crystal height by three-dimensional periodicity of single crystal layer. Additionally is provided the analysis of ferromagnetic resonance phenomenon for two-dimensional and three-dimensional structures. For the unsaturated magnetization of three-dimensional crystal the several pronounced resonance frequencies were detected.

Three-Dimensional Flows

CERN Document Server

Araujo, Vitor; Viana, Marcelo

2010-01-01

In this book, the authors present the elements of a general theory for flows on three-dimensional compact boundaryless manifolds, encompassing flows with equilibria accumulated by regular orbits. The book aims to provide a global perspective of this theory and make it easier for the reader to digest the growing literature on this subject. This is not the first book on the subject of dynamical systems, but there are distinct aspects which together make this book unique. Firstly, this book treats mostly continuous time dynamical systems, instead of its discrete counterpart, exhaustively treated

Three-diemensional materials science: An intersection of three-dimensional reconstructions and simulations

DEFF Research Database (Denmark)

Thornton, Katsuyo; Poulsen, Henning Friis

2008-01-01

The recent development of experimental techniques that rapidly reconstruct the three-dimensional microstructures of solids has given rise to new possibilities for developing a deeper understanding of the evolution of microstructures and the effects of microstructures on materials properties. Comb...... an overview of this emerging field of materials science, as well as brief descriptions of selected methods and their applicability.......The recent development of experimental techniques that rapidly reconstruct the three-dimensional microstructures of solids has given rise to new possibilities for developing a deeper understanding of the evolution of microstructures and the effects of microstructures on materials properties....... Combined with three-dimensional (3D) simulations and analyses that are capable of handling the complexity of these microstructures, 3D reconstruction, or tomography, has become a powerful tool that provides clear insights into materials processing and properties. This introductory article provides...

New method for solving three-dimensional Schroedinger equation

International Nuclear Information System (INIS)

Melezhik, V.S.

1990-01-01

The method derived recently for solving a multidimensional scattering problem is applied to a three-dimensional Schroedinger equation. As compared with direct three-dimensional calculations of finite elements and finite differences, this approach gives sufficiently accurate upper and lower approximations to the helium-atom binding energy, which demonstrates its efficiency. 15 refs.; 1 fig.; 2 tabs

Resonance fluorescence based two- and three-dimensional atom localization

Science.gov (United States)

Wahab, Abdul; Rahmatullah; Qamar, Sajid

2016-06-01

Two- and three-dimensional atom localization in a two-level atom-field system via resonance fluorescence is suggested. For the two-dimensional localization, the atom interacts with two orthogonal standing-wave fields, whereas for the three-dimensional atom localization, the atom interacts with three orthogonal standing-wave fields. The effect of the detuning and phase shifts associated with the corresponding standing-wave fields is investigated. A precision enhancement in position measurement of the single atom can be noticed via the control of the detuning and phase shifts.

Method for coupling two-dimensional to three-dimensional discrete ordinates calculations

International Nuclear Information System (INIS)

Thompson, J.L.; Emmett, M.B.; Rhoades, W.A.; Dodds, H.L. Jr.

1985-01-01

A three-dimensional (3-D) discrete ordinates transport code, TORT, has been developed at the Oak Ridge National Laboratory for radiation penetration studies. It is not feasible to solve some 3-D penetration problems with TORT, such as a building located a large distance from a point source, because (a) the discretized 3-D problem is simply too big to fit on the computer or (b) the computing time (and corresponding cost) is prohibitive. Fortunately, such problems can be solved with a hybrid approach by coupling a two-dimensional (2-D) description of the point source, which is assumed to be azimuthally symmetric, to a 3-D description of the building, the region of interest. The purpose of this paper is to describe this hybrid methodology along with its implementation and evaluation in the DOTTOR (Discrete Ordinates to Three-dimensional Oak Ridge Transport) code

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

International Nuclear Information System (INIS)

Clore, G.M.; Gronenborn, A.M.; Nilges, M.; Ryan, C.A.

1987-01-01

The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 1 H NMR spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional NMR techniques to identify through-bond and through-space (<5 A) connectivities. A set of 309 approximate interproton distance restraints is derived from the two-dimensional nuclear Overhauser enhancement spectra and used as the basis of a three-dimensional structure determination by a combination of metric matrix distance geometry and restrained molecular dynamics calculations. A total of 11 converged distance geometry structures were computed and refined by using restrained molecular dynamics. The average atomic root mean square (rms) difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 +/- 0.3 A for residues 2-39 and 0.9 +/- 0.2 A for residues 5-37. The corresponding values for all atoms are 1.9 +/- 0.3 and 1.4 +/- 0.2 A, respectively. The computed structures are very close to the X-ray structure of CPI in its complex with carboxypeptidase, and the backbone atomic rms difference between the mean of the computed structures and the X-ray structure is only 1.2 A. Nevertheless, there are some real differences present which are evidenced by significant deviations between the experimental upper interproton distance limits and the corresponding interproton distances derived from the X-ray structure. These principally occur in two regions, residues 18-20 and residues 28-30, the latter comprising part of the region of secondary contact between CPI and carboxypeptidase in the X-ray structure

Three-dimensional imagery by encoding sources of X rays

International Nuclear Information System (INIS)

Magnin, Isabelle

1987-01-01

This research thesis addresses the theoretical and practical study of X ray coded sources, and thus notably aims at exploring whether it would be possible to transform a standard digital radiography apparatus (as those operated in radiology hospital departments) into a low cost three-dimensional imagery system. The author first recalls the principle of conventional tomography and improvement attempts, and describes imagery techniques based on the use of encoding openings and source encoding. She reports the modelling of an imagery system based on encoded sources of X ray, and addresses the original notion of three-dimensional response for such a system. The author then addresses the reconstruction method by considering the reconstruction of a plane object, of a multi-plane object, and of real three-dimensional object. The frequency properties and the tomographic capacities of various types of source codes are analysed. She describes a prototype tomography apparatus, and presents and discusses three-dimensional actual phantom reconstructions. She finally introduces a new principle of dynamic three-dimensional radiography which implements an acquisition technique by 'gating code'. The acquisition principle should allow the reconstruction of volumes animated by periodic deformations, such as the heart for example [fr

Three-dimensional oscillator and Coulomb systems reduced from Kaehler spaces

International Nuclear Information System (INIS)

Nersessian, Armen; Yeranyan, Armen

2004-01-01

We define the oscillator and Coulomb systems on four-dimensional spaces with U(2)-invariant Kaehler metric and perform their Hamiltonian reduction to the three-dimensional oscillator and Coulomb systems specified by the presence of Dirac monopoles. We find the Kaehler spaces with conic singularity, where the oscillator and Coulomb systems on three-dimensional sphere and two-sheet hyperboloid originate. Then we construct the superintegrable oscillator system on three-dimensional sphere and hyperboloid, coupled to a monopole, and find their four-dimensional origins. In the latter case the metric of configuration space is a non-Kaehler one. Finally, we extend these results to the family of Kaehler spaces with conic singularities

Supersymmetric quantum mechanics in three-dimensional space, 1

International Nuclear Information System (INIS)

Ui, Haruo

1984-01-01

As a direct generalization of the model of supersymmetric quantum mechanics by Witten, which describes the motion of a spin one-half particle in the one-dimensional space, we construct a model of the supersymmetric quantum mechanics in the three-dimensional space, which describes the motion of a spin one-half particle in central and spin-orbit potentials in the context of the nonrelativistic quantum mechanics. With the simplest choice of the (super) potential, this model is shown to reduce to the model of the harmonic oscillator plus constant spin-orbit potential of unit strength of both positive and negative signs, which was studied in detail in our recent paper in connection with ''accidental degeneracy'' as well as the ''graded groups''. This simplest model is discussed in some detail as an example of the three-dimensional supersymmetric quantum mechanical system, where the supersymmetry is an exact symmetry of the system. More general choice of a polynomial superpotential is also discussed. It is shown that the supersymmetry cannot be spontaneously broken for any polynomial superpotential in our three-dimensional model; this result is contrasted to the corresponding one in the one-dimensional model. (author)

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.

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.

Proton Environments in Biomimetic Calcium Phosphates Formed from Mesoporous Bioactive CaO-SiO2-P2O5 Glasses in Vitro: Insights from Solid-State NMR.

Science.gov (United States)

Mathew, Renny; Turdean-Ionescu, Claudia; Yu, Yang; Stevensson, Baltzar; Izquierdo-Barba, Isabel; García, Ana; Arcos, Daniel; Vallet-Regí, María; Edén, Mattias

2017-06-22

When exposed to body fluids, mesoporous bioactive glasses (MBGs) of the CaO-SiO 2 -P 2 O 5 system develop a bone-bonding surface layer that initially consists of amorphous calcium phosphate (ACP), which transforms into hydroxy-carbonate apatite (HCA) with a very similar composition as bone/dentin mineral. Information from various 1 H-based solid-state nuclear magnetic resonance (NMR) experiments was combined to elucidate the evolution of the proton speciations both at the MBG surface and within each ACP/HCA constituent of the biomimetic phosphate layer formed when each of three MBGs with distinct Ca, Si, and P contents was immersed in a simulated body fluid (SBF) for variable periods between 15 min and 30 days. Directly excited magic-angle-spinning (MAS) 1 H NMR spectra mainly reflect the MBG component, whose surface is rich in water and silanol (SiOH) moieties. Double-quantum-single-quantum correlation 1 H NMR experimentation at fast MAS revealed their interatomic proximities. The comparatively minor H species of each ACP and HCA component were probed selectively by heteronuclear 1 H- 31 P NMR experimentation. The initially prevailing ACP phase comprises H 2 O and "nonapatitic" HPO 4 2- /PO 4 3- groups, whereas for prolonged MBG soaking over days, a well-progressed ACP → HCA transformation was evidenced by a dominating O 1 H resonance from HCA. We show that 1 H-detected 1 H → 31 P cross-polarization NMR is markedly more sensitive than utilizing powder X-ray diffraction or 31 P NMR for detecting the onset of HCA formation, notably so for P-bearing (M)BGs. In relation to the long-standing controversy as to whether bone mineral comprises ACP and/or forms via an ACP precursor, we discuss a recently accepted structural core-shell picture of both synthetic and biological HCA, highlighting the close relationship between the disordered surface layer and ACP.

Three-dimensional theory for light-matter interaction

DEFF Research Database (Denmark)

Sørensen, Martin Westring; Sørensen, Anders Søndberg

2008-01-01

We present a full quantum mechanical three dimensional theory describing an electromagnetic field interacting with an ensemble of identical atoms. The theory is constructed such that it describes recent experiments on light-matter quantum interfaces, where the quantum fluctuations of light...... to a dressed state picture, where the light modes are solutions to the diffraction problem, and develop a perturbative expansion in the fluctuations. The fluctuations are due to quantum fluctuations as well as the random positions of the atoms. In this perturbative expansion we show how the quantum...... fluctuations are mapped between atoms and light while the random positioning of the atoms give rise to decay due to spontaneous emission. Furthermore we identify limits, where the full three dimensional theory reduce to the one dimensional theory typically used to describe the interaction....

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

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

Energy Technology Data Exchange (ETDEWEB)

Rosato, Antonio [University of Florence, Department of Chemistry and Magnetic Resonance Center (Italy); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Fogh, Rasmus H.; Ragan, Timothy J. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H. [University of Georgia, Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium (United States); Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H. [University of Toronto, Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium (Canada); Kennedy, Michael [Miami University, Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (United States); Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.edu [The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers (United States); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

2015-08-15

The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

International Nuclear Information System (INIS)

Rosato, Antonio; Vranken, Wim; Fogh, Rasmus H.; Ragan, Timothy J.; Tejero, Roberto; Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H.; Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H.; Kennedy, Michael; Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T.; Vuister, Geerten W.

2015-01-01

The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged

Three dimensional contact/impact methodology

International Nuclear Information System (INIS)

Kulak, R.F.

1987-01-01

The simulation of three-dimensional interface mechanics between reactor components and structures during static contact or dynamic impact is necessary to realistically evaluate their structural integrity to off-normal loads. In our studies of postulated core energy release events, we have found that significant structure-structure interactions occur in some reactor vessel head closure designs and that fluid-structure interactions occur within the reactor vessel. Other examples in which three-dimensional interface mechanics play an important role are: (1) impact response of shipping casks containing spent fuel, (2) whipping pipe impact on reinforced concrete panels or pipe-to-pipe impact after a pipe break, (3) aircraft crash on secondary containment structures, (4) missiles generated by turbine failures or tornados, and (5) drops of heavy components due to lifting accidents. The above is a partial list of reactor safety problems that require adequate treatment of interface mechanics and are discussed in this paper

Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

Energy Technology Data Exchange (ETDEWEB)

Boonsri, Pornthip [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Herdendorf, Timothy J.; Miziorko, Henry M. [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Hannongbua, Supa [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Sem, Daniel S., E-mail: daniel.sem@cuw.edu [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)

2013-01-04

Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

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.

PINE-SPARKY.2 for automated NMR-based protein structure research.

Science.gov (United States)

Lee, Woonghee; Markley, John L

2018-05-01

Nuclear magnetic resonance (NMR) spectroscopy, along with X-ray crystallography and cryoelectron microscopy, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models. PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers to the SBGrid (https://sbgrid.org). For a detailed description of the program, see http://www.nmrfam.wisc.edu/pine-sparky2.htm. whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu. Supplementary data are available at Bioinformatics online.

Three-dimensional friction measurement during hip simulation.

Directory of Open Access Journals (Sweden)

Robert Sonntag

Full Text Available Wear of total hip replacements has been the focus of many studies. However, frictional effects, such as high loading on intramodular connections or the interface to the bone, as well as friction associated squeaking have recently increased interest about the amount of friction that is generated during daily activities. The aim of this study was thus to establish and validate a three-dimensional friction setup under standardized conditions.A standard hip simulator was modified to allow for high precision measurements of small frictional effects in the hip during three-dimensional hip articulation. The setup was verified by an ideal hydrostatic bearing and validated with a static-load physical pendulum and an extension-flexion rotation with a dynamic load profile. Additionally, a pendulum model was proposed for screening measurement of frictional effects based on the damping behavior of the angular oscillation without the need for any force/moment transducer. Finally, three-dimensional friction measurements have been realized for ceramic-on-polyethylene bearings of three different sizes (28, 36 and 40 mm.A precision of less than 0.2 Nm during three-dimensional friction measurements was reported, while increased frictional torque (resultant as well as taper torque was measured for larger head diameters. These effects have been confirmed by simple pendulum tests and the theoretical model. A comparison with current literature about friction measurements is presented.This investigation of friction is able to provide more information about a field that has been dominated by the reduction of wear. It should be considered in future pre-clinical testing protocols given by international organizations of standardization.

Diffraction limited focusing with controllable arbitrary three-dimensional polarization

International Nuclear Information System (INIS)

Chen, Weibin; Zhan, Qiwen

2010-01-01

We propose a new approach that enables full control over the three-dimensional state of polarization and the field distribution near the focus of a high numerical aperture objective lens. By combining the electric dipole radiation and a vectorial diffraction method, the input field at the pupil plane for generating arbitrary three-dimensionally oriented linear polarization at the focal point with a diffraction limited spot size is found analytically by solving the inverse problem. Arbitrary three-dimensional elliptical polarization can be obtained by introducing a second electric dipole oriented in the orthogonal plane with appropriate amplitude and phase differences

Three-dimensional CT imaging of soft-tissue anatomy

International Nuclear Information System (INIS)

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

1988-01-01

Three-dimensional display of computed tomographic data has been limited to skeletal structures. This was in part related to the reconstruction algorithm used, which relied on a binary classification scheme. A new algorithm, volumetric rendering with percentage classification, provides the ability to display three-dimensional images of muscle and soft tissue. A review was conducted of images in 35 cases in which muscle and/or soft tissue were part of the clinical problem. In all cases, individual muscle groups could be clearly identified and discriminated. Branching vessels in the range of 2.3 mm could be identified. Similarly, lymph nodes could be clearly defined. High-resolution three-dimensional images were found to be useful both in providing an increased understanding of complex muscle and soft tissue anatomy and in surgical planning

THREE DIMENSIONAL GRAPHICAL REPRESENTATION OF QUALITY

Directory of Open Access Journals (Sweden)

Vineet V. Kumar

2014-03-01

Full Text Available Quality is an important aspect for every firm in modern era of competition. Every product has tough competition in terms of market reach. The factor, which actually makes any product long run in market, is quality and hence quality is the stepping-stone for success of any firm. For everyone meaning of quality is different. We have seen several economists who have defined quality by considering different factors, but what all of them have common in them is Customer satisfaction. Customer satisfaction is the ultimate result of quality. In three-dimensional graphical representation of quality, optimum quality is obtained by using three-dimensional graph by considering some important factors governing quality of any product, limiting factor, and customer satisfaction.

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

Application status of three-dimensional CT reconstruction in hepatobiliary surgery

Directory of Open Access Journals (Sweden)

JIANG Chao

2017-02-01

Full Text Available With the development of imaging technology, three-dimensional CT reconstruction has been widely used in hepatobiliary surgery. Three-dimensional CT reconstruction can divide and reconstruct two-dimensional images into three-dimensional images and clearly show the location of lesion and its relationship with the intrahepatic bile duct system. It has an important value in the preoperative assessment of liver volume, diagnosis and treatment decision-making process, intraoperative precise operation, and postoperative individualized management, and promotes the constant development of hepatobiliary surgery and minimally invasive technology, and therefore, it holds promise for clinical application.

Utility of three-dimensional method for diagnosing meniscal lesions

International Nuclear Information System (INIS)

Ohshima, Suguru; Nomura, Kazutoshi; Hirano, Mako; Hashimoto, Noburo; Fukumoto, Tetsuya; Katahira, Kazuhiro

1998-01-01

MRI of the knee is a useful method for diagnosing meniscal tears. Although the spin echo method is usually used for diagnosing meniscal tears, we examined the utility of thin slice scan with the three-dimensional method. We reviewed 70 menisci in which arthroscopic findings were confirmed. In this series, sensitivity was 90.9% for medial meniscal injuries and 68.8% for lateral meniscal injuries. There were 3 meniscal tears in which we could not detect tears on preoperative MRI. We could find tears in two of these cases when re-evaluated using the same MRI. In conclusion, we can get the same diagnostic rate with the three-dimensional method compared with the spin echo method. Scan time of the three-dimensional method is 3 minutes, on the other hand that of spin echo method in 17 minutes. This slice scan with three-dimensional method is useful for screening meniscal injuries before arthroscopy. (author)

Three-dimensional features on oscillating microbubbles streaming flows

Science.gov (United States)

Rossi, Massimiliano; Marin, Alvaro G.; Wang, Cheng; Hilgenfeldt, Sascha; Kähler, Christian J.

2013-11-01

Ultrasound-driven oscillating micro-bubbles have been used as active actuators in microfluidic devices to perform manifold tasks such as mixing, sorting and manipulation of microparticles. A common configuration consists in side-bubbles, created by trapping air pockets in blind channels perpendicular to the main channel direction. This configuration results in bubbles with a semi-cylindrical shape that creates a streaming flow generally considered quasi two-dimensional. However, recent experiments performed with three-dimensional velocimetry methods have shown how microparticles can present significant three-dimensional trajectories, especially in regions close to the bubble interface. Several reasons will be discussed such as boundary effects of the bottom/top wall, deformation of the bubble interface leading to more complex vibrational modes, or bubble-particle interactions. In the present investigation, precise measurements of particle trajectories close to the bubble interface will be performed by means of 3D Astigmatic Particle Tracking Velocimetry. The results will allow us to characterize quantitatively the three-dimensional features of the streaming flow and to estimate its implications in practical applications as particle trapping, sorting or mixing.

S³ HMBC hetero: Spin-State-Selective HMBC for accurate measurement of long-range heteronuclear coupling constants

DEFF Research Database (Denmark)

Hoeck, Casper; Gotfredsen, Charlotte Held; Sørensen, Ole W.

2017-01-01

A novel method, Spin-State-Selective (S3) HMBC hetero, for accurate measurement of heteronuclear coupling constants is introduced. The method extends the S3 HMBC technique for measurement of homonuclear coupling constants by appending a pulse sequence element that interchanges the polarization...

Integration of Computed Tomography and Three-Dimensional Echocardiography for Hybrid Three-Dimensional Printing in Congenital Heart Disease.

Science.gov (United States)

Gosnell, Jordan; Pietila, Todd; Samuel, Bennett P; Kurup, Harikrishnan K N; Haw, Marcus P; Vettukattil, Joseph J

2016-12-01

Three-dimensional (3D) printing is an emerging technology aiding diagnostics, education, and interventional, and surgical planning in congenital heart disease (CHD). Three-dimensional printing has been derived from computed tomography, cardiac magnetic resonance, and 3D echocardiography. However, individually the imaging modalities may not provide adequate visualization of complex CHD. The integration of the strengths of two or more imaging modalities has the potential to enhance visualization of cardiac pathomorphology. We describe the feasibility of hybrid 3D printing from two imaging modalities in a patient with congenitally corrected transposition of the great arteries (L-TGA). Hybrid 3D printing may be useful as an additional tool for cardiologists and cardiothoracic surgeons in planning interventions in children and adults with CHD.

Three-dimensional image reconstruction from stereo DSA

International Nuclear Information System (INIS)

Sakamoto, Kiyoshi; Kotoura, Noriko; Umehara, Takayoshi; Yamada, Eiji; Inaba, Tomohiro; Itou, Hiroshi

1999-01-01

The technique of interventional radiology has spread rapidly in recent years, and three-dimensional information from blood vessel images is being sought to enhance examinations. Stereo digital subtraction angiography (DSA) and rotational DSA were developed for that purpose. However, it is difficult with stereo DSA to observe the image pair during examination and to obtain positional information on blood vessels. Further, the exposure dose is increased in rotational DSA when many mask images need to be collected, and the patient is required to hold his or her breath for a long duration. We therefore devised a technique to construct three-dimensional blood vessel images by employing geometrical information extracted from stereo DSA images using the right and left images. We used a judgment method based on the correlation coefficient, although we had to extract an equal blood vessel from the right and left images to determine the three-dimensional coordinates of the blood vessel. The reconstructed three-dimensional blood vessels were projected from various angles, again by using a virtual focus, and new images were created. These image groups were displayed as rotational images by the animation display function incorporated in the DSA device. This system can observe blood vessel images of the same phase at a free angle, although the image quality is inferior to that of rotational DSA. In addition, because collection of the mask images is reduced, exposure dose can be decreased. Further, the system offers enhanced safety because no mechanical movement of the imaging system is involved. (author)

A DETERMINISTIC METHOD FOR TRANSIENT, THREE-DIMENSIONAL NUETRON TRANSPORT

International Nuclear Information System (INIS)

S. GOLUOGLU, C. BENTLEY, R. DEMEGLIO, M. DUNN, K. NORTON, R. PEVEY I.SUSLOV AND H.L. DODDS

1998-01-01

A deterministic method for solving the time-dependent, three-dimensional Boltzmam transport equation with explicit representation of delayed neutrons has been developed and evaluated. The methodology used in this study for the time variable of the neutron flux is known as the improved quasi-static (IQS) method. The position, energy, and angle-dependent neutron flux is computed deterministically by using the three-dimensional discrete ordinates code TORT. This paper briefly describes the methodology and selected results. The code developed at the University of Tennessee based on this methodology is called TDTORT. TDTORT can be used to model transients involving voided and/or strongly absorbing regions that require transport theory for accuracy. This code can also be used to model either small high-leakage systems, such as space reactors, or asymmetric control rod movements. TDTORT can model step, ramp, step followed by another step, and step followed by ramp type perturbations. It can also model columnwise rod movement can also be modeled. A special case of columnwise rod movement in a three-dimensional model of a boiling water reactor (BWR) with simple adiabatic feedback is also included. TDTORT is verified through several transient one-dimensional, two-dimensional, and three-dimensional benchmark problems. The results show that the transport methodology and corresponding code developed in this work have sufficient accuracy and speed for computing the dynamic behavior of complex multidimensional neutronic systems

Summary of three-dimensional animation creation based on ethnic culture element

Directory of Open Access Journals (Sweden)

Shao Zhaopo

2016-01-01

Full Text Available three-dimensional animation is a product combined by technology and art. It is an artistic ex-pression form combining painting, film & television, digital technology, music, and literature. As an audio and visual art, three-dimensional animation has its own unique culture-loading function, technical aesthetic charac-teristics, and requirements for national art expression. This paper aims to find the method to combine digital technology and national art in combination of three-dimensional animation short film creation, and hopes to clear the road for the cultivation of domestic three-dimensional animation quality project.

Three-dimensional spiral CT during arterial portography: comparison of three rendering techniques.

Science.gov (United States)

Heath, D G; Soyer, P A; Kuszyk, B S; Bliss, D F; Calhoun, P S; Bluemke, D A; Choti, M A; Fishman, E K

1995-07-01

The three most common techniques for three-dimensional reconstruction are surface rendering, maximum-intensity projection (MIP), and volume rendering. Surface-rendering algorithms model objects as collections of geometric primitives that are displayed with surface shading. The MIP algorithm renders an image by selecting the voxel with the maximum intensity signal along a line extended from the viewer's eye through the data volume. Volume-rendering algorithms sum the weighted contributions of all voxels along the line. Each technique has advantages and shortcomings that must be considered during selection of one for a specific clinical problem and during interpretation of the resulting images. With surface rendering, sharp-edged, clear three-dimensional reconstruction can be completed on modest computer systems; however, overlapping structures cannot be visualized and artifacts are a problem. MIP is computationally a fast technique, but it does not allow depiction of overlapping structures, and its images are three-dimensionally ambiguous unless depth cues are provided. Both surface rendering and MIP use less than 10% of the image data. In contrast, volume rendering uses nearly all of the data, allows demonstration of overlapping structures, and engenders few artifacts, but it requires substantially more computer power than the other techniques.

Three-dimensional reconstruction of the pigeon inner ear

NARCIS (Netherlands)

Hofman, R.; Segenhout, J. M.; Wit, H. P.

2009-01-01

Three-dimensional reconstructions of the inner ear of the pigeon (Columba livia domestica), from two-dimensional images, obtained with (conventional) light microscopy or orthogonal-plane fluorescence optical sectioning (OPFOS), are presented. The results are compared with available information on

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.

Three-dimensional magnetophotonic crystals based on artificial opals

Science.gov (United States)

Baryshev, A. V.; Kodama, T.; Nishimura, K.; Uchida, H.; Inoue, M.

2004-06-01

We fabricated and experimentally investigated three-dimensional magnetophotonic crystals (3D MPCs) based on artificial opals. Opal samples with three-dimensional dielectric lattices were impregnated with different types of magnetic material. Magnetic and structural properties of 3D MPCs were studied by field emission scanning electron microscopy, x-ray diffraction analysis, and vibrating sample magnetometer. We have shown that magnetic materials synthesized in voids of opal lattices and the composites obtained have typical magnetic properties.

Three-dimensional magnetophotonic crystals based on artificial opals

International Nuclear Information System (INIS)

Baryshev, A.V.; Kodama, T.; Nishimura, K.; Uchida, H.; Inoue, M.

2004-01-01

We fabricated and experimentally investigated three-dimensional magnetophotonic crystals (3D MPCs) based on artificial opals. Opal samples with three-dimensional dielectric lattices were impregnated with different types of magnetic material. Magnetic and structural properties of 3D MPCs were studied by field emission scanning electron microscopy, x-ray diffraction analysis, and vibrating sample magnetometer. We have shown that magnetic materials synthesized in voids of opal lattices and the composites obtained have typical magnetic properties

Heteronuclear proton assisted recoupling

Science.gov (United States)

De Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Eddy, Matt; Megy, Simon; Böckmann, Anja; Griffin, Robert G.

2011-03-01

We describe a theoretical framework for understanding the heteronuclear version of the third spin assisted recoupling polarization transfer mechanism and demonstrate its potential for detecting long-distance intramolecular and intermolecular 15N-13C contacts in biomolecular systems. The pulse sequence, proton assisted insensitive nuclei cross polarization (PAIN-CP) relies on a cross term between 1H-15N and 1H-13C dipolar couplings to mediate zero- and/or double-quantum 15N-13C recoupling. In particular, using average Hamiltonian theory we derive effective Hamiltonians for PAIN-CP and show that the transfer is mediated by trilinear terms of the form N±C∓Hz (ZQ) or N±C±Hz (DQ) depending on the rf field strengths employed. We use analytical and numerical simulations to explain the structure of the PAIN-CP optimization maps and to delineate the appropriate matching conditions. We also detail the dependence of the PAIN-CP polarization transfer with respect to local molecular geometry and explain the observed reduction in dipolar truncation. In addition, we demonstrate the utility of PAIN-CP in structural studies with 15N-13C spectra of two uniformly 13C,15N labeled model microcrystalline proteins—GB1, a 56 amino acid peptide, and Crh, a 85 amino acid domain swapped dimer (MW = 2 × 10.4 kDa). The spectra acquired at high magic angle spinning frequencies (ωr/2π > 20 kHz) and magnetic fields (ω0H/2π = 700-900 MHz) using moderate rf fields, yield multiple long-distance intramonomer and intermonomer 15N-13C contacts. We use these distance restraints, in combination with the available x-ray structure as a homology model, to perform a calculation of the monomer subunit of the Crh protein.

Magnetohydrodynamic study of three-dimensional instability of the spontaneous fast magnetic reconnection

International Nuclear Information System (INIS)

Shimizu, T.; Kondoh, K.; Ugai, M.; Shibata, K.

2009-01-01

Three-dimensional instability of the spontaneous fast magnetic reconnection is studied with magnetohydrodynamic (MHD) simulation, where the two-dimensional model of the spontaneous fast magnetic reconnection is destabilized in three dimension. Generally, in two-dimensional magnetic reconnection models, every plasma condition is assumed to be uniform in the sheet current direction. In such two-dimensional MHD simulations, the current sheet destabilized by the initial resistive disturbance can be developed to fast magnetic reconnection by a current driven anomalous resistivity. In this paper, the initial resistive disturbance includes a small amount of fluctuations in the sheet current direction, i.e., along the magnetic neutral line. The other conditions are the same as that of previous two-dimensional MHD studies for fast magnetic reconnection. Accordingly, we may expect that approximately two-dimensional fast magnetic reconnection occurs in the MHD simulation. In fact, the fast magnetic reconnection activated on the first stage of the simulation is two dimensional. However, on the subsequent stages, it spontaneously becomes three dimensional and is strongly localized in the sheet current direction. The resulting three-dimensional fast magnetic reconnection intermittently ejects three-dimensional magnetic loops. Such intermittent ejections of the three-dimensional loops are similar to the intermittent downflows observed in the solar flares. The ejection of the three-dimensional loops seems to be random but, numerically and theoretically, it is shown that the aspect ratio of the ejected loops is limited under a criterion.

Possibility of estimating three-dimensional mandibular morphology by cephalogram analysis

International Nuclear Information System (INIS)

Kim, S.; Motegi, Etsuko; Kikuchi, Yu; Yamaguchi, Hideharu; Takaki, Takashi; Shibahara, Takahiko

2007-01-01

The purpose of this study was to investigate the possibility of a surmise of three-dimensional mandibular morphology by two-dimensional cephalogram analysis. The materials were three-dimensional CT and cephalogram of 20 female mandibular prognathism patients (average age: 25.20±7.49) before there orthognathic surgery. Mandibular bone volume and sponge bone width were calculated from three-dimensional images constructed from CT images using imaging software (Real Intage, KGT inc.). There was a positive correlation (r=0.72) between mandibular volume value and mandibular ramus width. There was a positive correlation between sponge bone width at the site of the mandibular cuspid and mandibular ramus width and SNB angle (r=0.80), and between sponge bone width at the site of the mandibular molar and symphysis height and mandibular ramus width (r=0.81). It was thought that these results will be useful for a surmise of three-dimensional mandibular morphology by cephalogram analysis. (author)

Three-dimensional interpretation of TEM soundings

Science.gov (United States)

Barsukov, P. O.; Fainberg, E. B.

2013-07-01

We describe the approach to the interpretation of electromagnetic (EM) sounding data which iteratively adjusts the three-dimensional (3D) model of the environment by local one-dimensional (1D) transformations and inversions and reconstructs the geometrical skeleton of the model. The final 3D inversion is carried out with the minimal number of the sought parameters. At each step of the interpretation, the model of the medium is corrected according to the geological information. The practical examples of the suggested method are presented.

Heteronuclear 2D NMR studies on an engineered insulin monomer: Assignments and characterization of the receptor-binding surface by selective 2H and 13C labeling with application to protein design

International Nuclear Information System (INIS)

Weiss, M.A.; Hua, Qingxin; Lynch, C.S.; Shoelson, S.E.; Frank, B.H.

1991-01-01

Insulin provides an important model for the application of genetic engineering to rational protein design and has been well characterized in the crystal state. However, self-association of insulin in solution has precluded complementary 2D NMR study under physiological conditions. The authors demonstrate here that such limitations may be circumvented by the use of a monomeric analogue that contains three amino acid substitutions on the protein surface (HisB10 → Asp, ProB28 → Lys, and LysB29 → Pro); this analogue (designated DKP-insulin) retains native receptor-binding potency. Comparative 1 H NMR studies of native human insulin and a series of three related analogues-(i) the singly substituted analogue [HisB10→Asp], (ii) the doubly substituted analogue [ProB28→Lys; LysB29→Pro], and (iii) DKP-insulin-demonstrate progressive reduction in concentration-dependent line-broadening in accord with the results of analytical ultracentrifugation. Extensive nonlocal interactions are observed in the NOESY spectrum of DKP-insulin, indicating that this analogue adopts a compact and stably folded structure as a monomer in overall accord with crystal models. Site-specific 2 H and 13 C isotopic labels are introduced by semisynthesis as probes for the structure and dynamics of the receptor-binding surface. These studies confirm and extend under physiological conditions the results of a previous 2D NMR analysis of native insulin in 20% acetic acid. Implications for the role of protein flexibility in receptor recognition are discussed with application to the design of novel insulin analogues

Cânfora: um bom modelo para ilustrar técnicas de RMN Camphor: a good model for illustrating NMR techniques

Directory of Open Access Journals (Sweden)

Julliane Diniz Yoneda

2007-01-01

Full Text Available The use of Nuclear Magnetic Resonance spectroscopy to establish the three-dimensional structures of molecules is an important component of modern Chemistry courses. The combination of techniques that can be used for this purpose is conveniently illustrated by their application to the camphor molecule. This paper presents applications of several techniques used in NMR spectral interpretation in an increasing order of complexity. The result of individual experiments is illustrated in order to familiarize the user with the way connectivity through bonds and through space is established from 1D/2D-NMR spectra and molecular stereochemistry is determined from different NMR experiments.

Three-dimensional teletherapy treatment planning

International Nuclear Information System (INIS)

Panthaleon van Eck, R.B. van.

1986-01-01

This thesis deals with physical/mathematical backgrounds of computerized teletherapy treatment planning. The subjects discussed in this thesis can be subdivided into three main categories: a) Three-dimensional treatment planning. A method is evaluated which can be used for the purpose of simulation and optimization of dose distributions in three dimensions. b) The use of Computed Tomography. The use of patient information obtained from Computed Tomography for the purpose of dose computations is evaluated. c) Dose computational models for photon- and electron beams. Models are evaluated which provide information regarding the way in which the radiation dose is distributed in the patient (viz. is absorbed and/or dispersed). (Auth.)

Three-dimensional imaging technology offers promise in medicine.

Science.gov (United States)

Karako, Kenji; Wu, Qiong; Gao, Jianjun

2014-04-01

Medical imaging plays an increasingly important role in the diagnosis and treatment of disease. Currently, medical equipment mainly has two-dimensional (2D) imaging systems. Although this conventional imaging largely satisfies clinical requirements, it cannot depict pathologic changes in 3 dimensions. The development of three-dimensional (3D) imaging technology has encouraged advances in medical imaging. Three-dimensional imaging technology offers doctors much more information on a pathology than 2D imaging, thus significantly improving diagnostic capability and the quality of treatment. Moreover, the combination of 3D imaging with augmented reality significantly improves surgical navigation process. The advantages of 3D imaging technology have made it an important component of technological progress in the field of medical imaging.

Identification of Hepatoprotective Constituents in Limonium tetragonum and Development of Simultaneous Analysis Method using High-performance Liquid Chromatography

Science.gov (United States)

Lee, Jae Sun; Kim, Yun Na; Kim, Na-Hyun; Heo, Jeong-Doo; Yang, Min Hye; Rho, Jung-Rae; Jeong, Eun Ju

2017-01-01

Background: Limonium tetragonum, a naturally salt-tolerant halophyte, has been studied recently and is of much interest to researchers due to its potent antioxidant and hepatoprotective activities. Objective: In the present study, we attempted to elucidate bioactive compounds from ethyl acetate (EtOAc) soluble fraction of L. tetragonum extract. Furthermore, the simultaneous analysis method of bioactive EtOAc fraction of L. tetragonum has been developed using high-performance liquid chromatography (HPLC). Materials and Methods: Thirteen compounds have been successfully isolated from EtOAc fraction of L. tetragonum, and the structures of 1–13 were elucidated by extensive one-dimensional and two-dimensional spectroscopic methods including 1H-NMR, 13C-NMR, 1H-1H COSY, heteronuclear single quantum coherence, heteronuclear multiple bond correlation, and nuclear Overhauser effect spectroscopy. Hepatoprotection of the isolated compounds against liver fibrosis was evaluated by measuring inhibition on hepatic stellate cells (HSCs) undergoing proliferation. Results: Compounds 1–13 were identified as gallincin (1), apigenin-3-O-β-D-galactopyranoside (2), quercetin (3), quercetin-3-O-β-D-galactopyranoside (4), (−)-epigallocatechin (5), (−)-epigallocatechin-3-gallate (6), (−)-epigallocatechin-3-(3″-O-methyl) gallate (7), myricetin-3-O-β-D-galactopyranoside (8), myricetin-3-O-(6″-O-galloyl)-β-D-galactopyranoside (9), myricetin-3-O-α-L-rhamnopyranoside (10), myricetin-3-O-(2″-O-galloyl)-α-L-rhamnopyranoside (11), myricetin-3-O-(3″-O-galloyl)-α-L-rhamnopyranoside (12), and myricetin-3-O-α-L-arabinopyranoside (13), respectively. All compounds except for 4, 8, and 10 are reported for the first time from this plant. Conclusion: Myricetin glycosides which possess galloyl substituent (9, 11, and 12) showed most potent inhibitory effects on the proliferation of HSCs. SUMMARY In the present study, we have successfully isolated 13 compounds from bioactive fraction

Three-dimensional echocardiographic assessment of the repaired mitral valve.

Science.gov (United States)

Maslow, Andrew; Mahmood, Feroze; Poppas, Athena; Singh, Arun

2014-02-01

This study examined the geometric changes of the mitral valve (MV) after repair using conventional and three-dimensional echocardiography. Prospective evaluation of consecutive patients undergoing mitral valve repair. Tertiary care university hospital. Fifty consecutive patients scheduled for elective repair of the mitral valve for regurgitant disease. Intraoperative transesophageal echocardiography. Assessments of valve area (MVA) were performed using two-dimensional planimetry (2D-Plan), pressure half-time (PHT), and three-dimensional planimetry (3D-Plan). In addition, the direction of ventricular inflow was assessed from the three-dimensional imaging. Good correlations (r = 0.83) and agreement (-0.08 +/- 0.43 cm(2)) were seen between the MVA measured with 3D-Plan and PHT, and were better than either compared to 2D-Plan. MVAs were smaller after repair of functional disease repaired with an annuloplasty ring. After repair, ventricular inflow was directed toward the lateral ventricular wall. Subgroup analysis showed that the change in inflow angle was not different after repair of functional disease (168 to 171 degrees) as compared to those presenting with degenerative disease (168 to 148 degrees; p<0.0001). Three-dimensional imaging provides caregivers with a unique ability to assess changes in valve function after mitral valve repair. Copyright © 2014 Elsevier Inc. All rights reserved.

Tactical Routing Using Two-Dimensional and Three-Dimensional Views of Terrain

National Research Council Canada - National Science Library

St

2001-01-01

Consoles for military and civilian occupations such as air warfare, command and control, air traffic control, piloting, and meteorological forecasting will be capable of displaying three-dimensional (3-D) perspective views...

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

Crystallization of a self-assembled three-dimensional DNA nanostructure

International Nuclear Information System (INIS)

Rendek, Kimberly N.; Fromme, Raimund; Grotjohann, Ingo; Fromme, Petra

2013-01-01

In this work, the crystallization of a self-assembling three-dimensional B-DNA nanostructure is described. The powerful and specific molecular-recognition system present in the base-pairing of DNA allows for the design of a plethora of nanostructures. In this work, the crystallization of a self-assembling three-dimensional B-DNA nanostructure is described. The DNA nanostructure consists of six single-stranded oligonucleotides that hybridize to form a three-dimensional tetrahedron of 80 kDa in molecular mass and 20 bp on each edge. Crystals of the tetrahedron have been successfully produced and characterized. These crystals may form the basis for an X-ray structure of the tetrahedron in the future. Nucleotide crystallography poses many challenges, leading to the fact that only 1352 X-ray structures of nucleic acids have been solved compared with more than 80 000 protein structures. In this work, the crystallization optimization for three-dimensional tetrahedra is also described, with the eventual goal of producing nanocrystals to overcome the radiation-damage obstacle by the use of free-electron laser technology in the future

Three Dimensional Energy Transmitting Boundary in the Time Domain

Directory of Open Access Journals (Sweden)

Naohiro eNakamura

2015-11-01

Full Text Available Although the energy transmitting boundary is accurate and efficient for the FEM earthquake response analysis, it could be applied in the frequency domain only. In the previous papers, the author proposed an earthquake response analysis method using the time domain energy transmitting boundary for two dimensional problems. In this paper, this technique is expanded for three dimensional problems. The inner field is supposed to be a hexahedron shape and the approximate time domain boundary is explained, first. Next, two dimensional anti-plane time domain boundary is studied for a part of the approximate three dimensional boundary method. Then, accuracy and efficiency of the proposed method are confirmed by example problems.

A method of image improvement in three-dimensional imaging

International Nuclear Information System (INIS)

Suto, Yasuzo; Huang, Tewen; Furuhata, Kentaro; Uchino, Masafumi.

1988-01-01

In general, image interpolation is required when the surface configurations of such structures as bones and organs are three-dimensionally constructed from the multi-sliced images obtained by CT. Image interpolation is a processing method whereby an artificial image is inserted between two adjacent slices to make spatial resolution equal to slice resolution in appearance. Such image interpolation makes it possible to increase the image quality of the constructed three-dimensional image. In our newly-developed algorithm, we have converted the presently and subsequently sliced images to distance images, and generated the interpolation images from these two distance images. As a result, compared with the previous method, three-dimensional images with better image quality have been constructed. (author)

Usefulness Of Three-Dimensional Printing Models for Patients with Stoma Construction

Directory of Open Access Journals (Sweden)

Tetsuro Tominaga

2016-04-01

Full Text Available The use of patient-specific organ models in three-dimensional printing systems could be helpful for the education of patients and medical students. The aim of this study was to clarify whether the use of patient-specific stoma models is helpful for patient education. From January 2014 to September 2014, 5 patients who underwent colorectal surgery and for whom a temporary or permanent stoma had been created were involved in this study. Three-dimensional stoma models and three-dimensional face plates were created. The patients’ ages ranged from 59 to 81 years. Four patients underwent stoma construction because of rectal cancer, and 1 underwent stoma construction because of colon stenosis secondary to recurrent cancer. All patients were educated about their stoma and potential stoma-associated problems using three-dimensional stoma models, and all practiced cutting face plates using three-dimensional face plates. The models were also used during medical staff conferences to discuss current issues. All patients understood their problems and finally became self-reliant. The recent availability of three-dimensional printers has enabled the creation of many organ models, and full-scale stoma and face plate models are now available for patient education on cutting an appropriately individualized face plate. Thus, three-dimensional printers could enable fewer skin problems than are currently associated with daily stomal care.

Interaction-induced decay of a heteronuclear two-atom system

Science.gov (United States)

Xu, Peng; Yang, Jiaheng; Liu, Min; He, Xiaodong; Zeng, Yong; Wang, Kunpeng; Wang, Jin; Papoular, D. J.; Shlyapnikov, G. V.; Zhan, Mingsheng

2015-01-01

Two-atom systems in small traps are of fundamental interest for understanding the role of interactions in degenerate cold gases and for the creation of quantum gates in quantum information processing with single-atom traps. One of the key quantities is the inelastic relaxation (decay) time when one of the atoms or both are in a higher hyperfine state. Here we measure this quantity in a heteronuclear system of 87Rb and 85Rb in a micro optical trap and demonstrate experimentally and theoretically the presence of both fast and slow relaxation processes, depending on the choice of the initial hyperfine states. This experimental method allows us to single out a particular relaxation process thus provides an extremely clean platform for collisional physics studies. Our results have also implications for engineering of quantum states via controlled collisions and creation of two-qubit quantum gates. PMID:26199051

A general framework to quantify the effect of restricted diffusion on the NMR signal with applications to double pulsed field gradient NMR experiments.

Science.gov (United States)

Ozarslan, Evren; Shemesh, Noam; Basser, Peter J

2009-03-14

Based on a description introduced by Robertson, Grebenkov recently introduced a powerful formalism to represent the diffusion-attenuated NMR signal for simple pore geometries such as slabs, cylinders, and spheres analytically. In this work, we extend this multiple correlation function formalism by allowing for possible variations in the direction of the magnetic field gradient waveform. This extension is necessary, for example, to incorporate the effects of imaging gradients in diffusion-weighted NMR imaging scans and in characterizing anisotropy at different length scales via double pulsed field gradient (PFG) experiments. In cylindrical and spherical pores, respectively, two- and three-dimensional vector operators are employed whose form is deduced from Grebenkov's results via elementary operator algebra for the case of cylinders and the Wigner-Eckart theorem for the case of spheres. The theory was validated by comparison with known findings and with experimental double-PFG data obtained from water-filled microcapillaries.

A general framework to quantify the effect of restricted diffusion on the NMR signal with applications to double pulsed field gradient NMR experiments

Science.gov (United States)

Özarslan, Evren; Shemesh, Noam; Basser, Peter J.

2009-03-01

Based on a description introduced by Robertson, Grebenkov recently introduced a powerful formalism to represent the diffusion-attenuated NMR signal for simple pore geometries such as slabs, cylinders, and spheres analytically. In this work, we extend this multiple correlation function formalism by allowing for possible variations in the direction of the magnetic field gradient waveform. This extension is necessary, for example, to incorporate the effects of imaging gradients in diffusion-weighted NMR imaging scans and in characterizing anisotropy at different length scales via double pulsed field gradient (PFG) experiments. In cylindrical and spherical pores, respectively, two- and three-dimensional vector operators are employed whose form is deduced from Grebenkov's results via elementary operator algebra for the case of cylinders and the Wigner-Eckart theorem for the case of spheres. The theory was validated by comparison with known findings and with experimental double-PFG data obtained from water-filled microcapillaries.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system

Energy Technology Data Exchange (ETDEWEB)

Ikeya, Teppei [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany); Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune [Tokyo Metropolitan University, Graduate School of Science (Japan)], E-mail: kainosho@nmr.chem.metro-u.ac.jp; Guentert, Peter [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany)], E-mail: guentert@em.uni-frankfurt.de

2009-08-15

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly {sup 13}C/{sup 15}N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the {sup 13}C-edited and {sup 15}N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system

International Nuclear Information System (INIS)

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Guentert, Peter

2009-01-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13 C/ 15 N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the 13 C-edited and 15 N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

Science.gov (United States)

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Three-dimensional ultrasound strain imaging of skeletal muscles

NARCIS (Netherlands)

Gijsbertse, Kaj; Sprengers, Andre M.; Nillesen, Maartje; Hansen, Hendrik H.G.; Verdonschot, Nico; De Korte, Chris L.

2015-01-01

Muscle contraction is characterized by large deformation and translation, which requires a multi-dimensional imaging modality to reveal its behavior. Previous work on ultrasound strain imaging of the muscle contraction was limited to 2D and bi-plane techniques. In this study, a three-dimensional

Homonuclear long-range correlation spectra from HMBC experiments by covariance processing.

Science.gov (United States)

Schoefberger, Wolfgang; Smrecki, Vilko; Vikić-Topić, Drazen; Müller, Norbert

2007-07-01

We present a new application of covariance nuclear magnetic resonance processing based on 1H--13C-HMBC experiments which provides an effective way for establishing indirect 1H--1H and 13C--13C nuclear spin connectivity at natural isotope abundance. The method, which identifies correlated spin networks in terms of covariance between one-dimensional traces from a single decoupled HMBC experiment, derives 13C--13C as well as 1H--1H spin connectivity maps from the two-dimensional frequency domain heteronuclear long-range correlation data matrix. The potential and limitations of this novel covariance NMR application are demonstrated on two compounds: eugenyl-beta-D-glucopyranoside and an emodin-derivative. Copyright (c) 2007 John Wiley & Sons, Ltd.

Exact solutions in three-dimensional gravity

CERN Document Server

Garcia-Diaz, Alberto A

2017-01-01

A self-contained text, systematically presenting the determination and classification of exact solutions in three-dimensional Einstein gravity. This book explores the theoretical framework and general physical and geometrical characteristics of each class of solutions, and includes information on the researchers responsible for their discovery. Beginning with the physical character of the solutions, these are identified and ordered on the basis of their geometrical invariant properties, symmetries, and algebraic classifications, or from the standpoint of their physical nature, for example electrodynamic fields, fluid, scalar field, or dilaton. Consequently, this text serves as a thorough catalogue on 2+1 exact solutions to the Einstein equations coupled to matter and fields, and on vacuum solutions of topologically massive gravity with a cosmological constant. The solutions are also examined from different perspectives, enabling a conceptual bridge between exact solutions of three- and four-dimensional gravit...

Fine hierarchy of the V-O bonds by advanced solid state NMR: novel Pb4(VO2)(PO4)3 structure as a textbook case.

Science.gov (United States)

Tricot, Grégory; Mentré, Olivier; Cristol, Sylvain; Delevoye, Laurent

2012-12-17

We report here a complete structural characterization of a new lead Pb(4)(VO(2))(PO(4))(3) vanadophosphate compound by single crystal X-ray diffraction and (51)V and (31)P solid-state NMR spectroscopy. Although structural data are commonly used for the estimation of bond lengths and further delimitation of the true coordination number (e.g., octahedral: 6 versus 5 + 1 versus 4 + 2), we show here for the first time by solid-state NMR a more accurate appreciation of the V-O bonding scheme in this complex oxide which appears well adapted to the full series of vanado-phosphate materials. The direct characterization of V-O-P bridges through the J-mediated correlation (51)V{(31)P} heteronuclear multiple quantum coherence (J-HMQC) technique allows a contrasted hierarchy of the V-O electronic delocalization and indirectly supports the presence or not of the V-O bond. In the reported lead vanado-phosphate structure, the two vanadium polyhedra that have been assigned to octahedra from a bond length point of view have been finally reclassified as tetra- and penta-coordinated units on the basis of the solid-state NMR results. More generally, we believe that the improved characterization of interatomic bonds in various vanado-phosphate structures by solid-state NMR will contribute to a better understanding of the structure/property relationships in this important class of materials.

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

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

Three-dimensional reacting shock–bubble interaction

NARCIS (Netherlands)

Diegelmann, Felix; Hickel, S.; Adams, Nikolaus A.

2017-01-01

We investigate a reacting shock–bubble interaction through three-dimensional numerical simulations with detailed chemistry. The convex shape of the bubble focuses the shock and generates regions of high pressure and temperature, which are sufficient to ignite the diluted stoichiometric

Collapse in a forced three-dimensional nonlinear Schrodinger equation

DEFF Research Database (Denmark)

Lushnikov, P.M.; Saffman, M.

2000-01-01

We derive sufficient conditions for the occurrence of collapse in a forced three-dimensional nonlinear Schrodinger equation without dissipation. Numerical studies continue the results to the case of finite dissipation.......We derive sufficient conditions for the occurrence of collapse in a forced three-dimensional nonlinear Schrodinger equation without dissipation. Numerical studies continue the results to the case of finite dissipation....

Eustachian tube three-dimensional reconstruction of secretory otitis media

International Nuclear Information System (INIS)

Yu Yafeng; Zhou Weirong; Bao Xueping; Li Min; Hu Zhenmin

2006-01-01

Objective: To study relationship between Eustachian tube and secretory otitis media and to explore the pathogeny of secretory otitis by three-dimensional reconstruction of Eustachian tube. Methods: Thirty cases of secretory otitis media (male 19, female 11) were selected randomly. Everyone was checked by otoscope and audiometry. Their bilateral Eustachian tubes were scanning by helix CT while making Valsalva's action. All images were passed on to work station to make three-dimensional reconstruction. Results: Four patients were found have Eustachian tube diseases, while most of patients' Eustachian tubes ventilated normally. Conclusions: Three-dimensional reconstruction of Eustachian tube can open out some pathogens of some secretory otitis medias. It will be helpful to diagnosis and therapy of secretory otitis media. (authors)

Computerized three-dimensional normal atlas

International Nuclear Information System (INIS)

Mano, Isamu; Suto, Yasuzo; Suzuki, Masataka; Iio, Masahiro.

1990-01-01

This paper presents our ongoing project in which normal human anatomy and its quantitative data are systematically arranged in a computer. The final product, the Computerized Three-Dimensional Normal Atlas, will be able to supply tomographic images in any direction, 3-D images, and coded information on organs, e.g., anatomical names, CT numbers, and T 1 and T 2 values. (author)

Three-Dimensional Shallow Water Acoustics

Science.gov (United States)

2016-03-30

medium properties, so horizontal refraction and reflection of sound can occur and produce significant three-dimensional (3-D) sound propagation ...by the environmental factors existing commonly in the continental shelf and shelfbreak areas, such as slopes, submarine canyons, sub-bottom layers ...surface waves, internal waves and shelfbreak fronts. 15. SUBJECT TERMS Continental Shelf; 3-D Acoustics , Surface Waves, Sound Propagation 16

Application of CRAFT in two-dimensional NMR data processing.

Science.gov (United States)

Krishnamurthy, Krish; Sefler, Andrea M; Russell, David J

2017-03-01

Two-dimensional (2D) data are typically truncated in both dimensions, but invariably and severely so in the indirect dimension. These truncated FIDs and/or interferograms are extensively zero filled, and Fourier transformation of such zero-filled data is always preceded by a rapidly decaying apodization function. Hence, the frequency line width in the spectrum (at least parallel to the evolution dimension) is almost always dominated by the apodization function. Such apodization-driven line broadening in the indirect (t 1 ) dimension leads to the lack of clear resolution of cross peaks in the 2D spectrum. Time-domain analysis (i.e. extraction of frequency, amplitudes, line width, and phase parameters directly from the FID, in this case via Bayesian modeling into a tabular format) of NMR data is another approach for spectral resonance characterization and quantification. The recently published complete reduction to amplitude frequency table (CRAFT) technique converts the raw FID data (i.e. time-domain data) into a table of frequencies, amplitudes, decay rate constants, and phases. CRAFT analyses of time-domain data require minimal or no apodization prior to extraction of the four parameters. We used the CRAFT processing approach for the decimation of the interferograms and compared the results from a variety of 2D spectra against conventional processing with and without linear prediction. The results show that use of the CRAFT technique to decimate the t 1 interferograms yields much narrower spectral line width of the resonances, circumventing the loss of resolution due to apodization. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Three dimensional CT imaging of ossicular chain: a preliminary study

International Nuclear Information System (INIS)

Hu Chunhong; Zhong Shenbin; Fu Yindi; Zhu Wei; Wang Xueyuan; Chen Jianhua; Ding Yi

2001-01-01

Objective: To analysis the features of normal and abnormal ossicular chain in three dimensional images and asses the best parameters and its usefulness in diagnosis and treatment of chronic otitis media (COM). Methods: All patients, including 43 patients with normal ears and 24 ears with COM, were examined using spiral CT with inner ear software, 1-mm slice width and 1 pitch. SSD method was used in three dimensional reconstruction and the threshold was 100-300 Hu. Results: In normal cases, Malleus, incus, stapes crura, incudomalleal joints and incudostapedial joints were displayed well, but stapes footplate unsatisfactorily. The disruption of the ossicular chain showed in three-dimensional images in cases of chronic otitis media was in accord with that seen in the operation. Conclusion: It is very important for imaging with high quality through selecting proper parameters, and three-dimensional image can provide valuable information for surgery

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

Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

International Nuclear Information System (INIS)

Marassi, Francesca M.; Ding, Yi; Schwieters, Charles D.; Tian, Ye; Yao, Yong

2015-01-01

The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential

Three dimensional digital imaging of environmental data

International Nuclear Information System (INIS)

Nichols, R.L.; Eddy, C.A.

1991-01-01

The Environmental Sciences Section (ESS) of the Savannah River Laboratory has recently acquired the computer hardware (Silicon Graphics Personal Iris Workstations) and software (Dynamic Graphics, Interactive Surface and Volume Modeling) to perform three dimensional analysis of hydrogeologic data. Three dimensional digital imaging of environmental data is a powerful technique that can be used to incorporate field, analytical, and modeling results from geologic, hydrologic, ecologic, and chemical studies into a comprehensive model for visualization and interpretation. This report covers the contamination of four different sites of the Savannah River Plant. Each section of this report has a computer graphic display of the concentration of contamination in the groundwater and/or sediments of each site

Three-dimensional Imaging, Visualization, and Display

CERN Document Server

Javidi, Bahram; Son, Jung-Young

2009-01-01

Three-Dimensional Imaging, Visualization, and Display describes recent developments, as well as the prospects and challenges facing 3D imaging, visualization, and display systems and devices. With the rapid advances in electronics, hardware, and software, 3D imaging techniques can now be implemented with commercially available components and can be used for many applications. This volume discusses the state-of-the-art in 3D display and visualization technologies, including binocular, multi-view, holographic, and image reproduction and capture techniques. It also covers 3D optical systems, 3D display instruments, 3D imaging applications, and details several attractive methods for producing 3D moving pictures. This book integrates the background material with new advances and applications in the field, and the available online supplement will include full color videos of 3D display systems. Three-Dimensional Imaging, Visualization, and Display is suitable for electrical engineers, computer scientists, optical e...

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

Three-dimensional radiation treatment planning

International Nuclear Information System (INIS)

Mohan, R.

1989-01-01

A major aim of radiation therapy is to deliver sufficient dose to the tumour volume to kill the cancer cells while sparing the nearby health organs to prevent complications. With the introduction of devices such as CT and MR scanners, radiation therapy treatment planners have access to full three-dimensional anatomical information to define, simulate, and evaluate treatments. There are a limited number of prototype software systems that allow 3D treatment planning currently in use. In addition, there are more advanced tools under development or still in the planning stages. They require sophisticated graphics and computation equipment, complex physical and mathematical algorithms, and new radiation treatment machines that deliver dose very precisely under computer control. Components of these systems include programs for the identification and delineation of the anatomy and tumour, the definition of radiation beams, the calculation of dose distribution patterns, the display of dose on 2D images and as three dimensional surfaces, and the generation of computer images to verify proper patient positioning in treatment. Some of these functions can be performed more quickly and accurately if artificial intelligence or expert systems techniques are employed. 28 refs., figs

Three-dimensional cooling of muons

CERN Document Server

Vsevolozhskaya, T A

2000-01-01

The simultaneous ionization cooling of muon beams in all three - the longitudinal and two transverse - directions is considered in a scheme, based on bent lithium lenses with dipole constituent of magnetic field in them, created by a special configuration of current-carrying rod. An analysis of three-dimensional cooling is performed with the use of kinetic equation method. Results of numerical calculation for a specific beam line configuration are presented together with results of computer simulation using the Moliere distribution to describe the Coulomb scattering and the Vavilov distribution used to describe the ionization loss of energy.

Vibrational spectra and thermal rectification in three-dimensional anharmonic lattices

International Nuclear Information System (INIS)

Lan Jinghua; Li Baowen

2007-01-01

We study thermal rectification in a three-dimensional model consisting of two segments of anharmonic lattices. One segment consists of layers of harmonic oscillator arrays coupled to a substrate potential, which is a three-dimensional Frenkel-Kontorova model, and the other segment is a three-dimensional Fermi-Pasta-Ulam model. We study the vibrational bands of the two lattices analytically and numerically, and find that, by choosing the system parameters properly, the rectification can be as high as a few thousands, which is high enough to be observed in experiment. Possible experiments in nanostructures are discussed

Synthesis and magnetic properties of heteronuclear 3d-4f compound

International Nuclear Information System (INIS)

Cristovao, B.; Ferenc, W.

2007-01-01

A novel heteronuclear 3d-4f compound having formula NdCu 3 L 3 ·13H 2 O (where H 3 L = Schiff base derived from 5-bromosalicylaldehyde and glycylglycine and L 3 = C 11 H 8 N 2 O 4 Br) was obtained. It was characterized by elemental and thermal analyses and magnetic measurements. The Cu(II)-Nd(III) compound is stable up to 323 K. During dehydration process the water molecules are lost in two stages. The magnetic susceptibility data for this complex change with temperature according to the Curie-Weiss law with Θ = -35 K. The magnetic moment values decrease from 5.00μ B at 303 K to 4.38μB at 76 K. (author)

Characterizing College Science Assessments: The Three-Dimensional Learning Assessment Protocol

Science.gov (United States)

Underwood, Sonia M.; Matz, Rebecca L.; Posey, Lynmarie A.; Carmel, Justin H.; Caballero, Marcos D.; Fata-Hartley, Cori L.; Ebert-May, Diane; Jardeleza, Sarah E.; Cooper, Melanie M.

2016-01-01

Many calls to improve science education in college and university settings have focused on improving instructor pedagogy. Meanwhile, science education at the K-12 level is undergoing significant changes as a result of the emphasis on scientific and engineering practices, crosscutting concepts, and disciplinary core ideas. This framework of “three-dimensional learning” is based on the literature about how people learn science and how we can help students put their knowledge to use. Recently, similar changes are underway in higher education by incorporating three-dimensional learning into college science courses. As these transformations move forward, it will become important to assess three-dimensional learning both to align assessments with the learning environment, and to assess the extent of the transformations. In this paper we introduce the Three-Dimensional Learning Assessment Protocol (3D-LAP), which is designed to characterize and support the development of assessment tasks in biology, chemistry, and physics that align with transformation efforts. We describe the development process used by our interdisciplinary team, discuss the validity and reliability of the protocol, and provide evidence that the protocol can distinguish between assessments that have the potential to elicit evidence of three-dimensional learning and those that do not. PMID:27606671

Characterizing College Science Assessments: The Three-Dimensional Learning Assessment Protocol.

Science.gov (United States)

Laverty, James T; Underwood, Sonia M; Matz, Rebecca L; Posey, Lynmarie A; Carmel, Justin H; Caballero, Marcos D; Fata-Hartley, Cori L; Ebert-May, Diane; Jardeleza, Sarah E; Cooper, Melanie M

2016-01-01

Many calls to improve science education in college and university settings have focused on improving instructor pedagogy. Meanwhile, science education at the K-12 level is undergoing significant changes as a result of the emphasis on scientific and engineering practices, crosscutting concepts, and disciplinary core ideas. This framework of "three-dimensional learning" is based on the literature about how people learn science and how we can help students put their knowledge to use. Recently, similar changes are underway in higher education by incorporating three-dimensional learning into college science courses. As these transformations move forward, it will become important to assess three-dimensional learning both to align assessments with the learning environment, and to assess the extent of the transformations. In this paper we introduce the Three-Dimensional Learning Assessment Protocol (3D-LAP), which is designed to characterize and support the development of assessment tasks in biology, chemistry, and physics that align with transformation efforts. We describe the development process used by our interdisciplinary team, discuss the validity and reliability of the protocol, and provide evidence that the protocol can distinguish between assessments that have the potential to elicit evidence of three-dimensional learning and those that do not.

Three dimensional imaging technique for laser-plasma diagnostics

International Nuclear Information System (INIS)

Jiang Shaoen; Zheng Zhijian; Liu Zhongli

2001-01-01

A CT technique for laser-plasma diagnostic and a three-dimensional (3D) image reconstruction program (CT3D) have been developed. The 3D images of the laser-plasma are reconstructed by using a multiplication algebraic reconstruction technique (MART) from five pinhole camera images obtained along different sight directions. The technique has been used to measure the three-dimensional distribution of X-ray of laser-plasma experiments in Xingguang II device, and the good results are obtained. This shows that a CT technique can be applied to ICF experiments

Three dimensional imaging technique for laser-plasma diagnostics

Energy Technology Data Exchange (ETDEWEB)

Shaoen, Jiang; Zhijian, Zheng; Zhongli, Liu [China Academy of Engineering Physics, Chengdu (China)

2001-04-01

A CT technique for laser-plasma diagnostic and a three-dimensional (3D) image reconstruction program (CT3D) have been developed. The 3D images of the laser-plasma are reconstructed by using a multiplication algebraic reconstruction technique (MART) from five pinhole camera images obtained along different sight directions. The technique has been used to measure the three-dimensional distribution of X-ray of laser-plasma experiments in Xingguang II device, and the good results are obtained. This shows that a CT technique can be applied to ICF experiments.

Three-dimensional Reciprocal Structures: Morphology, Concepts, Generative Rules

DEFF Research Database (Denmark)

Parigi, Dario; Pugnale, Alberto

2012-01-01

, causing every configuration to develop naturally out-of the plane. The structures presented here were developed and built by the students of the Master of Science in “Architectural Design” during a two week long workshop organized at Aalborg University in the fall semester 2011.......This paper present seven different three dimensional structures based on the principle of structural reciprocity with superimposition joint and standardized un-notched elements. Such typology could be regarded as being intrinsically three-dimensional because elements sit one of the top of the other...

Flukacad/Pipsicad: three-dimensional interfaces between Fluka and Autocad

International Nuclear Information System (INIS)

Helmut Vincke

2001-01-01

FLUKA is a widely used 3-D particle transport program. Up to now there was no possibility to display the simulation geometry or the calculated tracks in three dimensions. Even with FLUKA there exists only an option to picture two-dimensional views through the geometry used. This paper covers the description of two interface programs between the particle transport code FLUKA and the CAD program AutoCAD. These programs provide a three-dimensional facility not only for illustrating the simulated FLUKA geometry (FLUKACAD), but also for picturing simulated particle tracks (PIPSICAD) in a three-dimensional set-up. Additionally, the programming strategy for connecting FLUKA with AutoCAD is shown. A number of useful features of the programs themselves, but also of AutoCAD in the context of FLUKACAD and PIPSICAD, are explained. (authors)

Usefulness of three dimensional reconstructive images for thoracic trauma induced fractures

Energy Technology Data Exchange (ETDEWEB)

Koh, Kyung Hun; Kim, Dong Hun; Kim, Young Sook; Byun, Joo Nam [Chosun University Hospital, Gwangju (Korea, Republic of)

2006-09-15

We wanted to evaluate the usefulness of three-dimensional reconstructive images using multidetector computed tomography (MDCT) for thoracic traumatic patients visiting emergency room. 76 patients with fractures of the 105 patients who visited our emergency room with complaints of thoracic trauma were analyzed retrospectively. All the patients had thoracic MDCT performed and the three-dimensional reconstructive images were taken. The fractures were confirmed by axial CT, the clinical information, whole body bone scanning and the multiplanar reformation images. Plain x-ray images were analyzed by the fractured sites in a blind comparison of two radiologists' readings, and then that finding was compared with the axial CT scans and the three-dimensional reconstructive images. The fracture sites were rib (n 68), sternum (n = 14), clavicle (n = 6), scapula (n = 3), spine (n = 5) and combined fractures (n = 14). Plain x-ray and axial CT scans had a correspondency of 0.555 for the rib fractures. Axial CT scans and the three-dimensional reconstructive images had a correspondency of .952. For sternal fractures, those values were 0.692 and 0.928, respectively. The axial CT scans and three-dimensional reconstructive images showed sensitivities of 94% and 91% for rib and other fractures, respectively, and 93% and 100% for sternal fracture, respectively. Three-dimensional reconstructive image had an especially high sensitivity for the diagnosis of sternal fracture. While evaluating thoracic trauma at the emergency room, the three-dimensional reconstructive image was useful to easily diagnose the extent of fracture and it was very sensitive for detecting sternal fracture.

Usefulness of three dimensional reconstructive images for thoracic trauma induced fractures

International Nuclear Information System (INIS)

Koh, Kyung Hun; Kim, Dong Hun; Kim, Young Sook; Byun, Joo Nam

2006-01-01

We wanted to evaluate the usefulness of three-dimensional reconstructive images using multidetector computed tomography (MDCT) for thoracic traumatic patients visiting emergency room. 76 patients with fractures of the 105 patients who visited our emergency room with complaints of thoracic trauma were analyzed retrospectively. All the patients had thoracic MDCT performed and the three-dimensional reconstructive images were taken. The fractures were confirmed by axial CT, the clinical information, whole body bone scanning and the multiplanar reformation images. Plain x-ray images were analyzed by the fractured sites in a blind comparison of two radiologists' readings, and then that finding was compared with the axial CT scans and the three-dimensional reconstructive images. The fracture sites were rib (n 68), sternum (n = 14), clavicle (n = 6), scapula (n = 3), spine (n = 5) and combined fractures (n = 14). Plain x-ray and axial CT scans had a correspondency of 0.555 for the rib fractures. Axial CT scans and the three-dimensional reconstructive images had a correspondency of .952. For sternal fractures, those values were 0.692 and 0.928, respectively. The axial CT scans and three-dimensional reconstructive images showed sensitivities of 94% and 91% for rib and other fractures, respectively, and 93% and 100% for sternal fracture, respectively. Three-dimensional reconstructive image had an especially high sensitivity for the diagnosis of sternal fracture. While evaluating thoracic trauma at the emergency room, the three-dimensional reconstructive image was useful to easily diagnose the extent of fracture and it was very sensitive for detecting sternal fracture

Three-dimensional accuracy of plastic transfer impression copings for three implant systems.

Science.gov (United States)

Teo, Juin Wei; Tan, Keson B; Nicholls, Jack I; Wong, Keng Mun; Uy, Joanne

2014-01-01

The purpose of this study was to compare the three-dimensional accuracy of indirect plastic impression copings and direct implant-level impression copings from three implant systems (Nobel Biocare [NB], Biomet 3i [3i], and Straumann [STR]) at three interimplant buccolingual angulations (0, 8, and 15 degrees). Two-implant master models were used to simulate a three-unit implant fixed partial denture. Test models were made from Impregum impressions using direct implant-level impression copings (DR). Abutments were then connected to the master models for impressions using the plastic impression copings (INDR) at three different angulations for a total of 18 test groups (n = 5 in each group). A coordinate measuring machine was used to measure linear distortions, three-dimensional (3D) distortions, angular distortions, and absolute angular distortions between the master and test models. Three-way analysis of variance showed that the implant system had a significant effect on 3D distortions and absolute angular distortions in the x- and y-axes. Interimplant angulation had a significant effect on 3D distortions and absolute angular distortions in the y-axis. Impression technique had a significant effect on absolute angular distortions in the y-axis. With DR, the NB and 3i systems were not significantly different. With INDR, 3i appeared to have less distortion than the other systems. Interimplant angulations did not significantly affect the accuracy of NBDR, 3iINDR, and STRINDR. The accuracy of INDR and DR was comparable at all interimplant angulations for 3i and STR. For NB, INDR was comparable to DR at 0 and 8 degrees but was less accurate at 15 degrees. Three-dimensional accuracy of implant impressions varied with implant system, interimplant angulation, and impression technique.

Phase Diagrams of Three-Dimensional Anderson and Quantum Percolation Models Using Deep Three-Dimensional Convolutional Neural Network

Science.gov (United States)

Mano, Tomohiro; Ohtsuki, Tomi

2017-11-01

The three-dimensional Anderson model is a well-studied model of disordered electron systems that shows the delocalization-localization transition. As in our previous papers on two- and three-dimensional (2D, 3D) quantum phase transitions [J. Phys. Soc. Jpn. 85, 123706 (2016), 86, 044708 (2017)], we used an image recognition algorithm based on a multilayered convolutional neural network. However, in contrast to previous papers in which 2D image recognition was used, we applied 3D image recognition to analyze entire 3D wave functions. We show that a full phase diagram of the disorder-energy plane is obtained once the 3D convolutional neural network has been trained at the band center. We further demonstrate that the full phase diagram for 3D quantum bond and site percolations can be drawn by training the 3D Anderson model at the band center.

Three dimensional force prediction in a model linear brushless dc motor

Energy Technology Data Exchange (ETDEWEB)

Moghani, J.S.; Eastham, J.F.; Akmese, R.; Hill-Cottingham, R.J. (Univ. of Bath (United Kingdom). School of Electronic and Electric Engineering)

1994-11-01

Practical results are presented for the three axes forces produced on the primary of a linear brushless dc machine which is supplied from a three-phase delta-modulated inverter. Conditions of both lateral alignment and lateral displacement are considered. Finite element analysis using both two and three dimensional modeling is compared with the practical results. It is shown that a modified two dimensional model is adequate, where it can be used, in the aligned position and that the full three dimensional method gives good results when the machine is axially misaligned.

Visual Interpretation with Three-Dimensional Annotations (VITA): three-dimensional image interpretation tool for radiological reporting.

Science.gov (United States)

Roy, Sharmili; Brown, Michael S; Shih, George L

2014-02-01

This paper introduces a software framework called Visual Interpretation with Three-Dimensional Annotations (VITA) that is able to automatically generate three-dimensional (3D) visual summaries based on radiological annotations made during routine exam reporting. VITA summaries are in the form of rotating 3D volumes where radiological annotations are highlighted to place important clinical observations into a 3D context. The rendered volume is produced as a Digital Imaging and Communications in Medicine (DICOM) object and is automatically added to the study for archival in Picture Archiving and Communication System (PACS). In addition, a video summary (e.g., MPEG4) can be generated for sharing with patients and for situations where DICOM viewers are not readily available to referring physicians. The current version of VITA is compatible with ClearCanvas; however, VITA can work with any PACS workstation that has a structured annotation implementation (e.g., Extendible Markup Language, Health Level 7, Annotation and Image Markup) and is able to seamlessly integrate into the existing reporting workflow. In a survey with referring physicians, the vast majority strongly agreed that 3D visual summaries improve the communication of the radiologists' reports and aid communication with patients.

Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations

International Nuclear Information System (INIS)

Bernado, Pau; Fernandes, Miguel X.; Jacobs, Doris M.; Fiebig, Klaus; Garcia de la Torre, Jose; Pons, Miquel

2004-01-01

Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion.The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1

Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations

Energy Technology Data Exchange (ETDEWEB)

Bernado, Pau [Institut de Biologie Structurale, Jean Pierre Ebel (France); Fernandes, Miguel X. [Universidad de Murcia, Departamento de Quimica Fisica, Facultad de Quimica (Spain); Jacobs, Doris M. [Johann Wolfgang Goethe-Universitaet Frankfurt, Institut fuer Organische Chemie und Chemische Biologie (Germany); Fiebig, Klaus [Affinium Pharmaceuticals (Canada); Garcia de la Torre, Jose [Universidad de Murcia, Departamento de Quimica Fisica, Facultad de Quimica (Spain); Pons, Miquel [Laboratori de RMN de Biomolecules, Parc Cientific de Barcelona (Spain)], E-mail: mpons@ub.edu

2004-05-15

Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion.The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1.

Three-dimensional Simulation of Backward Raman Amplification

International Nuclear Information System (INIS)

Balakin, A.A.; Fraiman, G.M.; Fisch, N.J.

2005-01-01

Three-dimensional (3-D) simulations for the Backward Raman Amplification (BRA) are presented. The images illustrate the effects of pump depletion, pulse diffraction, non-homogeneous plasma density, and plasma ionization

A pulse programmable parahydrogen polarizer using a tunable electromagnet and dual channel NMR spectrometer

Science.gov (United States)

Coffey, Aaron M.; Shchepin, Roman V.; Feng, Bibo; Colon, Raul D.; Wilkens, Ken; Waddell, Kevin W.; Chekmenev, Eduard Y.

2017-11-01

Applications of parahydrogen induced polarization (PHIP) often warrant conversion of the chemically-synthesized singlet-state spin order into net heteronuclear magnetization. In order to obtain optimal yields from the overall hyperpolarization process, catalytic hydrogenation must be tightly synchronized to subsequent radiofrequency (RF) transformations of spin order. Commercial NMR consoles are designed to synchronize applied waves on multiple channels and consequently are well-suited as controllers for these types of hyperpolarization experiments that require tight coordination of RF and non-RF events. Described here is a PHIP instrument interfaced to a portable NMR console operating with a static field electromagnet in the milliTesla regime. In addition to providing comprehensive control over chemistry and RF events, this setup condenses the PHIP protocol into a pulse-program that in turn can be readily shared in the manner of traditional pulse sequences. In this device, a TTL multiplexer was constructed to convert spectrometer TTL outputs into 24 VDC signals. These signals then activated solenoid valves to control chemical shuttling and reactivity in PHIP experiments. Consolidating these steps in a pulse-programming environment speeded calibration and improved quality assurance by enabling the B0/B1 fields to be tuned based on the direct acquisition of thermally polarized and hyperpolarized NMR signals. Performance was tested on the parahydrogen addition product of 2-hydroxyethyl propionate-1-13C-d3, where the 13C polarization was estimated to be P13C = 20 ± 2.5% corresponding to 13C signal enhancement approximately 25 million-fold at 9.1 mT or approximately 77,000-fold 13C enhancement at 3 T with respect to thermally induced polarization at room temperature.

Three dimensional transport model for toroidal plasmas

International Nuclear Information System (INIS)

Copenhauer, C.

1980-12-01

A nonlinear MHD model, developed for three-dimensional toroidal geometries (asymmetric) and for high β (β approximately epsilon), is used as a basis for a three-dimensional transport model. Since inertia terms are needed in describing evolving magnetic islands, the model can calculate transport, both in the transient phase before nonlinear saturation of magnetic islands and afterwards on the resistive time scale. In the β approximately epsilon ordering, the plasma does not have sufficient energy to compress the parallel magnetic field, which allows the Alfven wave to be eliminated in the reduced nonlinear equations, and the model then follows the slower time scales. The resulting perpendicular and parallel plasma drift velocities can be identified with those of guiding center theory

Three dimensional imaging in cardiac nuclear medicine

International Nuclear Information System (INIS)

Torizuka, Kanji; Ishii, Yasushi; Yonekura, Yoshiharu; Yamamoto, Kazutaka; Tamaki, Takeyoshi

1981-01-01

Methods to obtain three dimensional images of the heart were reviewed. Gated three dimensional display reconstructed from images using bidirectional collimator, was a useful method to detect akinesis of the heart wall. Tomographic observation of the heart can be carried out by a pinhole collimator to image ischemia with high sensitivity. However the focusing plane must be carefully selected to prevent false positives. In the case of emission CT (ECT), utilization of positron emitters gave a quantitative image without correction, whereas single photon ECT needed the correction due to the absorption of γ-ray. Though the reliability of the images by ECT was high, the time required for data acquisition was much longer than that by a 7 pinhole or bidirectional collimator. (Nakanishi, T.)

[Three-dimensional computer aided design for individualized post-and-core restoration].

Science.gov (United States)

Gu, Xiao-yu; Wang, Ya-ping; Wang, Yong; Lü, Pei-jun

2009-10-01

To develop a method of three-dimensional computer aided design (CAD) of post-and-core restoration. Two plaster casts with extracted natural teeth were used in this study. The extracted teeth were prepared and scanned using tomography method to obtain three-dimensional digitalized models. According to the basic rules of post-and-core design, posts, cores and cavity surfaces of the teeth were designed using the tools for processing point clouds, curves and surfaces on the forward engineering software of Tanglong prosthodontic system. Then three-dimensional figures of the final restorations were corrected according to the configurations of anterior teeth, premolars and molars respectively. Computer aided design of 14 post-and-core restorations were finished, and good fitness between the restoration and the three-dimensional digital models were obtained. Appropriate retention forms and enough spaces for the full crown restorations can be obtained through this method. The CAD of three-dimensional figures of the post-and-core restorations can fulfill clinical requirements. Therefore they can be used in computer-aided manufacture (CAM) of post-and-core restorations.

Three-dimensional propagation in near-field tomographic X-ray phase retrieval

International Nuclear Information System (INIS)

Ruhlandt, Aike; Salditt, Tim

2016-01-01

An extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions is presented, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality

Three dimensional reconstruction of tomographic images of the retina

International Nuclear Information System (INIS)

Glittenberg, C.; Zeiler, F.; Falkner, C.; Binder, S.; Povazay, B.; Hermann, B.; Drexler, W.

2007-01-01

The development of a new display system for the three-dimensional visualization of tomographic images in ophthalmology. Specifically, a system that can use stacks of B-mode scans from an ultrahigh resolution optical tomography examination to vividly display retinal specimens as three-dimensional objects. Several subroutines were programmed in the rendering and raytracing program Cinema 4D XL 9.102 Studio Bundle (Maxon Computer Inc., Friedrichsburg, Germany), which could process stacks of tomographic scans into three-dimensional objects. Ultrahigh resolution optical coherence tomography examinations were performed on patients with various retinal pathologies and post processed with the subroutines that had been designed. All ultrahigh resolution optical coherence tomographies were performed with a titanium: sapphire based ultra broad bandwidth (160 nm) femtosecond laser system (INTEGRAL, Femtolasers Productions GmbH. Vienna Austria) with an axial resolution of 3 μm. A new three dimensional display system for tomographic images in ophthalmology was developed, which allows a highly vivid display of physiological and pathological structures of the retina. The system also distinguishes itself through its high interactivity and adaptability. This new display system allows the visualization of physiological and pathological structures of the retina in a new way, which will give us new insight into their morphology and development. (author) [de

Clinical significance of three-dimensional sonohysterography

International Nuclear Information System (INIS)

Lee, Eun Hye; Lee, Mi Hwa; Lee, Chan; Kim, Jong Wook; Shin, Myung Choel

1999-01-01

To evaluate the usefulness of three dimensional sonohysterography (3D SHG) in the evaluation of uterine endometrial and submucosal lesions in comparison with conventional two-dimensional sonohysterography (2D SHG). Our series consisted of 26 patients (mean aged 41 years) who complained of uterine bleeding, menorrhagia, or dysmenorrhea. 2D SHG was performed, and then 3D SHG was done after the volume mode was switched on. Simultaneous display of three perpendicular two-dimensional planes and surface rendering of findings on particular section were obtained. We analyzed whether the endometrium was thickened or not, and the location, size, shape, echogenicity, posterior shadowing, and echogenic rim of the focal lesion. The results were compared with the pathologic findings or MRI. There were submucosal myomas (n=12), intramural myomas (n=2), endometrial polyps (n=7), placental polyp (n=1), and normal endometrial cavities (n=4) on SHG. Nineteen cases were confirmed by pathologic findings or MRI. The results were correlated in 89% (17/19) of the cases. We misdiagnosed 2 cases: focal endometrial hyperplasia and choriocarcinoma were misdiagnosed as endometrial polyp and placental polyp, respectively. Imaging diagnoses were same in the techniques. Comparing with 2D SHG, 3D SHG provided a subjective display of pathologic findings and an additional information about spatial relationship between focal lesion and surroundings.

Clinical significance of three-dimensional sonohysterography

Energy Technology Data Exchange (ETDEWEB)

Lee, Eun Hye; Lee, Mi Hwa; Lee, Chan; Kim, Jong Wook; Shin, Myung Choel [Pochon Cha University College of Medicine, Pochon (Korea, Republic of)

1999-12-15

To evaluate the usefulness of three dimensional sonohysterography (3D SHG) in the evaluation of uterine endometrial and submucosal lesions in comparison with conventional two-dimensional sonohysterography (2D SHG). Our series consisted of 26 patients (mean aged 41 years) who complained of uterine bleeding, menorrhagia, or dysmenorrhea. 2D SHG was performed, and then 3D SHG was done after the volume mode was switched on. Simultaneous display of three perpendicular two-dimensional planes and surface rendering of findings on particular section were obtained. We analyzed whether the endometrium was thickened or not, and the location, size, shape, echogenicity, posterior shadowing, and echogenic rim of the focal lesion. The results were compared with the pathologic findings or MRI. There were submucosal myomas (n=12), intramural myomas (n=2), endometrial polyps (n=7), placental polyp (n=1), and normal endometrial cavities (n=4) on SHG. Nineteen cases were confirmed by pathologic findings or MRI. The results were correlated in 89% (17/19) of the cases. We misdiagnosed 2 cases: focal endometrial hyperplasia and choriocarcinoma were misdiagnosed as endometrial polyp and placental polyp, respectively. Imaging diagnoses were same in the techniques. Comparing with 2D SHG, 3D SHG provided a subjective display of pathologic findings and an additional information about spatial relationship between focal lesion and surroundings.

Prognostic value of three-dimensional ultrasound for fetal hydronephrosis

Science.gov (United States)

WANG, JUNMEI; YING, WEIWEN; TANG, DAXING; YANG, LIMING; LIU, DONGSHENG; LIU, YUANHUI; PAN, JIAOE; XIE, XING

2015-01-01

The present study evaluated the prognostic value of three-dimensional ultrasound for fetal hydronephrosis. Pregnant females with fetal hydronephrosis were enrolled and a novel three-dimensional ultrasound indicator, renal parenchymal volume/kidney volume, was introduced to predict the postnatal prognosis of fetal hydronephrosis in comparison with commonly used ultrasound indicators. All ultrasound indicators of fetal hydronephrosis could predict whether postnatal surgery was required for fetal hydronephrosis; however, the predictive performance of renal parenchymal volume/kidney volume measurements as an individual indicator was the highest. In conclusion, ultrasound is important in predicting whether postnatal surgery is required for fetal hydronephrosis, and the three-dimensional ultrasound indicator renal parenchymal volume/kidney volume has a high predictive performance. Furthermore, the majority of cases of fetal hydronephrosis spontaneously regress subsequent to birth, and the regression time is closely associated with ultrasound indicators. PMID:25667626

Imaging unsteady three-dimensional transport phenomena

Indian Academy of Sciences (India)

2014-01-05

Jan 5, 2014 ... The image data can be jointly analysed with the physical laws governing transport and principles of image formation. Hence, with the experiment suitably carried out, three-dimensional physical domains with unsteady processes can be accommodated. Optical methods promise to breach the holy grail of ...

Usefulness Of Three-Dimensional Printing Models for Patients with Stoma Construction

OpenAIRE

Tominaga, Tetsuro; Takagi, Katsunori; Takeshita, Hiroaki; Miyamoto, Tomo; Shimoda, Kozue; Matsuo, Ayano; Matsumoto, Keitaro; Hidaka, Shigekazu; Yamasaki, Naoya; Sawai, Terumitsu; Nagayasu, Takeshi

2016-01-01

The use of patient-specific organ models in three-dimensional printing systems could be helpful for the education of patients and medical students. The aim of this study was to clarify whether the use of patient-specific stoma models is helpful for patient education. From January 2014 to September 2014, 5 patients who underwent colorectal surgery and for whom a temporary or permanent stoma had been created were involved in this study. Three-dimensional stoma models and three-dimensional face ...

Loop expansion in massless three-dimensional QED

International Nuclear Information System (INIS)

Guendelman, E.I.; Radulovic, Z.M.

1983-01-01

It is shown how the loop expansion in massless three-dimensional QED can be made finite, up to three loops, by absorbing the infrared divergences in a gauge-fixing term. The same method removes leading and first subleading singularities to all orders of perturbation theory, and all singularities of the fermion self-energy to four loops

[Application Progress of Three-dimensional Laser Scanning Technology in Medical Surface Mapping].

Science.gov (United States)

Zhang, Yonghong; Hou, He; Han, Yuchuan; Wang, Ning; Zhang, Ying; Zhu, Xianfeng; Wang, Mingshi

2016-04-01

The booming three-dimensional laser scanning technology can efficiently and effectively get spatial three-dimensional coordinates of the detected object surface and reconstruct the image at high speed,high precision and large capacity of information.Non-radiation,non-contact and the ability of visualization make it increasingly popular in three-dimensional surface medical mapping.This paper reviews the applications and developments of three-dimensional laser scanning technology in medical field,especially in stomatology,plastic surgery and orthopedics.Furthermore,the paper also discusses the application prospects in the future as well as the biomedical engineering problems it would encounter with.

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...

Three-dimensional transesophageal echocardiography of the atrial septal defects

Directory of Open Access Journals (Sweden)

Romero-Cárdenas Ángel

2008-07-01

Full Text Available Abstract Transesophageal echocardiography has advantages over transthoracic technique in defining morphology of atrial structures. Even though real time three-dimensional echocardiographic imaging is a reality, the off-line reconstruction technique usually allows to obtain higher spatial resolution images. The purpose of this study was to explore the accuracy of off-line three-dimensional transesophageal echocardiography in a spectrum of atrial septal defects by comparing them with representative anatomic specimens.

8. Nuclear magnetic resonance users meeting; 1. Luso-Brazilian NMR meeting. Abstracts

International Nuclear Information System (INIS)

2001-01-01

The NMR Users Meeting is held every year in Brazil and its eighth edition took place from May 7 - 11, 2001 together with the first Luso-Brazilian Meeting on Nuclear Magnetic Resonance. The extended abstracts book comprise: ten major conferences, four plenary lectures delivered by enterprise representatives (three from USA and one from Germany), six talks about the state-of-the-art of NMR methods (especially bi and tri-dimensional new techniques) and summaries of results from one hundred and twenty four research works. Among these research results which have been discussed, one hundred and sixteen were presented as congress panels/posters and eight as oral communications. The major topics of the scientific and technological research works are thus distributed: 63% in chemical sciences (mainly structural elucidation and stereochemistry of organic compounds and dynamical studies of chemical reactions), 19% in materials science (including petroleum), 8% in applied life sciences (agricultural and food sciences, biological sciences and medicine), 8% about theoretical aspects related to nuclear magnetic resonance and 2% regarding improvements in NMR instrumental techniques

Symmetries, integrals, and three-dimensional reductions of Plebanski's second heavenly equation

International Nuclear Information System (INIS)

Neyzi, F.; Sheftel, M. B.; Yazici, D.

2007-01-01

We study symmetries and conservation laws for Plebanski's second heavenly equation written as a first-order nonlinear evolutionary system which admits a multi-Hamiltonian structure. We construct an optimal system of one-dimensional subalgebras and all inequivalent three-dimensional symmetry reductions of the original four-dimensional system. We consider these two-component evolutionary systems in three dimensions as natural candidates for integrable systems

Upper bound on the capacity of constrained three-dimensional codes

DEFF Research Database (Denmark)

Forchhammer, Søren

2000-01-01

An upper bound on the capacity of constrained three-dimensional codes is presented. The bound for two-dimensional codes of Calkin and Wilf (see SIAM Journal of Discrete Mathematics, vol.11, no.1, p.54-60, 1998) was extended to three dimensions by Nagy and Zeger. Both bounds apply to first order s...

Teaching veterinary obstetrics using three-dimensional animation technology.

Science.gov (United States)

Scherzer, Jakob; Buchanan, M Flint; Moore, James N; White, Susan L

2010-01-01

In this three-year study, test scores for students taught veterinary obstetrics in a classroom setting with either traditional media (photographs, text, and two-dimensional graphical presentations) were compared with those for students taught by incorporating three-dimensional (3D) media (linear animations and interactive QuickTime Virtual Reality models) into the classroom lectures. Incorporation of the 3D animations and interactive models significantly increased students' scores on essay questions designed to assess their comprehension of the subject matter. This approach to education may help to better prepare students for dealing with obstetrical cases during their final clinical year and after graduation.

Three-dimensional wax patterning of paper fluidic devices.

Science.gov (United States)

Renault, Christophe; Koehne, Jessica; Ricco, Antonio J; Crooks, Richard M

2014-06-17

In this paper we describe a method for three-dimensional wax patterning of microfluidic paper-based analytical devices (μPADs). The method is rooted in the fundamental details of wax transport in paper and provides a simple way to fabricate complex channel architectures such as hemichannels and fully enclosed channels. We show that three-dimensional μPADs can be fabricated with half as much paper by using hemichannels rather than ordinary open channels. We also provide evidence that fully enclosed channels are efficiently isolated from the exterior environment, decreasing contamination risks, simplifying the handling of the device, and slowing evaporation of solvents.

Estimation of three-dimensional radar tracking using modified extended kalman filter

Science.gov (United States)

Aditya, Prima; Apriliani, Erna; Khusnul Arif, Didik; Baihaqi, Komar

2018-03-01

Kalman filter is an estimation method by combining data and mathematical models then developed be extended Kalman filter to handle nonlinear systems. Three-dimensional radar tracking is one of example of nonlinear system. In this paper developed a modification method of extended Kalman filter from the direct decline of the three-dimensional radar tracking case. The development of this filter algorithm can solve the three-dimensional radar measurements in the case proposed in this case the target measured by radar with distance r, azimuth angle θ, and the elevation angle ϕ. Artificial covariance and mean adjusted directly on the three-dimensional radar system. Simulations result show that the proposed formulation is effective in the calculation of nonlinear measurement compared with extended Kalman filter with the value error at 0.77% until 1.15%.

Three-Dimensional Structure Determination of Botulinum Toxin

National Research Council Canada - National Science Library

Stevens, Ray

1997-01-01

...) Based on the structure of the neurotoxin, understand the toxins mechanism of action. We have accomplished the first goal of determining the three-dimensional structure of the 150 kD botulinum neurotoxin serotype...

Three-Dimensional Structure Determination of Botulinum Toxin

National Research Council Canada - National Science Library

Stevens, Ray

1998-01-01

...) Based on the structure of the neurotoxin, understand the toxins mechanism of action. We have accomplished the first goal of determining the three-dimensional structure of the 150 kD botulinum neurotoxin serotype...

Three-dimensional MRI of the glenoid labrum

International Nuclear Information System (INIS)

Loehr, S.P.; Pope, T.L. Jr.; Martin, D.F.; Link, K.M.; Monu, J.U.V.; Hunter, M.; Reboussin, D.

1995-01-01

The objective of this study was to assess the accuracy of three-dimensional (3D) magnetic resonance imaging (MRI) reformation in the evaluation of tears of the glenoid labrum complex (GLC). Fifty-five shoulders were evaluated by MRI using standard spin-echo sequences. Gradient-refocused-echo axial projections were used to assess the GLC on the two-dimensional (2D) studies. Three-dimensional Fourier transform multiplanar gradient-recalled imaging with a resolution of 0.7 mm was also performed in all patients. Independent analyses of the anterior and posterior labra were performed in a blinded manner for both the 2D and 3D studies by three experienced musculoskeletal radiologists. Observations of the imaging studies were compared with the videoarthroscopic findings. The appearance of the GLC was rated on a scale of 0 to 4 (0-2=normal, 3, 4=abnormal or torn). The diagnostic confidence was averaged from the three reader's scores. Anterior labral tears were effectively detected with sensitivities of 89% and 96% and specificities of 96% and 100% (P<0.0001) for the 2D and 3D studies, respectively. For posterior labral tears, the sensitivity and specificity of the 2D method were 47% and 98%, respectively. The sensitivity and specificity of the 3D volume sequence were 53% and 98%, respectively. The lower sensitivity of both imaging methods for detecting posterior labral tears may be influenced by the smaller number (n=5) of arthroscopically confirmed cases in our study and reflects the difficulty of visualizing the posteroinferior borders of the GLC with present MRI techniques. (orig.)

Infrared magneto-spectroscopy of two-dimensional and three-dimensional massless fermions: A comparison

Energy Technology Data Exchange (ETDEWEB)

Orlita, M., E-mail: milan.orlita@lncmi.cnrs.fr [Laboratoire National des Champs Magnétiques Intenses, CNRS-UJF-UPS-INSA, 38042 Grenoble (France); Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2 (Czech Republic); Faugeras, C.; Barra, A.-L.; Martinez, G.; Potemski, M. [Laboratoire National des Champs Magnétiques Intenses, CNRS-UJF-UPS-INSA, 38042 Grenoble (France); Basko, D. M. [LPMMC UMR 5493, Université Grenoble 1/CNRS, B.P. 166, 38042 Grenoble (France); Zholudev, M. S. [Laboratoire Charles Coulomb (L2C), UMR CNRS 5221, GIS-TERALAB, Université Montpellier II, 34095 Montpellier (France); Institute for Physics of Microstructures, RAS, Nizhny Novgorod GSP-105 603950 (Russian Federation); Teppe, F.; Knap, W. [Laboratoire Charles Coulomb (L2C), UMR CNRS 5221, GIS-TERALAB, Université Montpellier II, 34095 Montpellier (France); Gavrilenko, V. I. [Institute for Physics of Microstructures, RAS, Nizhny Novgorod GSP-105 603950 (Russian Federation); Mikhailov, N. N.; Dvoretskii, S. A. [A.V. Rzhanov Institute of Semiconductor Physics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090 (Russian Federation); Neugebauer, P. [Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart (Germany); Berger, C. [School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Institut Néel/CNRS-UJF BP 166, F-38042 Grenoble Cedex 9 (France); Heer, W. A. de [School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

2015-03-21

Here, we report on a magneto-optical study of two distinct systems hosting massless fermions—two-dimensional graphene and three-dimensional HgCdTe tuned to the zero band gap condition at the point of the semiconductor-to-semimetal topological transition. Both materials exhibit, in the quantum regime, a fairly rich magneto-optical response, which is composed from a series of intra- and interband inter-Landau level resonances with for massless fermions typical √(B) dependence. The impact of the system's dimensionality and of the strength of the spin-orbit interaction on the optical response is also discussed.

Three dimensional system integration

CERN Document Server

Papanikolaou, Antonis; Radojcic, Riko

2010-01-01

Three-dimensional (3D) integrated circuit (IC) stacking is the next big step in electronic system integration. It enables packing more functionality, as well as integration of heterogeneous materials, devices, and signals, in the same space (volume). This results in consumer electronics (e.g., mobile, handheld devices) which can run more powerful applications, such as full-length movies and 3D games, with longer battery life. This technology is so promising that it is expected to be a mainstream technology a few years from now, less than 10-15 years from its original conception. To achieve thi

Turbulence in Three Dimensional Simulations of Magnetopause Reconnection

Science.gov (United States)

Drake, J. F.; Price, L.; Swisdak, M.; Burch, J. L.; Cassak, P.; Dahlin, J. T.; Ergun, R.

2017-12-01

We present two- and three-dimensional particle-in-cell simulations of the 16 October 2015 MMS magnetopause reconnection event. While the two-dimensional simulation is laminar, turbulence develops at both the x-line and along the magnetic separatrices in the three-dimensional simulation. This turbulence is electromagnetic in nature, is characterized by a wavevector k given by kρ e ˜(m_e/m_i)0.25 with ρ e the electron Larmor radius, and appears to have the ion pressure gradient as its source of free energy. Taken together, these results suggest the instability is a variant of the lower-hybrid drift instability. The turbulence produces electric field fluctuations in the out-of-plane direction (the direction of the reconnection electric field) with an amplitude of around ± 10 mV/m, which is much greater than the reconnection electric field of around 0.1 mV/m. Such large values of the out-of-plane electric field have been identified in the MMS data. The turbulence in the simulation controls the scale lengths of the density profile and current layers in asymmetric reconnection, driving them closer to √ {ρ eρ_i } than the ρ e or de scalings seen in 2D reconnection simulations, where de is the electron inertial length. The turbulence is strong enough to make the magnetic field around the reconnection island chaotic and produces both anomalous resistivity and anomalous viscosity. Each contribute significantly to breaking the frozen-in condition in the electron diffusion region. The crescent-shaped features in velocity space seen both in MMS observations and in two-dimensional simulations survive, even in the turbulent environment of the three-dimensional system. We compare and contrast these results to a three-dimensional simulation of the 8 December 2015 MMS magnetopause reconnection event in which the reconnecting and out-of-plane guide fields are comparable. LHDI is still present in this event, although its appearance is modified by the presence of the guide

Two- and three-dimensional CT evaluation of sacral and pelvic anomalies

International Nuclear Information System (INIS)

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

1988-01-01

Pelvic anomalies are difficult to evaluate with standard techniques. Detailed knowledge of the existing pelvic structures and musculature is essential for successful repair. The authors evaluated 12 patients with complex malformations of the pelvis using two- and three-dimensional imaging. The anomalies included bladder exstrophy (n = 4), cloacal exstrophy (n = 1), duplicated and absent sacrum (n = 3), myelomeningoceles (n = 2), and diastrophic dwarfism (n = 2). The two-dimensional images consisted of sequential coronal and sagittal reconstructions that could be reviewed dynamically on screen. Three-dimensional images were generated on the Pixar imaging computer with use of volumetric rendering. Two- and three-dimensional CT proved complementary in the evaluation of pelvic anomalies, providing optimal information from transaxial CT data

Three-dimensional stellarator equilibrium as an ohmic steady state

International Nuclear Information System (INIS)

Park, W.; Monticello, D.A.; Strauss, H.; Manickam, J.

1985-07-01

A stable three-dimensional stellarator equilibrium can be obtained numerically by a time-dependent relaxation method using small values of dissipation. The final state is an ohmic steady state which approaches an ohmic equilibrium in the limit of small dissipation coefficients. We describe a method to speed up the relaxation process and a method to implement the B vector . del p = 0 condition. These methods are applied to obtain three-dimensional heliac equilibria using the reduced heliac equations

Self-assembled three-dimensional and compressible interdigitated thin-film supercapacitors and batteries

Science.gov (United States)

Nyström, Gustav; Marais, Andrew; Karabulut, Erdem; Wågberg, Lars; Cui, Yi; Hamedi, Mahiar M.

2015-01-01

Traditional thin-film energy-storage devices consist of stacked layers of active films on two-dimensional substrates and do not exploit the third dimension. Fully three-dimensional thin-film devices would allow energy storage in bulk materials with arbitrary form factors and with mechanical properties unique to bulk materials such as compressibility. Here we show three-dimensional energy-storage devices based on layer-by-layer self-assembly of interdigitated thin films on the surface of an open-cell aerogel substrate. We demonstrate a reversibly compressible three-dimensional supercapacitor with carbon nanotube electrodes and a three-dimensional hybrid battery with a copper hexacyanoferrate ion intercalating cathode and a carbon nanotube anode. The three-dimensional supercapacitor shows stable operation over 400 cycles with a capacitance of 25 F g−1 and is fully functional even at compressions up to 75%. Our results demonstrate that layer-by-layer self-assembly inside aerogels is a rapid, precise and scalable route for building high-surface-area 3D thin-film devices. PMID:26021485

A retrospective and prospective survey of three-dimensional transport calculations

International Nuclear Information System (INIS)

Nakahara, Yasuaki

1985-01-01

A retrospective survey is made on the three-dimensional radiation transport calculations. Introduction is given to computer codes based on the distinctive numerical methods such as the Monte Carlo, Direct Integration, Ssub(n) and Finite Element Methods to solve the three-dimensional transport equations. Prospective discussions are made on pros and cons of these methods. (author)

Early orthognathic surgery with three-dimensional image simulation during presurgical orthodontics in adults.

Science.gov (United States)

Kang, Sang-Hoon; Kim, Moon-Key; Park, Sun-Yeon; Lee, Ji-Yeon; Park, Wonse; Lee, Sang-Hwy

2011-03-01

To correct dentofacial deformities, three-dimensional skeletal analysis and computerized orthognathic surgery simulation are used to facilitate accurate diagnoses and surgical plans. Computed tomography imaging of dental occlusion can inform three-dimensional facial analyses and orthognathic surgical simulations. Furthermore, three-dimensional laser scans of a cast model of the predetermined postoperative dental occlusion can be used to increase the accuracy of the preoperative surgical simulation. In this study, we prepared cast models of planned postoperative dental occlusions from 12 patients diagnosed with skeletal class III malocclusions with mandibular prognathism and facial asymmetry that had planned to undergo bimaxillary orthognathic surgery during preoperative orthodontic treatment. The data from three-dimensional laser scans of the cast models were used in three-dimensional surgical simulations. Early orthognathic surgeries were performed based on three-dimensional image simulations using the cast images in several presurgical orthodontic states in which teeth alignment, leveling, and space closure were incomplete. After postoperative orthodontic treatments, intraoral examinations revealed that no patient had a posterior open bite or space. The two-dimensional and three-dimensional skeletal analyses showed that no mandibular deviations occurred between the immediate and final postoperative states of orthodontic treatment. These results showed that early orthognathic surgery with three-dimensional computerized simulations based on cast models of predetermined postoperative dental occlusions could provide early correction of facial deformities and improved efficacy of preoperative orthodontic treatment. This approach can reduce the decompensation treatment period of the presurgical orthodontics and contribute to efficient postoperative orthodontic treatments.

Reliability of tunnel angle in ACL reconstruction: two-dimensional versus three-dimensional guide technique.

Science.gov (United States)

Leiter, Jeff R S; de Korompay, Nevin; Macdonald, Lindsey; McRae, Sheila; Froese, Warren; Macdonald, Peter B

2011-08-01

To compare the reliability of tibial tunnel position and angle produced with a standard ACL guide (two-dimensional guide) or Howell 65° Guide (three-dimensional guide) in the coronal and sagittal planes. In the sagittal plane, the dependent variables were the angle of the tibial tunnel relative to the tibial plateau and the position of the tibial tunnel with respect to the most posterior aspect of the tibia. In the coronal plane, the dependent variables were the angle of the tunnel with respect to the medial joint line of the tibia and the medial and lateral placement of the tibial tunnel relative to the most medial aspect of the tibia. The position and angle of the tibial tunnel in the coronal and sagittal planes were determined from anteroposterior and lateral radiographs, respectively, taken 2-6 months postoperatively. The two-dimensional and three-dimensional guide groups included 28 and 24 sets of radiographs, respectively. Tibial tunnel position was identified, and tunnel angle measurements were completed. Multiple investigators measured the position and angle of the tunnel 3 times, at least 7 days apart. The angle of the tibial tunnel in the coronal plane using a two-dimensional guide (61.3 ± 4.8°) was more horizontal (P guide (64.7 ± 6.2°). The position of the tibial tunnel in the sagittal plane was more anterior (P guide group compared to the three-dimensional guide group (43.3 ± 2.9%). The Howell Tibial Guide allows for reliable placement of the tibial tunnel in the coronal plane at an angle of 65°. Tibial tunnels were within the anatomical footprint of the ACL with either technique. Future studies should investigate the effects of tibial tunnel angle on knee function and patient quality of life. Case-control retrospective comparative study, Level III.

Three-dimensional characterization of stress corrosion cracks

DEFF Research Database (Denmark)

Lozano-Perez, S.; Rodrigo, P.; Gontard, Lionel Cervera

2011-01-01

the best spatial resolution. To illustrate the power of these techniques, different parts of dominant stress corrosion cracks in Ni-alloys and stainless steels have been reconstructed in 3D. All relevant microstructural features can now be studied in detail and its relative orientation respect......Understanding crack propagation and initiation is fundamental if stress corrosion cracking (SCC) mechanisms are to be understood. However, cracking is a three-dimensional (3D) phenomenon and most characterization techniques are restricted to two-dimensional (2D) observations. In order to overcome...

Two- and three-dimensional evaluation of the acetabulum in the pediatric patient

International Nuclear Information System (INIS)

Magid, D.; Fishman, E.K.; Sponseller, P.D.

1987-01-01

Complex anatomic structures such as the hip and acetabulum are best evaluated with the use of two- and three-dimensional reconstruction techniques and standard transaxial CT data. CT scans of children with various hip pathologies, including congenital hip dislocation, slipped capital femoral epiphyses, hip dysplasias, dwarfism, and acetabular fractures, were reviewed to determine the value of two- and three-dimensional imaging. The advantages of two-dimensional imaging techniques (sequential coronal/sagittal reconstruction) and three-dimensional valumetric imaging techniques (using real-time video display) are illustrated with specific examples

NMR structure of the glucose-dependent insulinotropic polypeptide fragment, GIP(1-30)amide

International Nuclear Information System (INIS)

Alana, Inigo; Hewage, Chandralal M.; G. Malthouse, J. Paul; Parker, Jeremy C.; Gault, Victor A.; O'Harte, Finbarr P.M.

2004-01-01

Glucose-dependent insulinotropic polypeptide is an incretin hormone that stimulates insulin secretion and reduces postprandial glycaemic excursions. The glucose-dependent action of GIP on pancreatic β-cells has attracted attention towards its exploitation as a potential drug for type 2 diabetes. Use of NMR or X-ray crystallography is vital to determine the three-dimensional structure of the peptide. Therefore, to understand the basic structural requirements for the biological activity of GIP, the solution structure of the major biologically active fragment, GIP(1-30)amide, was investigated by proton NMR spectroscopy and molecular modelling. The structure is characterised by a full length α-helical conformation between residues F 6 and A 28 . This structural information could play an important role in the design of therapeutic agents based upon GIP receptor agonists

Two-dimensional NMR evidence for cleavage of lignin and xylan substituents in wheat straw through hydrothermal pretreatment and enzymatic hydrolysis

DEFF Research Database (Denmark)

Yelle, Daniel J.; Kaparaju, Laxmi-Narasimha Prasad; Hunt, Christopher G.

2013-01-01

correlation spectroscopy, via an heteronuclear single quantum coherence experiment, revealed substantial lignin β-aryl ether cleavage, deacetylation via cleavage of the natural acetates at the 2-O- and 3-O-positions of xylan, and uronic acid depletion via cleavage of the (1 → 2)-linked 4-O....... g., further deacylation revealed by the depletion in ferulate and p-coumarate structures). Supplementary chemical analyses showed that the hydrothermal pretreatment increased the cellulose and lignin concentration with partial removal of extractives and hemicelluloses. The subsequent enzymatic...

NMR imaging

International Nuclear Information System (INIS)

Ouchi, Toshihiro; Steiner, R.E.

1984-01-01

Three epidermoid and two dermoid tumours, pathologically proven, were examined by NMR and CT scans. Although most brain tumours have a low signal with a long T 1 , a dermoid cyst and one of the two components of the other dermoid tumour had a high signal and therefore a short T 1 . All three epidermoid tumours had a low signal and a long T 1 . Because of the high level contrast between some of the tumours and cerebrospinal fluid, NMR is helpful to detect the lesion. Neither of the liquid fluid levels in the tumour cysts or floating fat in the subarachnoid space was recognized in one patients, but the fine leakage of the content from the epidermoid cyst into the lateral ventricle was detected on a saturation recovery 1000 image in one case. (author)

Dynamic three-dimensional display of common congenital cardiac defects from reconstruction of two-dimensional echocardiographic images.

Science.gov (United States)

Hsieh, K S; Lin, C C; Liu, W S; Chen, F L

1996-01-01

Two-dimensional echocardiography had long been a standard diagnostic modality for congenital heart disease. Further attempts of three-dimensional reconstruction using two-dimensional echocardiographic images to visualize stereotypic structure of cardiac lesions have been successful only recently. So far only very few studies have been done to display three-dimensional anatomy of the heart through two-dimensional image acquisition because such complex procedures were involved. This study introduced a recently developed image acquisition and processing system for dynamic three-dimensional visualization of various congenital cardiac lesions. From December 1994 to April 1995, 35 cases were selected in the Echo Laboratory here from about 3000 Echo examinations completed. Each image was acquired on-line with specially designed high resolution image grazmber with EKG and respiratory gating technique. Off-line image processing using a window-architectured interactive software package includes construction of 2-D ehcocardiographic pixel to 3-D "voxel" with conversion of orthogonal to rotatory axial system, interpolation, extraction of region of interest, segmentation, shading and, finally, 3D rendering. Three-dimensional anatomy of various congenital cardiac defects was shown, including four cases with ventricular septal defects, two cases with atrial septal defects, and two cases with aortic stenosis. Dynamic reconstruction of a "beating heart" is recorded as vedio tape with video interface. The potential application of 3D display of the reconstruction from 2D echocardiographic images for the diagnosis of various congenital heart defects has been shown. The 3D display was able to improve the diagnostic ability of echocardiography, and clear-cut display of the various congenital cardiac defects and vavular stenosis could be demonstrated. Reinforcement of current techniques will expand future application of 3D display of conventional 2D images.

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.

Superconductivity and the existence of Nambu's three-dimensional phase space mechanics

International Nuclear Information System (INIS)

Angulo, R.; Gonzalez-Bernardo, C.A.; Rodriguez-Gomez, J.; Kalnay, A.J.; Perez-M, F.; Tello-Llanos, R.A.

1984-01-01

Nambu proposed a generalization of hamiltonian mechanics such that three-dimensional phase space is allowed. Thanks to a recent paper by Holm and Kupershmidt we are able to show the existence of such three-dimensional phase space systems in superconductivity. (orig.)

Three-dimensional stereo by photometric ratios

International Nuclear Information System (INIS)

Wolff, L.B.; Angelopoulou, E.

1994-01-01

We present a methodology for corresponding a dense set of points on an object surface from photometric values for three-dimensional stereo computation of depth. The methodology utilizes multiple stereo pairs of images, with each stereo pair being taken of the identical scene but under different illumination. With just two stereo pairs of images taken under two different illumination conditions, a stereo pair of ratio images can be produced, one for the ratio of left-hand images and one for the ratio of right-hand images. We demonstrate how the photometric ratios composing these images can be used for accurate correspondence of object points. Object points having the same photometric ratio with respect to two different illumination conditions constitute a well-defined equivalence class of physical constraints defined by local surface orientation relative to illumination conditions. We formally show that for diffuse reflection the photometric ratio is invariant to varying camera characteristics, surface albedo, and viewpoint and that therefore the same photometric ratio in both images of a stereo pair implies the same equivalence class of physical constraints. The correspondence of photometric ratios along epipolar lines in a stereo pair of images under different illumination conditions is a correspondence of equivalent physical constraints, and the determination of depth from stereo can be performed. Whereas illumination planning is required, our photometric-based stereo methodology does not require knowledge of illumination conditions in the actual computation of three-dimensional depth and is applicable to perspective views. This technique extends the stereo determination of three-dimensional depth to smooth featureless surfaces without the use of precisely calibrated lighting. We demonstrate experimental depth maps from a dense set of points on smooth objects of known ground-truth shape, determined to within 1% depth accuracy

Three-dimensional metallic opals fabricated by double templating

International Nuclear Information System (INIS)

Yan Qingfeng; Nukala, Pavan; Chiang, Yet-Ming; Wong, C.C.

2009-01-01

We report a simple and cost-effective double templating method for fabricating large-area three-dimensional metallic photonic crystals of controlled thickness. A self-assembled polystyrene opal was used as the first template to fabricate a silica inverse opal on a gold-coated glass substrate via sol-gel processing. Gold was subsequently infiltrated to the pores of the silica inverse opal using electrochemical deposition. A high-quality three-dimensional gold photonic crystal was obtained after removal of the secondary template (silica inverse opal). The effects of template sphere size and deposition current density on the gold growth rate, and the resulting morphology and growth mechanism of the gold opal, were investigated.

Three-dimensional quadrupole lenses made with permanent magnets

International Nuclear Information System (INIS)

Ivanov, A.S.

1984-01-01

The performance of accelerator systems with quadrupole magnets can be improved by using permanent magnets in quadrupole lenses. This requires better methods for treating the three-dimensional nature of the magnetic fields and the nonlinear characteristics of the magnets. A numerical method is described for simulating three-dimensional magnetic fields and used to analyze quadrupole lenses and doublets with permanent magnets. The results, which are confirmed experimentally, indicate that both the quadrupole magnetic gradient and the effective field length are changed in permanent-magnet quadrupole lenses when the pole lengths and the gap between the lenses are varied while the other characteristics of the magnets remain unchanged

CFT description of three-dimensional Kerr-de Sitter spacetime

International Nuclear Information System (INIS)

Fjelstad, Jens; Hwang, Stephen; Maansson, Teresia

2002-01-01

We describe three-dimensional Kerr-de Sitter space using similar methods as recently applied to the BTZ black hole. A rigorous form of the classical connection between gravity in three dimensions and two-dimensional conformal field theory is employed, where the fundamental degrees of freedom are described in terms of two dependent SL(2,C) currents. In contrast to the BTZ case, however, quantization does not give the Bekenstein-Hawking entropy connected to the cosmological horizon of Kerr-de Sitter space

CFT description of three-dimensional Kerr-de Sitter spacetime

Energy Technology Data Exchange (ETDEWEB)

Fjelstad, Jens E-mail: jens.fjelstad@kau.se; Hwang, Stephen E-mail: stephen.hwang@kau.se; Maansson, Teresia E-mail: teresia@physto.se

2002-10-07

We describe three-dimensional Kerr-de Sitter space using similar methods as recently applied to the BTZ black hole. A rigorous form of the classical connection between gravity in three dimensions and two-dimensional conformal field theory is employed, where the fundamental degrees of freedom are described in terms of two dependent SL(2,C) currents. In contrast to the BTZ case, however, quantization does not give the Bekenstein-Hawking entropy connected to the cosmological horizon of Kerr-de Sitter space.

Radiological evaluation of the fetal face using three-dimensional ultrasound imaging

Directory of Open Access Journals (Sweden)

Bäumler M

2012-12-01

Full Text Available Marcel Bäumler,1–3 Michèle Bigorre,1,4 Jean-Michel Faure1,51CHU Montpellier, Centre de Compétence des Fentes Faciales, Hôpital Lapeyronie, Montpellier, 2Clinique du Parc, Imagerie de la Femme, Castelnau-le-Lez, 3Cabinet de Radiologie du Trident, Lunel, 4CHU Service de Chirurgie Plastique Pédiatrique, Hôpital Lapeyronie, Montpellier, 5CHU Montpellier, Service de Gynécologie-Obstétrique, Hôpital Arnaud de Villeneuve, Montpellier, FranceAbstract: This paper reviews screening and three-dimensional diagnostic ultrasound imaging of the fetal face. The different techniques available for analyzing biometric and morphological items of the profile, eyes, ears, lips, and hard and soft palate are commented on and briefly compared with the respective bi-dimensional techniques. The available literature supports the use of three-dimensional ultrasound in difficult prenatal diagnostic conditions because of its diagnostic accuracy, enabling improved safety of perinatal care. Globally, a marked increase has been observed in the accuracy of three-dimensional ultrasound in comparison with the bi-dimensional approach. Because there is no consensus about the performance of the different three-dimensional techniques, future studies are needed in order to compare them and to find the best technique for analysis of each of the respective facial elements. Universal prenatal standards may integrate these potential new findings in the future. At this time, the existing guidelines for prenatal facial screening should not be changed.Keywords: prenatal three-dimensional ultrasound, prenatal screening, prenatal diagnosis, cleft lip and palate, fetal profile, retrognathism

Research and Realization of Medical Image Fusion Based on Three-Dimensional Reconstruction

Institute of Scientific and Technical Information of China (English)

无

2007-01-01

A new medical image fusion technique is presented. The method is based on three-dimensional reconstruction. After reconstruction, the three-dimensional volume data is normalized by three-dimensional coordinate conversion in the same way and intercepted through setting up cutting plane including anatomical structure, as a result two images in entire registration on space and geometry are obtained and the images are fused at last.Compared with traditional two-dimensional fusion technique, three-dimensional fusion technique can not only resolve the different problems existed in the two kinds of images, but also avoid the registration error of the two kinds of images when they have different scan and imaging parameter. The research proves this fusion technique is more exact and has no registration, so it is more adapt to arbitrary medical image fusion with different equipments.

Three-dimensional Modeling of Type Ia Supernova Explosions

Science.gov (United States)

Khokhlov, Alexei

2001-06-01

A deflagration explosion of a Type Ia Supernova (SNIa) is studied using three-dimensional, high-resolution, adaptive mesh refinement fluid dynamic calculations. Deflagration speed in an exploding Chandrasekhar-mass carbon-oxygen white dwarf (WD) grows exponentially, reaches approximately 30the speed of sound, and then declines due to a WD expansion. Outermost layers of the WD remain unburned. The explosion energy is comparable to that of a Type Ia supernova. The freezing of turbulent motions by expansion appears to be a crucial physical mechanism regulating the strength of a supernova explosion. In contrast to one-dimensional models, three-dimensional calculations predict the formation of Si-group elements and pockets of unburned CO in the middle and in central regions of a supernova ejecta. This, and the presence of unburned outer layer of carbon-oxygen may pose problems for SNIa spectra. Explosion sensitivity to initial conditions and its relation to a diversity of SNIa is discussed.

Creating three-dimensional thermal maps

CSIR Research Space (South Africa)

Price

2011-11-01

Full Text Available stream_source_info Price_2011.pdf.txt stream_content_type text/plain stream_size 30895 Content-Encoding ISO-8859-1 stream_name Price_2011.pdf.txt Content-Type text/plain; charset=ISO-8859-1 Creating Three...-Dimensional Thermal Maps Mathew Price Cogency cc Cape Town Email: mathew@cogency.co.za Jeremy Green CSIR Centre for Mining Innovation Johannesburg Email: jgreen@csir.co.za John Dickens CSIR Centre for Mining Innovation Johannesburg Email: jdickens...

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.

Facile fabrication of the porous three-dimensional regenerated silk fibroin scaffolds

International Nuclear Information System (INIS)

Cao, Zhengbing; Wen, Jianchuan; Yao, Jinrong; Chen, Xin; Ni, Yusu; Shao, Zhengzhong

2013-01-01

In the present work, we report a new facile method to fabricate porous three-dimensional regenerated silk fibroin (RSF) scaffolds through n-butanol- and freezing-induced conformation transition and phase separation. The effects of RSF concentration, freezing temperature and n-butanol addition on the microstructure, the secondary structures of silk fibroin and apparent mechanical properties of the RSF scaffolds were investigated by SEM, 13 C CP-MAS NMR spectra and mechanical testing, respectively. By adjusting the RSF concentration and n-butanol addition, the pore size of the scaffold could be controlled in the range from of 10 μm to 350 μm with 84%–98% of porosity. The tensile strength of the wet scaffold reached the maximum of 755.2 ± 33.6 kPa when the concentration of RSF solution was increased to 15% w/w. Moreover, post-treatment with ethanol further induced conformation transition of RSF from random coil or helix to β-sheet. The porous scaffolds prepared by this facile and energy-saving method with good biocompatibility will have great potential for application in tissue engineering. Highlights: • A new facile and energy-saving method to fabricate porous silk fibroin scaffolds; • Freeze-drying step (a typical high energy consuming process) is unnecessary; • Morphology and mechanical properties of scaffolds were easily controlled; • Ethanol post-treatment can be used to tune the degradation behavior

three dimensional photoelastic investigations on thick rectangular

African Journals Online (AJOL)

user

1983-09-01

Sep 1, 1983 ... Thick rectangular plates are investigated by means of three-dimensional photoelasticity ... a thin plate theory and a higher order thick plate theory. 1. ..... number of fringes lest the accuracy of the results will be considerably.

Surgical accuracy of three-dimensional virtual planning

DEFF Research Database (Denmark)

Stokbro, Kasper; Aagaard, Esben; Torkov, Peter

2016-01-01

This retrospective study evaluated the precision and positional accuracy of different orthognathic procedures following virtual surgical planning in 30 patients. To date, no studies of three-dimensional virtual surgical planning have evaluated the influence of segmentation on positional accuracy...... and transverse expansion. Furthermore, only a few have evaluated the precision and accuracy of genioplasty in placement of the chin segment. The virtual surgical plan was compared with the postsurgical outcome by using three linear and three rotational measurements. The influence of maxillary segmentation...

Three-dimensional interconnected nickel phosphide networks with hollow microstructures and desulfurization performance

International Nuclear Information System (INIS)

Zhang, Shuna; Zhang, Shujuan; Song, Limin; Wu, Xiaoqing; Fang, Sheng

2014-01-01

Graphical abstract: Three-dimensional interconnected nickel phosphide networks with hollow microstructures and desulfurization performance. - Highlights: • Three-dimensional Ni 2 P has been prepared using foam nickel as a template. • The microstructures interconnected and formed sponge-like porous networks. • Three-dimensional Ni 2 P shows superior hydrodesulfurization activity. - Abstract: Three-dimensional microstructured nickel phosphide (Ni 2 P) was fabricated by the reaction between foam nickel (Ni) and phosphorus red. The as-prepared Ni 2 P samples, as interconnected networks, maintained the original mesh structure of foamed nickel. The crystal structure and morphology of the as-synthesized Ni 2 P were characterized by X-ray diffraction, scanning electron microscopy, automatic mercury porosimetry and X-ray photoelectron spectroscopy. The SEM study showed adjacent hollow branches were mutually interconnected to form sponge-like networks. The investigation on pore structure provided detailed information for the hollow microstructures. The growth mechanism for the three-dimensionally structured Ni 2 P was postulated and discussed in detail. To investigate its catalytic properties, SiO 2 supported three-dimensional Ni 2 P was prepared successfully and evaluated for the hydrodesulfurization (HDS) of dibenzothiophene (DBT). DBT molecules were mostly hydrogenated and then desulfurized by Ni 2 P/SiO 2

Method and system for manipulating a digital representation of a three-dimensional object

DEFF Research Database (Denmark)

2010-01-01

A method of manipulating a three-dimensional virtual building block model by means of two-dimensional cursor movements, the virtual building block model including a plurality of virtual building blocks each including a number of connection elements for connecting the virtual building block...... with another virtual building block according to a set of connection rules, the method comprising positioning by means of cursor movements in a computer display area representing a two-dimensional projection of said model, a two-dimensional projection of a first virtual building block to be connected...... to the structure, resulting in a two-dimensional position; determining, from the two-dimensional position, a number of three-dimensional candidate positions of the first virtual building block in the three-dimensional coordinate system; selecting one of said candidate positions based on the connection rules...

Multi-particle three-dimensional coordinate estimation in real-time optical manipulation

DEFF Research Database (Denmark)

Dam, Jeppe Seidelin; Perch-Nielsen, Ivan R.; Palima, Darwin

2009-01-01

We have previously shown how stereoscopic images can be obtained in our three-dimensional optical micromanipulation system [J. S. Dam et al, Opt. Express 16, 7244 (2008)]. Here, we present an extension and application of this principle to automatically gather the three-dimensional coordinates for...

Conformations and Intermolecular Interactions in Cellulose/Silk Fibroin Blend Films: A Solid-State NMR Perspective.

Science.gov (United States)

Tian, Donglin; Li, Tao; Zhang, Rongchun; Wu, Qiang; Chen, Tiehong; Sun, Pingchuan; Ramamoorthy, Ayyalusamy

2017-06-29

Fabricating materials with excellent mechanical performance from the natural renewable and degradable biopolymers has drawn significant attention in recent decades due to the environmental concerns and energy crisis. As two of the most promising substitutes of synthetic polymers, silk fibroin (SF), and cellulose, have been widely used in the field of textile, biomedicine, biotechnology, etc. Particularly, the cellulose/SF blend film exhibits better strength and toughness than that of regenerated cellulose film. Herein, this study is aimed to understand the molecular origin of the enhanced mechanical properties for the cellulose/SF blend film, using solid-state NMR as a main tool to investigate the conformational changes, intermolecular interactions between cellulose and SF and the water organization. It is found that the content of the β-sheet structure is increased in the cellulose/SF blend film with respect to the regenerated SF film, accompanied by the reduction of the content of random coil structures. In addition, the strong hydrogen bonding interaction between the SF and cellulose is clearly elucidated by the two-dimensional (2D) 1 H- 13 C heteronuclear correlation (HETCOR) NMR experiments, demonstrating that the SF and cellulose are miscible at the molecular level. Moreover, it is also found that the -NH groups of SF prefer to form hydrogen bonds with the hydroxyl groups bonded to carbons C2 and C3 of cellulose, while the hydroxyl groups bonded to carbon C6 and the ether oxygen are less favorable for hydrogen bonding interactions with the -NH groups of SF. Interestingly, bound water is found to be present in the air-dried cellulose/SF blend film, which is predominantly associated with the cellulose backbones as determined by 2D 1 H- 13 C wide-line-separation (WISE) experiments with spin diffusion. This clearly reveals the presence of nanoheterogeneity in the cellulose/SF blend film, although cellulose and SF are miscible at a molecular level. Without doubt

Electron crystallography of three dimensional protein crystals

NARCIS (Netherlands)

Georgieva, Dilyana

2008-01-01

This thesis describes an investigation of the potential of electron diffraction for studying three dimensional sub-micro-crystals of proteins and pharmaceuticals. A prerequisite for using electron diffraction for structural studies is the predictable availability of tiny crystals. A method for

On-line analysis of algae in water by discrete three-dimensional fluorescence spectroscopy.

Science.gov (United States)

Zhao, Nanjing; Zhang, Xiaoling; Yin, Gaofang; Yang, Ruifang; Hu, Li; Chen, Shuang; Liu, Jianguo; Liu, Wenqing

2018-03-19

In view of the problem of the on-line measurement of algae classification, a method of algae classification and concentration determination based on the discrete three-dimensional fluorescence spectra was studied in this work. The discrete three-dimensional fluorescence spectra of twelve common species of algae belonging to five categories were analyzed, the discrete three-dimensional standard spectra of five categories were built, and the recognition, classification and concentration prediction of algae categories were realized by the discrete three-dimensional fluorescence spectra coupled with non-negative weighted least squares linear regression analysis. The results show that similarities between discrete three-dimensional standard spectra of different categories were reduced and the accuracies of recognition, classification and concentration prediction of the algae categories were significantly improved. By comparing with that of the chlorophyll a fluorescence excitation spectra method, the recognition accuracy rate in pure samples by discrete three-dimensional fluorescence spectra is improved 1.38%, and the recovery rate and classification accuracy in pure diatom samples 34.1% and 46.8%, respectively; the recognition accuracy rate of mixed samples by discrete-three dimensional fluorescence spectra is enhanced by 26.1%, the recovery rate of mixed samples with Chlorophyta 37.8%, and the classification accuracy of mixed samples with diatoms 54.6%.

Three-dimensional magnetic probe measurements of EXTRAP T1 equilibria

International Nuclear Information System (INIS)

Hedin, E.R.

1988-12-01

Internal probes are described for use in measuring the three orthogonal components of the magnetic field in the Extrap T1 device. The data analysis process for numerical processing of the probe signals is also explained. Results include radial and vertical profiles of the field components, three-dimensional field plots, inverse field strength contours, two-dimensional magnetic flux plots and toroidal current profiles. (author)

Three-dimensional dose-response models of risk for radiation injury carcinogenesis

International Nuclear Information System (INIS)

Raabe, O.G.

1988-01-01

The use of computer graphics in conjunction with three-dimensional models of dose-response relationships for chronic exposure to ionizing radiation dramaticly clarifies the separate and interactive roles of competing risks. The three dimensions are average dose rate, exposure time, and risk. As an example, the functionally injurious and carcinogenic responses after systemic uptake of Ra-226 by beagles, mice and people with consequent alpha particle irradiation of the bone are represented by three-dimensional dose-rate/time/response surfaces that demonstrate the contributions with the passage of time of the competing deleterious responses. These relationships are further evaluated by mathematical stripping with three-dimensional illustrations that graphically show the resultant separate contribution of each effect. Radiation bone injury predominates at high dose rates and bone cancer at intermediate dose rates. Low dose rates result in spontaneous deaths from natural aging, yielding a type of practical threshold for bone cancer induction. Risk assessment is benefited by the insights that become apparent with these three-dimensional models. The improved conceptualization afforded by them contributes to planning and evaluating epidemiological analyses and experimental studies

Induction of carcinoembryonic antigen expression in a three-dimensional culture system

Science.gov (United States)

Jessup, J. M.; Brown, D.; Fitzgerald, W.; Ford, R. D.; Nachman, A.; Goodwin, T. J.; Spaulding, G.

1994-01-01

MIP-101 is a poorly differentiated human colon carcinoma cell line established from ascites that produces minimal amounts of carcinoembryonic antigen (CEA), a 180 kDa glycoprotein tumor marker, and nonspecific cross-reacting antigen (NCA), a related protein that has 50 and 90 kDa isoforms, in vitro in monolayer culture. MIP-101 produces CEA when implanted into the peritoneum of nude mice but not when implanted into subcutaneous tissue. We tested whether MIP-101 cells may be induced to express CEA when cultured on microcarrier beads in three-dimensional cultures, either in static cultures as non-adherent aggregates or under dynamic conditions in a NASA-designed low shear stress bioreactor. MIP- 101 cells proliferated well under all three conditions and increased CEA and NCA production 3 - 4 fold when grown in three-dimensional cultures compared to MIP-101 cells growing logarithmically in monolayers. These results suggest that three-dimensional growth in vitro simulates tumor function in vivo and that three-dimensional growth by itself may enhance production of molecules that are associated with the metastatic process.

Characterization of lithium coordination sites with magic-angle spinning NMR

Science.gov (United States)

Haimovich, A.; Goldbourt, A.

2015-05-01

Lithium, in the form of lithium carbonate, is one of the most common drugs for bipolar disorder. Lithium is also considered to have an effect on many other cellular processes hence it possesses additional therapeutic as well as side effects. In order to quantitatively characterize the binding mode of lithium, it is required to identify the interacting species and measure their distances from the metal center. Here we use magic-angle spinning (MAS) solid-state NMR to study the binding site of lithium in complex with glycine and water (LiGlyW). Such a compound is a good enzyme mimetic since lithium is four-coordinated to one water molecule and three carboxylic groups. Distance measurements to carbons are performed using a 2D transferred echo double resonance (TEDOR) MAS solid-state NMR experiment, and water binding is probed by heteronuclear high-resolution proton-lithium and proton-carbon correlation (wPMLG-HETCOR) experiments. Both HETCOR experiments separate the main complex from impurities and non-specifically bound lithium species, demonstrating the sensitivity of the method to probe the species in the binding site. Optimizations of the TEDOR pulse scheme in the case of a quadrupolar nucleus with a small quadrupole coupling constant show that it is most efficient when pulses are positioned on the spin-1/2 (carbon-13) nucleus. Since the intensity of the TEDOR signal is not normalized, careful data analysis that considers both intensity and dipolar oscillations has to be performed. Nevertheless we show that accurate distances can be extracted for both carbons of the bound glycine and that these distances are consistent with the X-ray data and with lithium in a tetrahedral environment. The lithium environment in the complex is very similar to the binding site in inositol monophosphatase, an enzyme associated with bipolar disorder and the putative target for lithium therapy. A 2D TEDOR experiment applied to the bacterial SuhB gene product of this enzyme was designed

Atom-dimer scattering in a heteronuclear mixture with a finite intraspecies scattering length

Science.gov (United States)

Gao, Chao; Zhang, Peng

2018-04-01

We study the three-body problem of two ultracold identical bosonic atoms (denoted by B ) and one extra atom (denoted by X ), where the scattering length aB X between each bosonic atom and atom X is resonantly large and positive. We calculate the scattering length aad between one bosonic atom and the shallow dimer formed by the other bosonic atom and atom X , and investigate the effect induced by the interaction between the two bosonic atoms. We find that even if this interaction is weak (i.e., the corresponding scattering length aB B is of the same order of the van der Waals length rvdW or even smaller), it can still induce a significant effect for the atom-dimer scattering length aad. Explicitly, an atom-dimer scattering resonance can always occur when the value of aB B varies in the region with | aB B|≲ rvdW . As a result, both the sign and the absolute value of aad, as well as the behavior of the aad-aB X function, depends sensitively on the exact value of aB B. Our results show that, for a good quantitative theory, the intraspecies interaction is required to be taken into account for this heteronuclear system, even if this interaction is weak.

Three-dimensional demonstration of liver and spleen by computer graphics technique

International Nuclear Information System (INIS)

Kashiwagi, Toru; Azuma, Masayoshi; Katayama, Kazuhiro; Yoshioka, Hiroaki; Ishizu, Hiromi; Mitsutani, Natsuki; Koizumi, Takao; Takayama, Ichiro

1987-01-01

Three-dimensional demonstration system of the liver and spleen has been developed using computer graphics technique. Three-dimensional models were constructed from CT images of the organ surface. The three-dimensional images were displayed as wire-frame and/or solid models on the color CRT. The anatomical surface of the liver and spleen was realistically viewed from any direction. In liver cirrhosis, atrophy of the right lobe, hypertrophy of the left lobe and splenomegaly were displayed vividly. The liver and hepatoma were displayed as wire-frame and solid models respectively on the same image. This combined display clarified the intrahepatic location of hepatoma together with configuration of liver and hepatoma. Furthermore, superimposed display of three dimensional models and celiac angiogram enabled us to understand the location and configuration of lesions more easily than the original CT data or angiogram alone. Therefore, it is expected that this system is clinically useful for noninvasive evaluation of patho-morphological changes of the liver and spleen. (author)

Numerical Investigation of Three-dimensional Instability of Standing Waves

Science.gov (United States)

Zhu, Qiang; Liu, Yuming; Yue, Dick K. P.

2002-11-01

We study the three-dimensional instability of finite-amplitude standing waves under the influence of gravity using the transition matrix method. For accurate calculation of the transition matrices, we apply an efficient high-order spectral element method for nonlinear wave dynamics in complex domain. We consider two types of standing waves: (a) plane standing waves; and (b) standing waves in a circular tank. For the former, in addition to the confirmation of the side-band-like instability, we find a new three-dimensional instability for arbitrary base standing waves. The dominant component of the unstable disturbance is an oblique standing wave, with an arbitrary angle relative to the base flow, whose frequency is approximately equal to that of the base standing wave. Based on direct simulations, we confirm such a three-dimensional instability and show the occurrence of the Fermi-Pasta-Ulam recurrence phenomenon during nonlinear evolution. For the latter, we find that beyond a threshold wave steepness, the standing wave with frequency Ω becomes unstable to a small three-dimensional disturbance, which contains two dominant standing-wave components with frequencies ω1 and ω_2, provided that 2Ω ω1 + ω_2. The threshold wave steepness is found to decrease/increase as the radial/azimuthal wavenumber of the base standing wave increases. We show that the instability of standing waves in rectangular and circular tanks is caused by third-order quartet resonances between base flow and disturbance.

Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.

Science.gov (United States)

Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

2010-09-03

Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR - X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution.

NMR study of quasi-one-dimensional itinerant-electron magnets RMn{sub 4}Al{sub 8} (R=Y, Lu and Sc)

Energy Technology Data Exchange (ETDEWEB)

Muro, Y. [Graduate School of Material Science, University of Hyogo, Kamigori, Ako-gun, Hyogo 678-1297 (Japan)], E-mail: rk04j052@yahoo.co.jp; Nakamura, H.; Kohara, T. [Graduate School of Material Science, University of Hyogo, Kamigori, Ako-gun, Hyogo 678-1297 (Japan)

2008-04-01

{sup 55}Mn-NMR measurements, which revealed previously the presence of spin pseudogap in YMn{sub 4}Al{sub 8}, have been extended to LuMn{sub 4}Al{sub 8} and ScMn{sub 4}Al{sub 8}. Temperature (T) dependences of the Knight shift, K, and the nuclear spin-lattice relaxation rate, 1/T{sub 1}, are well explained by the same pseudogap model used to explain a broad maximum observed in the T-dependence of the susceptibility, indicating common nature in the spin excitation spectrum in the quasi-one-dimensional itinerant-electron compounds.

Three-dimensional metamaterials fabricated using Proton Beam Writing

Energy Technology Data Exchange (ETDEWEB)

Bettiol, A.A., E-mail: a.bettiol@nus.edu.sg [Centre for Ion Beam Applications, Department of Physics, National University of Singapore, 2 Science Dr. 3, Singapore 117542 (Singapore); Turaga, S.P.; Yan, Y.; Vanga, S.K. [Centre for Ion Beam Applications, Department of Physics, National University of Singapore, 2 Science Dr. 3, Singapore 117542 (Singapore); Chiam, S.Y. [NUS High School for Maths and Science, 20 Clementi Avenue 1, Singapore 129957 (Singapore)

2013-07-01

Proton Beam Writing (PBW) is a direct write lithographic technique that has recently been applied to the fabrication of three dimensional metamaterials. In this work, we show that the unique capabilities of PBW, namely the ability to fabricate arrays of high resolution, high aspect ratio microstructures in polymer or replicated into metal, is well suited to metamaterials research. We have also developed a novel method for selectively electroless plating silver directly onto polymer structures that were fabricated using PBW. This method opens up new avenues for utilizing PBW for making metamaterials and other sub-wavelength metallic structures. Several potential applications of three dimensional metamaterials fabricated using PBW are discussed, including sensing and negative refractive index materials.

SNAP-3D: a three-dimensional neutron diffusion code

International Nuclear Information System (INIS)

McCallien, C.W.J.

1975-10-01

A preliminary report is presented describing the data requirements of a one- two- or three-dimensional multi-group diffusion code, SNAP-3D. This code is primarily intended for neutron diffusion calculations but it can also carry out gamma calculations if the diffuse approximation is accurate enough. It is suitable for fast and thermal reactor core calculations and for shield calculations. It is assumed the reader is familiar with the older, two-dimensional code SNAP and can refer to the report [TRG-Report-1990], describing it. The present report concentrates on the enhancements to SNAP that have been made to produce the three-dimensional version, SNAP-3D, and is intended to act a a guide on data preparation until a single, comprehensive report can be published. (author)

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

On boundary conditions in three-dimensional AdS gravity

Energy Technology Data Exchange (ETDEWEB)

Miskovic, Olivera [Instituto de Fisica, P. Universidad Catolica de Valparaiso, Casilla 4059, Valparaiso (Chile) and Departamento de Fisica, P. Universidad Catolica de Chile, Casilla 306, Santiago 22 (Chile)]. E-mail: olivera.miskovic@ucv.cl; Olea, Rodrigo [Departamento de Fisica, P. Universidad Catolica de Chile, Casilla 306, Santiago 22 (Chile) and Centro Multidisciplinar de Astrofisica, CENTRA, Departamento de Fisica, Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon (Portugal)]. E-mail: rolea@fisica.ist.utl.pt

2006-09-07

A finite action principle for three-dimensional gravity with negative cosmological constant, based on a boundary condition for the asymptotic extrinsic curvature, is considered. The bulk action appears naturally supplemented by a boundary term that is one half the Gibbons-Hawking term, that makes the Euclidean action and the Noether charges finite without additional Dirichlet counterterms. The consistency of this boundary condition with the Dirichlet problem in AdS gravity and the Chern-Simons formulation in three dimensions, and its suitability for the higher odd-dimensional case, are also discussed.

Three-Dimensional Organization of Chromosome Territories in the Human Interphase Nucleus